@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.},
}

*Metagenomics/methods
Microbiota/genetics
Lakes/microbiology/virology
*Fresh Water/microbiology/virology
Ecosystem
Metagenome
*Viruses/genetics/classification
*Bacteria/genetics/virology
Pesticides
*Host Microbial Interactions/genetics
Stress, Physiological
Climate Change

@article {pmid40841245,
year = {2025},
author = {Antoniadou, C and Gavriilidis, E and Chatzopoulos, P and Gkouliavera, M and Skendros, P},
title = {Fever and inflammation of unknown origin in the 21st century.},
journal = {European journal of internal medicine},
volume = {},
number = {},
pages = {106443},
doi = {10.1016/j.ejim.2025.106443},
pmid = {40841245},
issn = {1879-0828},
abstract = {Fever and inflammation of unknown origin (FUO/IUO) remain challenging clinical syndromes today, in which the internists play a central role in orchestrating the diagnostic process and interpreting key findings. FUO and IUO share similar diagnostic evaluations and overlapping etiologies, although the relative frequencies of their causes may differ. The established five-category classification includes infectious diseases (INF), non-infectious inflammatory diseases (NIID), malignancies (MAL), miscellaneous (MISC) and undiagnosed illnesses (UI). The relative distribution of these categories varies depending on the FUO diagnostic criteria applied, as well as geographical region and socioeconomic factors. Although infectious diseases were historically the predominant cause of FUO, in recent years there has been a shift toward UI and NIID, especially in high-income settings. IUO is typically associated with a lower likelihood of infections compared to FUO, while the most common causes are mainly NIID. Meticulous medical history and clinical examination, aimed at identifying potential diagnostic clues (PDCs), remain pivotal to FUO/IUO diagnostics. Modern technologies such as PET/CT and next-generation sequencing (NGS) have advanced the diagnostic workup of FUO/IUO. However, they should be employed selectively, guided by PDCs, and with consideration of their limitations and cost-effectiveness. Emerging techniques, including metagenomic NGS and cytokine-based assays (e.g. IL-1β/DNA complex detection), show promising results in distinguishing sterile from infectious inflammation. Despite advancements in diagnostics and considering that UI now represent a leading cause of FUO in the European region, there remains an urgent need to deepen our understanding of underlying disease mechanisms and to develop novel, pathophysiology-based diagnostic tools.},
}

@article {pmid40841065,
year = {2025},
author = {Jia, M and Gao, Z and Hu, X and Feng, M and Liu, F and Huang, J and Zhang, R and Li, J and Zhang, G and Wang, Y},
title = {Wetland types shape microbial function related to soil phosphorus cycling based on metagenomics analysis.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {930-943},
doi = {10.1016/j.jes.2025.03.009},
pmid = {40841065},
issn = {1001-0742},
mesh = {*Wetlands ; *Phosphorus/analysis/metabolism ; *Soil Microbiology ; Metagenomics ; Soil/chemistry ; China ; *Environmental Monitoring ; },
abstract = {Limitations regarding phosphorus (P) are widespread in ecosystems. Understanding the impacts of the wetland types on microbially mediated soil P availability and cycling is essential for the effective management of wetlands. In this study, the Beidagang wetland, Baodi paddy field, and Dahuangpu wetland in Tianjin, China were chosen as representatives of the coastal wetland (B), constructed wetland (R), and swampy wetland (W), respectively. Sequential P extraction and metagenomics approaches were adopted to explore the soil P fraction and microbially regulated P cycle. Proteobacteria were the predominant microbes-related soil P cycle. IMPA, gph, rsbU_P, ugpQ, and glpK genes were dominant in organic P (Po) mineralization, while gcd, ppa, and ppx genes were dominant in inorganic P (Pi) solubilization. The salinity, NO3[-]-N concentration, the ratio of total carbon to total nitrogen (TC/TN), total carbon (TC), and the ratio of soil organic carbon to total P (SOC/TP) were the co-drivers of microbially mediated P cycle processes. Microbial network complexity-relate P cycle was the lowest in the coastal wetland. Salinity and NO3[-]-N exhibited a significant negative relation to the abundance of most genes-relate Pi solubilization and a remarkable positive correlation with the abundance of many genes-relate Po mineralization. These findings demonstrated that Po mineralization tended to occur in habitats with high salinity and nutrient imbalances, whereas the dissolution of Pi was prone to occur in low-salinity environments with relatively balanced soil nutrients. This study improves understanding of how salinity and soil nutrients jointly shape microbial-regulated soil P cycle in different types of wetlands.},
}

*Wetlands
*Phosphorus/analysis/metabolism
*Soil Microbiology
Metagenomics
Soil/chemistry
China
*Environmental Monitoring

@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.},
}

Anaerobiosis
*Microbiota
Metagenomics
*Temperature
*Metagenome
Archaea/genetics
Bacteria/genetics

@article {pmid40840611,
year = {2025},
author = {Guo, D and Liu, X and Zhang, Y and Li, Y and Hou, B and Duan, J},
title = {Combining Simulated Immersion and Statistical Analysis to Reveal Microbial Evidence of Corrosion Failure in Fuel Aluminum Alloys.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122511},
doi = {10.1016/j.envres.2025.122511},
pmid = {40840611},
issn = {1096-0953},
abstract = {Microbial contamination has caused engineering problems such as fuel deterioration, corrosion of maritime aviation aluminium alloys, and fuel tank leakage. By integrating metagenomic analysis of a fuel corrosion biofilm and microbial cultivation techniques, we selected ten types of microbial resources that might affect the deteriorated corrosion of aluminium alloys in aviation fuel for corrosion immersion simulation experiments. Through multidimensional analysis of corrosive microorganisms, medium environment, and material surfaces, the qualitative and quantitative microbial evidence for the failure of aluminium alloy in aviation fuel tanks was presented. The statistical analysis results indicated that anaerobic microorganisms exhibited a higher corrosiveness towards the 2024 T3 aluminium alloy than aerobic microorganisms. The corrosion extent of microorganisms was significantly influenced by the types of microorganisms present, as evidenced by the presence of potential corrosion-inhibiting microorganisms within the biofilm. In mixed microbial contamination, aerobic microorganisms accelerated fuel degradation and rust formation. In contrast, anaerobic microorganisms, particularly co-culture systems of Desulfovibrio bizertensis and Methanosarcine barkeri accelerated the pitting of aluminium alloy. The galvanic electrochemical effect was considered to be an important indicator for characterizing the corrosion of aluminium materials in fuel-water systems.},
}

@article {pmid40840604,
year = {2025},
author = {Tiwari, A and Jaén-Gil, A and Karavaeva, A and Gomiero, A and Ásmundsdóttir, ÁM and Silva, MJ and Salmivirta, E and Tran, TT and Sarekoski, A and Cook, J and Lood, R and Pitkänen, T and Krolicka, A},
title = {Antibiotic resistance genes, antibiotic residues, and microplastics in influent and effluent wastewater from treatment plants in Norway, Iceland, and Finland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122629},
doi = {10.1016/j.envres.2025.122629},
pmid = {40840604},
issn = {1096-0953},
abstract = {Monitoring antimicrobial resistance genes (ARGs) in wastewater influents (pre-treatment) and effluents (post-treatment) provides insights into community-level circulation, potential amplification during treatment, and risks associated with gene release into surface waters. Pollutants such as antibiotic residues and microplastics (MPs) may influence ARG dynamics, highlighting the need to assess their dynamics across wastewater environments. In this study, we analyzed ARGs and bacterial communities using Oxford Nanopore (ONP) metagenomics and qPCR in wastewater samples from Mekjarvik (Norway), Reykjavik (Iceland), and Mariehamn (Åland, Finland). Antibiotic residues were quantified via High-Performance Liquid Chromatography (HPLC), and MPs were characterized using Micro-Fourier Transform Infrared Spectroscopy (μ-FTIR) in Mekjarvik and Reykjavik. Metagenomic analysis identified 193 unique ARGs, with the highest average (±SD) in Reykjavik (66.3 ± 4.1), followed by Mekjarvik (61.3 ± 14.1) and Mariehamn (18.0 ± 2.2). ONP sequencing revealed that many ARGs were plasmid-associated, co-occurring with metal stress genes. Common plasmids were Col440I, IncQ2, and ColRNAI. Mercury-related genes dominated metal stress genes (64.9%), followed by multimetal (23.7%) and copper (6.4%). Of 45 antibiotics screened, only sulfamethoxazole and sulfapyridine were consistently detected. Polyethylene (∼60%) was the dominant MP type; Reykjavik influent had the highest MP load (8200 MPs/m[3]). While treatment reduced ARGs, antibiotic residues, and larger MPs, it was less effective against fine particles and key ARGs, including carbapenemase- and ESBL-associated genes. Clinically relevant ARGs and potential pathogens (e.g., Acinetobacter baumannii, Pseudomonas aeruginosa) persisted in effluents, highlighting risks to downstream ecosystems. These findings underscore the need for regular monitoring of both influents and effluents to assess treatment performance and safeguard environmental health.},
}

@article {pmid40840441,
year = {2025},
author = {Shi, Q and Kristiansen, K},
title = {Spatial dissimilarity analysis in single-cell transcriptomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101141},
doi = {10.1016/j.crmeth.2025.101141},
pmid = {40840441},
issn = {2667-2375},
abstract = {We develop the spatial dissimilarity method to uncover complex bivariate relationships in single-cell and spatial transcriptomics data, addressing challenges such as alternative splicing and allele-specific gene expression. Applying this method to detect alternative splicing in neurons demonstrates improved accuracy and sensitivity compared to existing tools, notably identifying neuron subtypes. In tumor cells, spatial dissimilarity analysis reveals somatic variants that emerge during tumor progression, validated through whole-exome sequencing. These findings highlight how allele-specific genetic variants contribute to the subclone architecture of cancer cells, offering insights into cellular heterogeneity. Applied on a human cell atlas, we uncover numerous cases of allele-specific expression of genes in normal cells. We provide a software package for spatial dissimilarity analysis to enable enhanced understanding of cellular complexity and gene expression dynamics under homeostatic conditions and during states of transitions.},
}

@article {pmid40840439,
year = {2025},
author = {He, X and Gao, Y and Zhang, Y and Yang, Z and Wang, C and Ma, Q and Lei, P and Yu, L and Fan, Y and Liu, R and Wang, W and Zhang, J and Ma, X and Zhu, F},
title = {Distinct Gut Microbial Signatures and Diminished Anti-Inflammatory Effect of Short-Chain Fatty Acids in Schizophrenia With Immune Activation.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf110},
pmid = {40840439},
issn = {1745-1701},
support = {82171505//National Natural Science Foundation of China/ ; 82230044//National Natural Science Foundation of China/ ; 82022023//National Natural Science Foundation of China/ ; 82271572//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: A subset of patients with schizophrenia (SCZ) exhibit subclinical immune activation. However, the gut microbial features of this subgroup and their interplay with the immune function remain poorly understood. This study aimed to identify the gut microbiome signature of immune-activated SCZ and elucidate the role of short-chain fatty acids (SCFAs) in the gut-immune crosstalk.

STUDY DESIGN: In this study, 297 patients with SCZ and 301 healthy controls (HCs) were assessed for 4 serum immune mediators. Immune-activated subgroups were classified based on these biomarkers. Fecal metagenomic sequencing, SCFA metabolomics, and in vitro peripheral blood mononuclear cells (PBMCs) stimulation experiments were performed to analyze the microbial composition, SCFA levels, and immune responses.

STUDY RESULTS: We found that 46.5% of the patients with SCZ exhibited elevated immune activation biomarker levels, which displayed unique bacterial signatures. Microbiome-based machine learning classifiers demonstrated robustness in SCZ and immune activation classification. Notably, microbial species abundance, functional metagenomics, and SCFA levels have confirmed an elevated capacity for SCFA production in patients with immune activation. Furthermore, in vitro PBMC stimulation experiments revealed a diminished anti-inflammatory effect of SCFAs in immune-activated patients when exposed to lipopolysaccharide-induced inflammation.

CONCLUSIONS: This study delineates the gut microbiome and SCFA metabolic profiles of immune-activated SCZ patients, revealing an association between gut microbiota dysbiosis, enhanced SCFA production capacity, and diminished anti-inflammatory effect of SCFA. These findings provide new insights into the underlying mechanisms and potential targeted treatments for SCZ patients with immune activation.},
}

@article {pmid40840192,
year = {2025},
author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH},
title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111392},
doi = {10.1016/j.ijfoodmicro.2025.111392},
pmid = {40840192},
issn = {1879-3460},
abstract = {Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.},
}

@article {pmid40838886,
year = {2025},
author = {Xie, T and Lin, D and Cai, XD and Ma, LJ and Wang, L and Cai, TG and Ye, YQ and Shen, LQ and Sun, MM and Ye, M and Neilson, R and Zhu, D},
title = {Nano-biochar regulates phage-host interactions, reducing antibiotic resistance genes in vermicomposting systems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {34},
pages = {e2511986122},
doi = {10.1073/pnas.2511986122},
pmid = {40838886},
issn = {1091-6490},
support = {Grant XDB0750400//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 42307033 and 42222701//the National Natural Science Foundation of China/ ; 2022A-163-G//the Ningbo Yongjiang Talent Project/ ; RESAS//the James Hutton Institute receives financial support from Scottish Government Rural and Environment Science and Analytical Services/ ; },
mesh = {Animals ; *Oligochaeta/virology/microbiology ; *Bacteriophages/physiology/genetics ; *Drug Resistance, Microbial/genetics ; *Composting/methods ; *Host Microbial Interactions ; Bacteria/genetics/virology ; Soil Microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {Biochar amendment reshapes microbial community dynamics in vermicomposting, but the mechanism of how phages respond to this anthropogenic intervention and regulate the dissemination of antibiotic resistance genes (ARGs) remains unclear. In this study, we used metagenomics, viromics, and laboratory validation to explore how nano-biochar affects phage-host interactions and ARGs dissemination in vermicomposting. Our results revealed distinct niche-specific phage life strategies. In vermicompost, lytic phages dominated and used a "kill-the-winner" strategy to suppress antibiotic-resistant bacteria (ARB). In contrast, lysogenic phages prevailed in the earthworm gut, adopting a "piggyback-the-winner" strategy that promoted ARGs transduction through mutualistic host interactions. Nano-biochar induced the conversion of lysogenic to lytic phages in the earthworm gut, while concurrently reducing the abundance of lysogenic phages and their encoded auxiliary metabolic genes carried by ARB. This shift disrupted phage-host mutualism and inhibited ARGs transmission via a "phage shunting" mechanism. In vitro validation with batch culture experiments further confirmed that lysogenic phages increased transduction of ARGs in the earthworm gut, while nano-biochar reduced the spread of ARGs by enhancing lysis infectivity. Our study constructs a mechanistic framework linking nano-biochar induced shifts in phage lifestyles that suppress ARG spread, offering insights into phage-host coadaptation and resistance mitigation strategies in organic waste treatment ecosystems.},
}

Animals
*Oligochaeta/virology/microbiology
*Bacteriophages/physiology/genetics
*Drug Resistance, Microbial/genetics
*Composting/methods
*Host Microbial Interactions
Bacteria/genetics/virology
Soil Microbiology
*Drug Resistance, Bacterial/genetics
Metagenomics

@article {pmid40838858,
year = {2025},
author = {Hashimoto, K and Fukushima, K and Matsumoto, Y and Saito, H and Funauchi, A and Hamada, N and Niitsu, T and Abe, Y and Yamauchi, J and Nitta, T and Motooka, D and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H},
title = {Molecular epidemiological surveillance for non-tuberculous mycobacterial pulmonary disease: a single-center prospective cohort study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0043625},
doi = {10.1128/spectrum.00436-25},
pmid = {40838858},
issn = {2165-0497},
abstract = {UNLABELLED: Bacterial species cultured from sputum change during treatment or observation for non-tuberculous mycobacterial pulmonary disease; however, strain-level changes remain unrecognized. Variable number tandem repeat typing is a standard technique for strain identification; nonetheless, its labor-intensive and time-consuming nature limits routine clinical use. Therefore, we aimed to elucidate species-subspecies and strain dynamics in non-tuberculous mycobacteria and develop a simple sequence-based strain-level determination method. We performed a single-center prospective cohort study of 112 patients with non-tuberculous mycobacterial pulmonary disease. Whole-genome sequencing was performed on two sputum samples collected at enrollment and at the end of follow-up, followed by variable number tandem repeat (VNTR) typing. We also developed a simple long-read sequencing-based digital VNTR (dVNTR) typing method and evaluated its efficacy. Our results demonstrate that core genome multi-locus sequencing typing revealed species/subspecies changes in 13 patients (11.6%); VNTR typing detected strain changes in 16 patients (14.3%) without species/subspecies changes. Overall, pathogen shifts occurred in 29 patients (shift [+] group, 25.9%), whereas 83 had no detectable pathogen shift (shift [-] group, 74.1%). Interestingly, macrolide and amikacin susceptibility changed in both groups, but resistance remained higher in shift (-) patients. dVNTR results aligned with those of conventional VNTR typing. In conclusion, since susceptibility factors remain unclear, routine species/subspecies identification and molecular typing, such as VNTR, are optimal for patient care. Core genome multi-locus sequencing typing with a dVNTR identified pathogen shifts, innovating non-tuberculous mycobacterial pulmonary disease management.Clinical TrialsThis study is registered with UMIN as UMIN 000056067.

IMPORTANCE: Pulmonary non-tuberculous mycobacterial disease is a chronic infection in which the causative pathogens may change at the species, subspecies, or strain level over time. Accurate tracking of these changes is essential for optimizing treatment; however, conventional clinical practice lacks efficient methods for monitoring such dynamics. Our study revealed pathogen changes in approximately one-quarter of patients over 1.5 years, prompting the development of a novel surveillance system that integrates next-generation sequencing for both species-subspecies identification and strain-level molecular epidemiology. This innovation enables real-time monitoring of pathogen dynamics, allowing clinicians to promptly adjust treatment strategies and improve patient care through more informed decision-making.},
}

@article {pmid40838847,
year = {2025},
author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P},
title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.},
journal = {Journal of medical virology},
volume = {97},
number = {8},
pages = {e70570},
doi = {10.1002/jmv.70570},
pmid = {40838847},
issn = {1096-9071},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; Aged ; Microbiota ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.},
}

Humans
*Virome
*Arthritis, Rheumatoid/diagnosis/virology
*Metagenomics
Male
Female
Middle Aged
*Palatine Tonsil/virology
Adult
*Viruses/genetics/classification/isolation & purification
Aged
Microbiota

@article {pmid40838747,
year = {2025},
author = {Acharya, SM and Yang, Y and Enalls, BC and Walian, PJ and Van Houghton, BD and Rosenblum, JS and Cath, TY and Tringe, SG and Chakraborty, R},
title = {Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/spectrum.00683-25},
pmid = {40838747},
issn = {2165-0497},
abstract = {UNLABELLED: Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines.

IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.},
}

@article {pmid40838736,
year = {2025},
author = {Fang, J and Chen, Z and Yu, Z and Shan, S and Hou, Y and Liu, L and Huang, J and Li, B and Guo, J},
title = {Biochar suppresses conjugative transfer of antibiotic resistance genes in manure-amended soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf187},
pmid = {40838736},
issn = {1751-7370},
abstract = {The environmental dissemination of antibiotic resistance genes (ARGs), particularly in manure-amended soils, poses a growing threat to public health due to the potential transfer of ARGs to humans and animals. Effective strategies are urgently needed to mitigate ARG spread in agricultural settings. Biochar, an eco-friendly soil amendment, shows promise for pollution control, yet its role in suppressing ARG horizontal gene transfer remains unclear. Here, metagenomic analysis showed that manure application significantly increased the relative abundance of ARGs in soil microbiota, whereas biochar amendment reduced it. To determine whether biochar suppresses ARG dissemination by inhibiting horizontal transfer, we established a soil microcosm. Manure application increased the conjugative transfer ratio by 3-fold, whereas biochar effectively suppressed this transfer reducing it to levels observed in unamended soils. Cell sorting and 16S rRNA gene amplicon sequencing demonstrated that biochar treatment reduced the diversity of transconjugant pools at both phylum and genus level. Transconjugants were primarily affiliated with Pseudomonadota, Bacillota, and Actinomycetota, with Massilia, Delftia, and Ammoniphilus being the most abundant genera in biochar treatment soil. Mechanistic investigations revealed that biochar-mediated inhibition of ARG transfer was linked to reduced ATP energy supply, decreased reactive oxygen species production, and lower cell membrane permeability, and diminished bioavailability of heavy metals and antibiotics. Additionally, biochar altered soil enzyme activity and microbial community structure, further limiting ARG dissemination. The findings provide insights into biochar-induced mitigation of ARG spread in manure-amended soils and highlight its potential as an effective strategy for controlling environmental ARG transmission.},
}

@article {pmid40837017,
year = {2025},
author = {Li, Q and Zhang, L and Li, R and Tang, J and Lin, B and Qin, C and Jiang, W and An, L and Zhang, F and Shi, X and Yang, S and Yang, Q and Chen, S},
title = {Metagenomics-based analysis of microbial community dynamics and flavor compound correlations during rice-flavor Baijiu brewing.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1638716},
pmid = {40837017},
issn = {2296-4185},
abstract = {This study aimed to explore the microbial contribution to flavor compound production by analysing the succession patterns and metabolic functional characteristics of microbial communities during Jiuqu preparation, saccharification, and fermentation processes of rice-flavor Baijiu (RFB). The physicochemical parameters during RFB fermentation were systematically monitored, and the volatile flavor profile was characterized using headspace solid-phase microextraction gas chromatography‒mass spectrometry (HS-SPME-GC-MS). Concurrently, metagenomic sequencing was employed to elucidate the microbial community structure and its temporal dynamics throughout the fermentation process. The results of the physicochemical parameters revealed that the reducing sugar content peaked at the end of saccharification and subsequently decreased throughout fermentation, whereas the total acid and total ester contents progressively increased, reaching maximum levels at the fermentation endpoint and maintaining stability. HS-SPME-GC-MS analysis revealed 84 volatile flavor compounds including phenylethanol, ethanol, dimethyl ether, isopentyl alcohol, and acetic acid. Notably, compounds such as L-ethyl lactate, diethyl succinate, and isobutanol were initially synthesized during saccharification and subsequently accumulated during fermentation, emerging as major flavor constituents. Ascomycota and Mucoromycota dominated the fungal community (average relative abundance >1%), whereas Firmicutes and Proteobacteria prevailed among the bacterial phyla. Six genera, Lichtheimia, Kluyveromyces, Lacticaseibacillus, Lactobacillus, Limosilactobacillus, and Schleiferilactobacillus were identified as primary contributors to flavor production during fermentation. Functional analysis revealed that microbial metabolism in fermented mash primarily involved amino acid and carbohydrate metabolism, with glycoside hydrolases (GHs) and glycosyl transferases (GTs) serving as key carbohydrate-active enzymes. This study could improve the comprehensive understanding of the brewing mechanism of RFB and provide a theoretical basis for the development and utilization of microbial resources in the fermented grains and the improvement of RFB quality.},
}

@article {pmid40836310,
year = {2025},
author = {Wang, X and Dong, Q and Huang, P and Yang, S and Gao, M and Zhang, C and Zhang, C and Deng, Y and Huang, Z and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and Consortium, C and Tang, L and Hu, S and Duan, Y and Sun, W and Chen, W and Zhai, Q and Kong, X and Chen, L},
title = {The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {188},
pmid = {40836310},
issn = {2049-2618},
support = {32270077//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Genome, Viral ; Feces/virology/microbiology ; *Genetic Variation ; *Polymorphism, Single Nucleotide ; *Viruses/genetics/classification/isolation & purification ; China ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.

RESULTS: Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome/genetics
Genome, Viral
Feces/virology/microbiology
*Genetic Variation
*Polymorphism, Single Nucleotide
*Viruses/genetics/classification/isolation & purification
China
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing

@article {pmid40836306,
year = {2025},
author = {Gao, H and Li, B and Guo, Z and Zheng, L and Chen, J and Liang, G},
title = {Highly accurate prophage island detection with PIDE.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {254},
pmid = {40836306},
issn = {1474-760X},
mesh = {*Prophages/genetics ; Humans ; *Software ; Genome, Bacterial ; Algorithms ; Metagenome ; *Genomic Islands ; Genome, Viral ; },
abstract = {As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify prophages through computational methods. Here, we introduce PIDE for identifying prophages from bacterial genomes or metagenome-assembled genomes. PIDE integrates a pre-trained protein language model and gene density clustering algorithm to distinguish prophages. Benchmarking with induced prophage sequencing datasets demonstrates that PIDE pinpoints prophages with precise boundaries. Applying PIDE to 4744 human gut representative genomes reveals 24,467 prophages with widespread functional capacity. PIDE is available at https://github.com/chyghy/PIDE , with model training code at https://zenodo.org/records/16457629 .},
}

*Prophages/genetics
Humans
*Software
Genome, Bacterial
Algorithms
Metagenome
*Genomic Islands
Genome, Viral

@article {pmid40836223,
year = {2025},
author = {Wibberg, D and Bakuła, Z and García-Cunchillos, I and Gawor, J and Gromadka, R and Karnkowska, A and Bielecki, J and Jagielski, T},
title = {Complete mitochondrial genomes of the Prototheca genus: comparative genomics and evolutionary insights.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {766},
pmid = {40836223},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; Phylogeny ; *Genomics/methods ; *Evolution, Molecular ; *Prototheca/genetics/classification ; Base Composition ; },
abstract = {BACKGROUND: Prototheca (Chlorophyta: Trebouxiophyceae) is a genus of non-photosynthetic microalgae that causes increasingly frequent infections in both humans and animals, collectively referred to as protothecosis The genetic landscape of the Prototheca algae has remained largely uncharted until recent advances in sequencing and genomics. In this study, a combination of Illumina and Oxford Nanopore technologies was employed for sequencing of 18 mitochondrial genomes, representing all currently recognized Prototheca species.

RESULTS: The genomes differed in terms of size and GC content, ranging from 38 kbp to 68 kbp and from 25 to 30%, respectively. The gene content and gene order within the mitochondrial DNA exhibited specific characteristics. The gene content was conserved but showed variable number of hypothetical proteins and a clustering tendency for nad genes. Noteworthy, most genes were located on the clockwise strand, with type I introns, containing long open reading frames encoding homing endonucleases, suggesting a mechanism for intron mobility and genome plasticity. Comparative genomic analyses and phylogenetic classification across the 21 core genes showed a close relationship between the mitochondrial genomes, as evidenced by average nucleotide identity (ANI) and average amino acid identity (AAI), supportive for the current cytb gene-based taxonomy. The phylogenetic tree constructed from concatenated alignments of the core genes confirmed the presence of three distinct Prototheca clades, indicating the polyphyletic nature of the genus.

CONCLUSIONS: In conclusion, this work provides another important step toward elucidating the genetics of Prototheca algae, serving as a framework for future studies on the phylogeny and evolution of these peculiar microorganisms.},
}

*Genome, Mitochondrial
Phylogeny
*Genomics/methods
*Evolution, Molecular
*Prototheca/genetics/classification
Base Composition

@article {pmid40835852,
year = {2025},
author = {Weber, J and Hillen, M and Seuberlich, T and Fürmann, A and Gurtner, C and Becker, J and Syring, C and Ruiters, MW and Alsaaod, M and Mazurek, L and Schüpbach, G and Steiner, A},
title = {Successful implementation of a risk assessment and mitigation program to control bovine digital dermatitis at the herd-level.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30577},
pmid = {40835852},
issn = {2045-2322},
abstract = {UNLABELLED: This nonrandomized clinical intervention study was designed as a prospective, multicenter group comparison to evaluate the efficacy of a risk assessment and mitigation program to control bovine digital dermatitis (BDD). The program was implemented over a 1-year period on 9 intervention (INT) farms and 10 control (CTR) farms. Mainstays of the program derived from results of a previous BDD risk factor analysis. All farms were visited monthly to assess within-herd BDD prevalences to perform risk assessments and to treat BDD lesions with salicylic acid paste. Bulk milk samples were collected every 4 months. Diagnosis of BDD was based on visual inspection (clinical scoring) of the feet. Risk-associated management practices were identified on each farm, and management changes expected to prevent further introduction or spread of BDD within INT farms were suggested and agreed upon with farmers of the INT farms. Lesional biopsies were taken from a subset of cows of the INT group before and 2 months after treatment for histopathological and molecular biological examination to confirm histological and bacteriological cure in addition to clinical cure. The initial BDD prevalences for the INT and CTR farms averaged 39.8% (IQR 16.2) and 41.0% (IQR 12.4) for overall BDD lesions, 25.9% (IQR 10.8) and 26.2% (IQR 14.5) for active BDD lesions, and 22.1% (IQR 6.9) and 23.7% (IQR 22.3) for chronic BDD lesions, respectively. After 1 year of implementation, overall BDD prevalences were reduced to 14.1% (IQR 8.2) on INT farms but remained at 41.6% (IQR 10.8) on CTR farms. A significant decline in bulk milk anti-Treponema antibodies over the 1-year period was found in INT as compared to CTR farms. Considering the results of the histopathological examination, of 16S metagenomic sequencing and of the Fluorescence in situ hybridization as indicators for healing, 6/7 (85.7%) selected lesions were cured 2 months post completion of treatment. The results of this study show that the described BDD control measures can markedly reduce the within-herd prevalence of BDD. The proposed procedure might provide the basis for a nationwide BDD mitigation program that could be of importance also beyond national borders.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-12093-5.},
}

@article {pmid40836093,
year = {2025},
author = {He, G and Wang, W and Chen, G and Xie, Y and Parks, JM and Davin, ME and Hettich, RL and Konstantinidis, KT and Löffler, FE},
title = {A novel bacterial protein family that catalyses nitrous oxide reduction.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40836093},
issn = {1476-4687},
abstract = {Nitrous oxide (N2O), a driver of global warming and climate change, has reached unprecedented concentrations in Earth's atmosphere[1]. Current N2O sources outpace N2O sinks, emphasizing the need for comprehensive understanding of processes that consume N2O. Microbes that express the enzyme N2O reductase (N2OR) convert N2O to climate change-neutral dinitrogen (N2). Known N2ORs belong to the canonical clade I and clade II NosZ reductases and are considered key enzymes for N2O reduction[2-4]. Here we report a previously unrecognized protein family with a role in N2O reduction, clade III lactonase-type N2OR (L-N2OR), which diverges in sequence from canonical NosZ but conserves three-dimensional protein structural features. Integrated physiological, metagenomic, proteomic and structural modelling studies demonstrate that L-N2ORs catalyse N2O reduction. L-N2OR genes occur in several phyla, predominantly in uncultured taxa with broad geographic distribution. Our findings expand the known diversity of N2ORs and implicate previously unrecognized taxa (for example, Nitrospinota) in N2O consumption. The expansion of N2OR diversity and the identification of a novel type of catalyst for N2O reduction advances the understanding of N2O sinks, has implications for greenhouse gas emission and climate change modelling, and expands opportunities for innovative biotechnologies aimed at curbing N2O emissions[5,6].},
}

@article {pmid40835708,
year = {2025},
author = {Chuchaona, W and Izquierdo-Lara, RW and Schapendonk, CME and Khongwichit, S and Koopmans, MPG and de Graaf, M and Poovorawan, Y},
title = {Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30672},
pmid = {40835708},
issn = {2045-2322},
support = {No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; No. 874735 (VEO)//The European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement/ ; },
mesh = {Humans ; Thailand ; *Gastroenteritis/virology ; *Coinfection/virology ; *Norovirus/genetics/isolation & purification ; Phylogeny ; Genome, Viral ; Metagenomics/methods ; *Caliciviridae Infections/virology ; *Enterovirus Infections/virology ; *Enterovirus A, Human/genetics/isolation & purification ; Male ; Genomics ; },
abstract = {Acute gastroenteritis (AGE) remains a significant global health concern, with noroviruses among the most prevalent viral pathogens. However, other enteric viruses also contribute substantially to the public health burden. This study provides the first molecular characterization of a co-infection involving a rarely reported enterovirus A76 (EV-A76) and a norovirus GI.6[P11] in a patient from Thailand. Metagenomic sequencing successfully identified complete viral genomes, revealing unique genetic variations. Phylogenetic analysis demonstrated that the EV-A76 strain shares high nucleotide similarity with a recently reported strain from Nepal, distinguishing it from previously identified recombinant strains. The amino acid sequence alignment of the complete EV-A76 genome revealed several distinctive amino acid substitutions compared to the most closely related strains. Notably, variations in the VP1 C-terminus and VP2 EF loop, known for high variability, were observed. These regions, crucial for epitope formation, are particularly susceptible to high-frequency mutations. This study reports the first documented co-infection of EV-A76 and norovirus GI.6[P11] in a single sample, identified through metagenomic sequencing in an AGE case in Thailand in 2023. The observed genetic variations highlight the necessity for ongoing monitoring of viral diversity to strengthen genomic surveillance and inform prevention strategies, especially for emerging pathogens with significant public health implications.},
}

Humans
Thailand
*Gastroenteritis/virology
*Coinfection/virology
*Norovirus/genetics/isolation & purification
Phylogeny
Genome, Viral
Metagenomics/methods
*Caliciviridae Infections/virology
*Enterovirus Infections/virology
*Enterovirus A, Human/genetics/isolation & purification
Male
Genomics

@article {pmid40835198,
year = {2025},
author = {Liu, Q and Wang, M and Xie, JW and Du, YT and Yin, ZG and Cai, JH and Zhao, MH and Jiang, YT and Zhang, HD},
title = {Macrogenome Analysis of Rodents from Heilongjiang Province, China.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107789},
doi = {10.1016/j.actatropica.2025.107789},
pmid = {40835198},
issn = {1873-6254},
abstract = {Rodents are carriers and hosts of numerous zoonotic pathogens, analysing the diversity of viruses and bacteria carried by rodents is important for predicting and reducing the risk of future outbreaks of zoonotic diseases. Heilongjiang is a border province in China with rich ecological resources. In this study, we characterized the zoonotic microbiota (viruses and bacteria) in wild rodents. Sixty-seven rodents representing two species (20 Apodemus peninsulae; 47 Myodes rufocanus) were collected in Hengdaohezi Town, Heilongjiang Province, China. Metagenomic sequencing was employed to characterize pathogen carriage in these reservoirs. The sequencing results showed that the annotated viruses covered 21 viral families, including family Arenaviridae and family Hantaviridae. The annotated bacteria cover 1051 bacterial genera, including genus Salmonella and genus Yersinia. Results of de novo assembly of extracted viral sequences using Megahit showed that 154 contigs were assembled from these two hosts, and 110 of these contigs were mapped to 19 viruses from eight families, including Rat arterivirus1, Amur virus and Lassa mammarenavirus, these results can provide a certain reference for the monitoring and control of rodents in Heilongjiang Province.},
}

@article {pmid40835141,
year = {2025},
author = {Bu, Q and Jiao, L and Liu, Y and Fan, N and Zhang, H and Xu, J and He, A and Xi, Y},
title = {H2O2-modified shrimp shell biochar enhances the digestion of cow manure to produce caproic acid.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133173},
doi = {10.1016/j.biortech.2025.133173},
pmid = {40835141},
issn = {1873-2976},
abstract = {Nitrogen-doped biochar materials can improve electron transfer efficiency through defects between carbon atoms. In this study, H2O2 was used to treat nitrogen-rich shrimp shell biochar to enhance its oxygen-containing functional group structure and improve the electron transfer efficiency of the anaerobic system by investigating the impact of H2O2 on caproic acid production. The results indicated that the concentration of caproic acid reached 29.7 g COD/L following the addition of 15 g/L of H2O2-modified shrimp shell biochar. These concentrations were 58.8 % and 31.4 % higher than those of the control group and the original biochar group, respectively. Mechanistic analysis revealed that H2O2-modified shrimp shell biochar (HBC) facilitated the enrichment of microorganisms linked to caproic acid production, enhanced interspecific electron transfer, and increased the abundance of enzymes related to reverse β-oxidation and fatty acid biosynthesis pathways. Ultimately, these findings pave the way for the development of more efficient processes to produce caproic acid.},
}

@article {pmid40835139,
year = {2025},
author = {Zhong, Y and He, J and Duan, S and Pan, X and Zou, X and Zhang, J and Su, Q and Ng, HY},
title = {Nitrogen-doped biochar supported magnetite enhances hydrolysis and methanogenesis during anaerobic digestion of waste activated sludge in continuously operated reactors: Metagenomic Approach.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133174},
doi = {10.1016/j.biortech.2025.133174},
pmid = {40835139},
issn = {1873-2976},
abstract = {While conductive materials (CMs) are known to enhance anaerobic digestion (AD), comparative efficacies of carbon- and iron-based CMs during AD of waste activated sludge (WAS) have not been investigated. In this study, a novel hybrid conductive material, namely nitrogen-doped biochar supported magnetite (Fe3O4@N-BC), was synthesized and applied in continuously operated up-flow anaerobic sludge blanket reactors. The addition of Fe3O4@N-BC increased methane production rate by 25 %, higher than that of Fe3O4 (19 %) and biochar (13 %). Chryseobacterium and Methanothrix were enriched as key bacteria and archaea responsible for hydrolysis and direct interspecies electron transfer (DIET) in methanogenesis, respectively. Fe3O4@N-BC enhanced hydrolase activities and the construction of e-pili network for electron transfer. Metagenomic data further revealed that electrons were efficiently transferred for CO2-to-CH4 conversion. The results highlight that Fe3O4@N-BC can improve CH4 production during AD of WAS by simultaneously enhancing hydrolysis and DIET in methanogenesis, thereby demonstrating its applicability in continuous AD reactors.},
}

@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.

METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.

RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR = 0.012), and two viral species were reduced in the low-response trajectory group.

CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}

@article {pmid40834840,
year = {2025},
author = {Jia, X and Zheng, Y and Li, D and Cai, J and Yang, J and Rao, Q and Ye, X},
title = {Diagnosis of Leishmania donovani infection via bronchoalveolar lavage fluid next-generation sequencing:A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {4},
pages = {117067},
doi = {10.1016/j.diagmicrobio.2025.117067},
pmid = {40834840},
issn = {1879-0070},
abstract = {Visceral leishmaniasis usually presents with fever, weight loss, enlargement of the spleen and liver, and anemia. Its diagnosis relies on etiological examination, typically by detecting Leishmania parasites in smears of bone marrow, splenic, or lymph node aspirates. We report a case of Leishmania infection presenting predominantly as interstitial pneumonia. The patient showed no significant improvement in pulmonary lesions after empirical antibiotic therapy. Targeted next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF) detected Leishmania donovani species complex. The pulmonary lesions gradually resolved following standard treatment with amphotericin B colloidal dispersion. Through a comprehensive review of previous studies, we examined the pulmonary manifestations of visceral leishmaniasis, encompassing both interstitial pneumonia and secondary parasitic lung infections. Based on our findings, we emphasize the need for enhanced clinical recognition of visceral leishmaniasis-related pulmonary complications among healthcare professionals. Furthermore, we addressed the limitations of this case report.},
}

@article {pmid40834737,
year = {2025},
author = {Xu, J and Gao, Y and Sheng, Z and Bi, X and Huang, S and Ng, HY},
title = {Calcium-loaded activated carbon microtubes as a structural framework of aerobic granules: crosslinking networks overcome native framework limitations.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124418},
doi = {10.1016/j.watres.2025.124418},
pmid = {40834737},
issn = {1879-2448},
abstract = {Aerobic granular sludge (AGS) technology is often constrained by slow granulation and structural instability, issues largely attributed to imbalances in filamentous bacteria and extracellular polymeric substances (EPS). In this study, calcium-loaded activated carbon microtubes (ACMTs-Ca) were developed as novel frameworks to enhance AGS formation and stability. The interfacial energy barrier between microorganisms and ACMTs-Ca was reduced by 67.43 % compared to that between microorganisms and conventional sludge. Incorporation of ACMTs-Ca significantly accelerated granulation kinetics, achieving mature granulation (89.36 % granules >200 μm, SVI30 = 48.35 mL·g[-1], SVI30/SVI5 = 99.15 %) within 30 d, in contrast to 140 d required by the control. AGS with ACMTs-Ca as the primary framework exhibited an 80 % enhancement in structural strength relative to the control. The improved structural integrity was attributed to the formation of a calcium-alginate coordination network with β-polysaccharides, thereby reducing dependence on filamentous bacteria for granule stability. Enhanced pollutant removal efficiencies were observed, with AGS-ACMTs-Ca system achieving COD, TN, and TP removal rates of 96 %, 80 %, and 99.48 %, respectively, facilitated by the enrichment of functional genera such as Candidatus_Competibacter, Thauera, and Flavobacterium. Metagenomic analysis revealed increased relative abundance of algE genes (associated with β-polysaccharide synthesis) alongside decreased abundance of genes involved in amino acid biosynthesis pathways. These abundance shifts suggest potential microbial regulation favoring EPS compositional changes toward calcium-stabilized frameworks. This study demonstrates the dual role of ACMTs-Ca in structural reinforcement and microbial niche regulation, offering a sustainable strategy for rapid and robust AGS cultivation.},
}

@article {pmid40834730,
year = {2025},
author = {Páez-Watson, T and Jansens, C and van Loosdrecht, MCM and Roy, S},
title = {Co-substrate utilisation in "Candidatus Accumulibacter" enhances metabolic fitness in dynamic environments.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124401},
doi = {10.1016/j.watres.2025.124401},
pmid = {40834730},
issn = {1879-2448},
abstract = {Optimizing resource use is essential for the survival and fitness of species in microbial communities ubiquitous in natural and engineered ecosystems. These ecosystems are often characterized by the simultaneous presence of multiple substrates such as volatile fatty acids, amino acids and sugars. Yet, the evaluation of metabolic potential for these microbial community members is predominantly based on single substrate utilisation. Metabolic and ecological implications of the interactions of multiple substrates, particularly in environments with changes in redox conditions and substrate availability, remain poorly understood. In this study, we investigate the metabolic interactions resulting from co-substrate utilization in polyphosphate-accumulating organisms within wastewater treatment systems. We combined experimental analysis of highly enriched "Ca. Accumulibacter" mixed cultures with genome-resolved metagenomics and conditional flux balance analysis (cFBA) to quantify the physiological relevance of co-substrate uptake. We observe that anaerobic co-substrate utilisation of acetate and aspartate result in metabolic interactions leading to optimized redox balance, reduced ATP losses and increased biomass yields by up to 8% compared to individual substrate use. Metabolic modelling revealed that these benefits emerge from the network topology, where the interaction of different metabolic routes gives rise to synergistic effects. Extending our analysis to additional substrate pairs, we classify metabolic interactions into three general types: (i) neutral, (ii) one-way synergistic and (iii) reciprocal synergistic. Our findings highlight the importance of metabolic interactions and cellular resource allocation strategies in dynamic microbial ecosystems. This study provides a broader ecological framework for understanding competitive metabolic strategies in environmental organisms. Co-substrate utilization can have direct implications for improving the yield or productivity of bioprocesses.},
}

@article {pmid40834728,
year = {2025},
author = {Bains, A and Dahal, S and Manna, B and Lyte, M and Yang, L and Singhal, N},
title = {L-norepinephrine induces community shift, oxidative stress response, metabolic reprogramming, and virulence potential in wastewater microbiomes.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124353},
doi = {10.1016/j.watres.2025.124353},
pmid = {40834728},
issn = {1879-2448},
abstract = {Neuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. l-norepinephrine (L-NE), which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and faeces. While extensive pure culture studies have established l-NE's capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of l-NE (1 × 10[-5] M to 1 × 10[-4] M), dextrose, and H2O2 in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, l-NE treatments achieved superior growth (10[8] CFU mL[-1]) while maintaining Pseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR, soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls, representing typical carbon substrate utilization, l-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, l-NE significantly enhanced autoinducer gene (luxS, qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal l-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.},
}

@article {pmid40834570,
year = {2025},
author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L},
title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127000},
doi = {10.1016/j.jenvman.2025.127000},
pmid = {40834570},
issn = {1095-8630},
abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.},
}

@article {pmid40834509,
year = {2025},
author = {Poshvina, DV and Balkin, AS and Dilbaryan, DS and Vasilchenko, AS},
title = {Unravelling the response of the soil microbiome to macrolactin A: A metagenomic study.},
journal = {Chemosphere},
volume = {387},
number = {},
pages = {144645},
doi = {10.1016/j.chemosphere.2025.144645},
pmid = {40834509},
issn = {1879-1298},
abstract = {The development of environmentally sustainable biopreparations for crop protection requires comprehensive assessment of their microbiome impacts. This study investigates how macrolactin A (McA)-a polyketide antibiotic produced by plant-beneficial Bacillus velezensis-shapes soil microbial communities and antibiotic resistance gene (ARG) profiles under various agricultural scenarios. Using high-throughput metagenomics and network analysis, we compared untreated soils with those exposed to two McA concentrations: a high dose (10 mg/kg soil, representing potential point-source accumulation) and a low dose (1 mg/kg, mimicking natural rhizosphere levels). While overall ARG α- and β-diversity remained stable, we observed significant taxonomic restructuring, with Pseudomonadota increasing by 1.36-2.15 % and Actinomycetota declining by 1.14-1.74 % across treatments. Resistome analysis showed dose-dependent ARG selection: control soils favored target alteration mechanism, whereas McA promoted efflux, inactivation, and protection mechanisms. Network analysis demonstrated disruption of complex ARG-host associations, as control-dominant genera belonging to Actinomycetota (Conexibacter, Baekduia, and Capillimicrobium) maintaining 16-21 ARGs per genome decreased, while genera belonging to Pseudomonadota (Bradyrhizobium, Mesorhizobium, Paraburkholderia, and Piscinibacter) with streamlined resistomes (1-2 ARGs) became prevalent. Functional gene profiling (COGs) and annotation of MAGs revealed dose-dependent restructuring: low-dose McA enriched chemotaxis systems and broad-spectrum efflux pumps, facilitating motile escape and energy-efficient resistance, whereas high-dose exposure selected for secondary metabolite synthesis, metal transporters, and cell wall remodeling genes, indicating defensive countermeasures. These findings demonstrate McA's biphasic selection: low doses favor avoidance strategies (efflux/motility), while high doses enforce biosynthetic defenses and structural resilience. The results support the hypothesis that narrow-spectrum antibiotics act as ecosystem engineers through metabolic trade-offs, highlighting the need to evaluate resistome restructuring in biocontrol agent risk assessments.},
}

@article {pmid40833948,
year = {2025},
author = {Kanyerezi, S and Guerfali, FZ and Anzaku, AA and Babaleye, OA and Calvert-Joshua, T and Nguinkal, JA and Amoo, OP and Atri, C and Khan, W and Saleh, I and Nisar, MI and Kasambula, AS and Morapedi, K and Mboowa, G},
title = {Correction: Wastewater metagenomics in Africa: Opportunities and challenges.},
journal = {PLOS global public health},
volume = {5},
number = {8},
pages = {e0005097},
doi = {10.1371/journal.pgph.0005097},
pmid = {40833948},
issn = {2767-3375},
abstract = {[This corrects the article DOI: 10.1371/journal.pgph.0004044.].},
}

@article {pmid40833852,
year = {2025},
author = {Vander Donck, L and Victor, M and Van Beeck, W and Van Rillaer, T and Dillen, J and Ahannach, S and Wittouck, S and Allonsius, CN and Lebeer, S},
title = {Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116171},
doi = {10.1016/j.celrep.2025.116171},
pmid = {40833852},
issn = {2211-1247},
abstract = {The human vagina is a unique microbiome, typically predominated by Lactobacillus species in healthy women. However, we currently lack an understanding of why lactobacilli predominate in this environment and how these bacteria interact, aspects that are crucial for developing microbiome-based therapeutics. In this study, we used cost-efficient synthetic communities (SynComs) to investigate the stability and dynamics of Lactobacillus-predominated vaginal communities from healthy women independent of host influence. Reproducible communities of Lactobacillus crispatus co-occurring with Limosilactobacillus species and Lactobacillus jensenii were established in top-down experiments. Co-occurrence was verified with compositional correlation patterns in metagenome sequencing data and reproduced through a bottom-up approach. This co-occurrence pattern was independent of strain selection, host factors, and inoculation ratio. Genome-scale metabolic models predicted potential cross-feeding involving amino acids (e.g., L-arginine, L-lysine, and γ-aminobutyric acid [GABA]) and vitamins as mechanisms mediating their co-occurrence. This study provides a framework for developing reproducible synthetic vaginal Lactobacillus communities and informs future microbiome-based therapies.},
}

@article {pmid40833800,
year = {2025},
author = {Kaspersen, HP and Estensmo, EL and Slettemeås, JS and Haverkamp, THA and Sjurseth, SK and Granstad, S and Sekse, C and Frederiksen, RF and Urdahl, AM},
title = {Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001466},
pmid = {40833800},
issn = {2057-5858},
mesh = {Animals ; *Monensin/pharmacology ; *Turkeys/microbiology ; *Bifidobacterium/drug effects/genetics/classification/isolation & purification ; Poultry Diseases/prevention & control/microbiology ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Norway ; Female ; Male ; Coccidiosis/veterinary/prevention & control ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Coccidiostats/pharmacology ; },
abstract = {Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of Bifidobacterium spp. was observed in the samples from monensin-exposed turkeys, including Bifidobacterium pullorum, Bifidobacterium longum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium animalis. Additionally, a decrease in Megamonas and Megasphaera species was detected in these samples. Further, species within the Clostridium genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of Bifidobacterium spp. in the caecum of turkeys, while decreasing the abundance of Megamonas and Megasphaera species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable Bifidobacterium spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of Bifidobacterium spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.},
}

Animals
*Monensin/pharmacology
*Turkeys/microbiology
*Bifidobacterium/drug effects/genetics/classification/isolation & purification
Poultry Diseases/prevention & control/microbiology
Cecum/microbiology
*Gastrointestinal Microbiome/drug effects
Norway
Female
Male
Coccidiosis/veterinary/prevention & control
Metagenomics
Anti-Bacterial Agents/pharmacology
*Coccidiostats/pharmacology

@article {pmid40833797,
year = {2025},
author = {O'Ferrall, AM and Juhász, A and Jones, S and Makaula, P and Namacha, G and Ame, S and Oguttu, D and Foo, A and Kayuni, SA and LaCourse, EJ and Musaya, J and Stothard, JR and Roberts, AP},
title = {Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001480},
pmid = {40833797},
issn = {2057-5858},
mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Snails/microbiology ; Fresh Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Uganda ; Tanzania ; United Kingdom ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Bacterial Proteins/genetics ; Bacteria/genetics ; },
abstract = {The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance. Here, we evaluate freshwater snails, which are geographically widespread aquatic invertebrates, as environmental reservoirs of ARGs. We collected faeces from eight gastropod genera at 15 freshwater locations across Malawi, Uganda, Zanzibar and the UK and conducted the first freshwater snail faecal metagenomic study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems. All ARGs that could be assembled into metagenome-assembled genomes (MAGs) were found within Proteobacteria, which dominated the faecal microbiomes and were strongly associated with the total ARG load. In Malawi, we linked bla OXA-181 (bla OXA-48-like), a previously mobilized carbapenemase gene, to Shewanella xiamenensis, the gene's known progenitor. We detected another bla OXA-48-like gene by read mapping from a sample in the UK. We identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations, with two mcr-7-like genes being found in an Aeromonas jandaei MAG in Uganda. Our findings highlight freshwater snail faeces as a One Health-relevant environmental reservoir of clinically important ARGs.},
}

Animals
*Feces/microbiology
*Metagenome
*Snails/microbiology
Fresh Water/microbiology
Anti-Bacterial Agents/pharmacology
Uganda
Tanzania
United Kingdom
*Drug Resistance, Bacterial/genetics
Metagenomics
Bacterial Proteins/genetics
Bacteria/genetics

@article {pmid40833630,
year = {2025},
author = {Sampasivam, Y and Razman, KK and Mazlan, NSM and Azizan, KA and Ahlawat, YK and Othman, R},
title = {Towards Sustainable Agarwood Production: Integrating Microbial Interactions, Anatomical Changes, and Metabolite Biosynthesis.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuaf025},
pmid = {40833630},
issn = {1476-5535},
abstract = {Agarwood is a highly valuable non-timber forest product mainly derived from the Aquilaria genus, widely traded in the perfumery, religious items, and traditional medicine industries. Naturally, agarwood forms within the xylem as part of the tree's defense mechanism against environmental stressors and microbial infection. The escalating demand for agarwood has led to the overexploitation of Aquilaria species, with some now classified as critically endangered. Despite advancements in artificial induction methods for sustainable agarwood supply, the intricate links between physiological and molecular mechanisms governing its formation remain poorly understood. This review addresses these knowledge gaps by examining the interplay between morphological changes in xylem structure during tylose formation and molecular alterations, particularly the biosynthesis of 2-(2-phenylethyl)chromones (PECs), key compounds in agarwood. Additionally, it integrates findings from multi-omics approaches including genomics, transcriptomics, proteomics, and metagenomics to reveal how secondary metabolite biosynthesis, including PECs and terpenes, is regulated across various Aquilaria species, regions, and induction techniques. The role of microbial communities, particularly endophytes such as Fusarium, in regulating agarwood formation is also discussed, emphasizing their involvement in both natural and artificial induction strategies. Furthermore, this review explores the role of reactive oxygen species (ROS) in mediating morphological and biochemical defense responses, alongside the functions of transcription factors (TFs), protein kinases, and signaling molecules in balancing defense and growth. However, the crosstalk between key genes such as chalcone synthases, MAPK, cytochromes, NADPH oxidases, TFs, and miRNAs require further study to fully understand the complex defense mechanisms in Aquilaria trees. Overall, this review aims to bridge the current knowledge gaps by linking morphological and biochemical changes in agarwood formation, particularly PEC biosynthesis, while proposing metabolite engineering using microbial hosts as a promising tool for sustainable and technology-driven agarwood production.},
}

@article {pmid40833501,
year = {2025},
author = {Annamalai, A and Sasikumar, R},
title = {Enzymatic valorization of fishery by-products: harnessing cold-adapted marine proteases for sustainable production of bioactive peptides.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {232},
pmid = {40833501},
issn = {1432-072X},
mesh = {*Peptide Hydrolases/metabolism/chemistry ; Cold Temperature ; Animals ; *Peptides/metabolism/chemistry ; Fisheries ; Fishes ; Aquatic Organisms/enzymology ; Aquaculture ; },
abstract = {The rapid expansion of aquaculture and fish processing industries has resulted in the annual generation of approximately 99 million tons of fishery byproducts, including heads, bones, skin, viscera, and fish scales. These residual biomasses are typically underutilized despite their richness in proteins, lipids, collagen, and other bioactive compounds. Recent advancements in enzymatic valorization, particularly through the application of cold-adapted marine proteases, have offered eco-efficient solutions for converting these byproducts into high-value bioactive peptides and nutraceutical ingredients. Cold-adapted proteases function efficiently at low temperatures, preserving thermolabile compounds, reducing energy input, and minimizing undesirable reactions. This review critically examines the biochemical composition of fishery by-products and explores the distinctive structural and catalytic properties of cold-adapted proteases. We highlight novel strategies for their discovery using metagenomics, bioinformatics and AI-assisted enzyme engineering. Process optimization aspects, including the use of membrane bioreactors, immobilization supports, and downstream purification techniques, are discussed, with an emphasis on improving the yield, stability, and scalability. The bioactivities of the derived peptides, such as antioxidant, ACE-inhibitory, antimicrobial, and anti-inflammatory effects, are summarized alongside their emerging functional roles in metabolic regulation and in wound healing. This article presents case studies, economic assessments, and regulatory considerations to evaluate the commercial viability of cold-adapted biocatalysis in the circular blue bioeconomy. Finally, technical limitations, such as enzyme deactivation, recovery, and cost-performance ratios, are critically analyzed, and future directions for sustainable marine biorefinery development are discussed.},
}

*Peptide Hydrolases/metabolism/chemistry
Cold Temperature
Animals
*Peptides/metabolism/chemistry
Fisheries
Fishes
Aquatic Organisms/enzymology
Aquaculture

@article {pmid40833454,
year = {2025},
author = {Fong, GY and Chan, KG and Goh, WL and Yap, ML},
title = {Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {134},
pmid = {40833454},
issn = {1572-9699},
support = {IPSR/RMC/UTARRF/2022-C1/Y01//Universiti Tunku Abdul Rahman/ ; },
mesh = {Animals ; *Columbidae/microbiology/virology ; *Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics ; Viruses/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification/drug effects ; Metagenome ; Malaysia ; *Microbiota ; Biodiversity ; Phylogeny ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.},
}

Animals
*Columbidae/microbiology/virology
*Feces/microbiology/virology
*Bacteria/genetics/classification/isolation & purification/drug effects
Metagenomics
Viruses/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification/drug effects
Metagenome
Malaysia
*Microbiota
Biodiversity
Phylogeny
*Drug Resistance, Microbial/genetics

@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0311924},
doi = {10.1128/spectrum.03119-24},
pmid = {40833093},
issn = {2165-0497},
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}

@article {pmid40832979,
year = {2025},
author = {Zhou, W and Fan, Y and Zhang, X and Liu, M and Jiang, S and Shang, E and Duan, J},
title = {Amelioration of Guishao Yigong Decoction on Colorectal Cancer Through the Integration of 16S rRNA Sequencing and Fecal Metabolomics.},
journal = {Biomedical chromatography : BMC},
volume = {39},
number = {10},
pages = {e70198},
doi = {10.1002/bmc.70198},
pmid = {40832979},
issn = {1099-0801},
support = {ZDXM-3-9//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; },
mesh = {Animals ; *Colorectal Neoplasms/metabolism/drug therapy/microbiology ; *Feces/chemistry/microbiology ; *Drugs, Chinese Herbal/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; *Metabolome/drug effects ; Male ; },
abstract = {Guishao Yigong Decoction (GYD), a classical formula, has been used to treat colorectal cancer (CRC) in clinical practices. However, its mechanism is still unclear. Increasing evidence suggests that the gut microbiota may serve as a potential target for treating CRC. Therefore, this study aims to elucidate the amelioration and potential mechanism of GYD on CRC by comprehensively analyzing the metagenome of gut microbiota and fecal metabolome. The results indicated that GYD significantly reduced the number and size of adenomas in the mouse colon, decreased spleen index, alleviated mouse emaciation and rectal bleeding, and protected the colonic barrier. 16S rRNA gene sequencing analysis revealed that GYD could markedly improve the dysbiosis of gut microbiota in CRC mice, increasing the abundance of beneficial bacteria and decreasing the abundance of pathogenic bacteria. Furthermore, the disordered fecal metabolic profiling of CRC mice was notably reversed by GYD. Following GYD administration, metabolites such as thiamine pyrophosphate, 3-methylpentanoic acid, and propanoic acid significantly increased, whereas 2-hydroxy-2-methylpropanoic acid, levodopa, and stearic acid remarkably decreased. Correlation analysis further indicated a close relationship between differential gut microbiota and metabolites. In conclusion, the amelioration of GYD on CRC might involve the regulation of gut microbiota and its metabolism.},
}

Animals
*Colorectal Neoplasms/metabolism/drug therapy/microbiology
*Feces/chemistry/microbiology
*Drugs, Chinese Herbal/pharmacology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/drug effects
Mice
Metabolomics/methods
*Metabolome/drug effects
Male

@article {pmid40832781,
year = {2025},
author = {Tian, Y and Xu, Q and Wu, Z and Wang, H and Hu, X and He, N and Li, H and Liu, B and Zhong, Y and Zhang, H and Wang, M and Xiao, L and Li, S and Zou, Y},
title = {Ameliorating Effect of Bifidobacterium breve CM02-09T on High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease in Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {16},
pages = {e70957},
doi = {10.1096/fj.202501250RR},
pmid = {40832781},
issn = {1530-6860},
support = {32100009//National Natural Science Foundation of China-Guangdong Joint Fund/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy ; *Diet, High-Fat/adverse effects ; Male ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Mice ; *Bifidobacterium breve/physiology ; *Gastrointestinal Microbiome ; Liver/metabolism/pathology ; },
abstract = {Evidences have demonstrated that the regulation of gut microbiota by probiotics can be utilized to prevent nonalcoholic fatty liver disease (NAFLD); Bifidobacterium was widely used as a potential therapeutic alternative for metabolic diseases. In this study, the probiotic functions of Bifidobacterium breve CM02-09T and its effects on NAFLD were investigated through genome annotation and high-fat diet (HFD)-induced mouse model. The genome of B. breve CM02-09T consists of a single circular chromosome of 2 372 890 bp. Eighteen male C57BL/6J mice were fed a normal chow diet (NCD), a high-fat diet, and a high-fat diet (HFD) with B. breve CM02-09T separately for 12 weeks. Histopathology, lipid content, biochemical markers in the liver and blood, and metagenomics were assessed and compared. Our results indicate that supplementation with B. breve CM02-09T alleviated liver damage, reduced fat accumulation in the liver and epididymal adipose tissue, decreased TNF-α concentration, and improved NAFLD activity scores. Metagenomic analysis revealed that administration of B. breve CM02-09T promoted a decreased Firmicutes/Bacteroidetes ratio (F/B), an increase in beneficial bacteria, and enhanced lipid metabolism functions. Correlation analysis between the differential species and NAFLD-related indicators suggested that the anti-NAFLD effect of B. breve CM02-09T is related to the gut microbiota. Therefore, B. breve CM02-09T attenuates NAFLD by modulating the gut microbiota and could be used as an alternative therapeutic strategy.},
}

Animals
*Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy
*Diet, High-Fat/adverse effects
Male
*Probiotics/pharmacology
Mice, Inbred C57BL
Mice
*Bifidobacterium breve/physiology
*Gastrointestinal Microbiome
Liver/metabolism/pathology

@article {pmid40832572,
year = {2025},
author = {Zhang, S and Wu, J and Wang, D and Song, J and Li, Y and Yin, C and Sun, C and Ding, S and Liu, T and Kou, Z},
title = {The First Imported Case of Zika Virus Infection - Shandong Province, China, 2025.},
journal = {China CDC weekly},
volume = {7},
number = {30},
pages = {1004-1008},
pmid = {40832572},
issn = {2096-7071},
abstract = {Zika virus (ZIKV) is transmitted primarily through mosquito vectors, including Aedes albopictus and Aedes aegypti, both of which are distributed across multiple provinces in China. Approximately 80% of ZIKV infections remain asymptomatic, while symptomatic cases typically manifest as mild, self-limiting illnesses lacking pathognomonic features. Common clinical presentations include maculopapular rash, low-grade fever, conjunctivitis, arthralgia, and myalgia.

WHAT IS ADDED BY THIS REPORT?: The clinical manifestations of ZIKV infection are nonspecific and may closely mimic other febrile illnesses, complicating differential diagnosis. This study documents the first laboratory-confirmed ZIKV infection case in Shandong Province. The patient exhibited fever accompanied by extensive subcutaneous petechiae, predominantly distributed across the chest and upper extremities.

This investigation provides a comprehensive epidemiological analysis and phylogenetic characterization of a ZIKV infection case imported from Thailand. In accordance with China's Border Health and Quarantine Law, international port cities must strengthen surveillance and diagnostic testing for imported infectious diseases. For cases presenting with unclear diagnoses, healthcare providers should prioritize obtaining detailed 30-day travel histories to evaluate potential exposure risks of imported infectious diseases.},
}

@article {pmid40832300,
year = {2025},
author = {Horvath, ERB and Winter, JM},
title = {SeqForge: A scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.12.669971},
pmid = {40832300},
issn = {2692-8205},
abstract = {BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST+ remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers.

RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST+ database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage.

CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.},
}

@article {pmid40832205,
year = {2025},
author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, T and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G},
title = {Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.30.615906},
pmid = {40832205},
issn = {2692-8205},
abstract = {Fecal microbiota transplantation (FMT) has revolutionized the treatment of recurrent Clostridioides difficile infection (rCDI) and is being evaluated across other diseases. Accurate tracking of bacterial strains that stably engraft in recipients is critical for understanding the determinants of strain engraftment, evaluating their correlation with clinical outcomes, and guiding the development of therapeutic bacterial consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. In this study, we described a novel framework, LongTrack, which uses long-read metagenomic assemblies and rigorous informatics tailored for FMT strain tracking. We highlighted LongTrack advantage over short-read approaches especially when multiple strains co-exist in the same sample. We showed LongTrack uncovered hundreds of engrafted strains across six FMT cases of rCDI and inflammatory bowel disease patients. Furthermore, long reads also allowed us to assess the genomic and epigenomic stability of engrafted strains during the 5-year follow-ups, revealing structural variations that may be associated with strain adaptation in a new host environment. Combined, our study advocates the use of long-read metagenomics and LongTrack to enhance strain tracking in future FMT studies, paving the way for the development of more effective defined biotherapeutic as an alternative to FMT.},
}

@article {pmid40832181,
year = {2025},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {A prevalent huge phage clade in human and animal gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.10.669567},
pmid = {40832181},
issn = {2692-8205},
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

@article {pmid40831761,
year = {2025},
author = {Nikaein, H and Sharifi-Zarchi, A},
title = {Multi-metric locality sensitive hashing enhances alignment accuracy of bisulfite sequencing reads: BisHash.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf144},
pmid = {40831761},
issn = {2635-0041},
abstract = {MOTIVATION: Locality-Sensitive Hashing (LSH) is a widely used algorithm for estimating similarity between large datasets in bioinformatics, with applications in genome assembly, sequence alignment, and metagenomics. However, traditional single-metric LSH approaches often lead to inefficiencies, particularly when handling biological data where regions may have diverse evolutionary histories or structural properties. This limitation can reduce accuracy in sequence alignment, variant calling, and functional analysis.

RESULTS: We propose Multi-Metric Locality-Sensitive Hashing (M2LSH), an extension of LSH that integrates multiple similarity metrics for more accurate analysis of complex biological data. By capturing diverse sequence and structural features, M2LSH improves performance in heterogeneous and evolutionarily diverse regions. Building on this, we introduce Multi-Metric MinHash (M3Hash), enhancing sequence alignment and similarity detection. As a proof of concept, we present BisHash, which applies M2LSH to bisulfite sequencing, a key method in DNA methylation analysis. Although not fully optimized, BisHash demonstrates superior accuracy, particularly in challenging scenarios like cancer studies where traditional approaches often fail. Our results highlight the potential of M2LSH and M3Hash to advance bioinformatics research.

The source code for BisHash and the test procedures for benchmarking aligners using simulated data are publicly accessible at https://github.com/hnikaein/bisHash.},
}

@article {pmid40830754,
year = {2025},
author = {Li, Q and Fan, X and Wang, K and Wu, X and Li, J and An, Y and Wei, P and Shi, W and Shan, Y and Chen, S and Zhao, G},
title = {Subdural empyema caused by Aggregatibacter segnis: a rare case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1042},
pmid = {40830754},
issn = {1471-2334},
support = {Z221100007422016//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; 82030037//National Natural Science Foundation of China/ ; 2023XACX0005//Science and Technology Innovation Program of Xiongan New Area/ ; ZLRK202319//Beijing Hospitals Authority Clinical medicine Development of special funding support/ ; 11000023T000002036286//Translational and Application Project of Brain-inspired and Network Neuroscience on Brain Disorders, Beijing Municipal Health Commission/ ; 2021ZD0201801//STI2030-Major Projects/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Empyema, Subdural/microbiology/diagnosis/drug therapy/surgery/diagnostic imaging ; Anti-Bacterial Agents/therapeutic use ; *Pasteurellaceae Infections/microbiology/diagnosis/drug therapy ; *Pasteurellaceae/isolation & purification/genetics ; Magnetic Resonance Imaging ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Aggregatibacter species are Gram-negative bacteria typically recognized as oral saprophytes in humans, with invasive infections uncommon in immunocompetent individuals. To the best our knowledge, this is the first reported case of subdural empyema attributed to Aggregatibacter segnis (A. segnis).

CASE PRESENTATION: A 50-year-old female was transferred to our hospital from a local facility due to headache, fever, and left-sided limb numbness. Initially suspected of subdural hematoma and viral encephalitis, she did not respond well to prior treatment. Cerebral computed tomography and magnetic resonance imaging revealed a subdural lesion in the frontal-temporal region and sinusitis. Virus-related tests, smear, and culture of cerebrospinal fluid (CSF) were negative. Craniotomy was performed to evacuate the subdual empyema, and A. segnis was detected in the culture of pus. The discrepancy between metagenomic next-generation sequencing (mNGS) and culture highlights diagnostic challenges in this pretreated patient. Antibiotic treatment was guided by culture results and mNGS. Clinical symptoms resolved gradually following surgery and administration of antibiotics.

CONCLUSIONS: This rare case suggested that A. segnis should be considered in the diagnosis of subdural empyema. Multimodal diagnostics, prompt neurosurgical management, and individualized antimicrobial stewardship are crucial in managing rare central nervous system infections.},
}

Humans
Female
Middle Aged
*Empyema, Subdural/microbiology/diagnosis/drug therapy/surgery/diagnostic imaging
Anti-Bacterial Agents/therapeutic use
*Pasteurellaceae Infections/microbiology/diagnosis/drug therapy
*Pasteurellaceae/isolation & purification/genetics
Magnetic Resonance Imaging
Tomography, X-Ray Computed

@article {pmid40830751,
year = {2025},
author = {Ahmad, AA and Fletcher, K and Hesford, N and Glendinning, L},
title = {Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {520},
pmid = {40830751},
issn = {1471-2180},
support = {BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Chancellor's Fellowship//University of Edinburgh/ ; },
}

@article {pmid40830497,
year = {2025},
author = {Marialva, EF and Martins-Campos, KM and de Almeida, VR and Ríos-Velasquez, CM and Tempone, AJ and Pessoa, FAC and Traub-Cseko, YM},
title = {Investigation of bacterial microbiota variability in two allopatric populations of Nyssomyia umbratilis, susceptible and nonsusceptible to Leishmania (Viannia) guyanensis infection in the Amazon region.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {354},
pmid = {40830497},
issn = {1756-3305},
mesh = {Animals ; *Psychodidae/microbiology/parasitology ; Brazil ; Female ; *Leishmania guyanensis/physiology ; *Insect Vectors/microbiology/parasitology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Humans ; },
abstract = {BACKGROUND: Sand flies of the species Nyssomyia umbratilis (Diptera: Psychodidae: Phlebotominae) are vectors of the parasite Leishmania (Viannia) guyanensis, one of the etiological agents of cutaneous leishmaniasis in the Amazon region. In addition, Ny. umbratilis is a cryptic species, with populations showing differences in their ability to transmit the parasite. For instance, populations of Ny. umbratilis from the Manacapuru municipality (MAN), located on the south bank of the Negro river, in the Amazonas state of Brazil, shows refractoriness to Leishmania infection, while populations from Rio Preto da Eva municipality (RPE), located on the north bank of the Negro river, are susceptible to infection. This lack of vectorial capacity may be caused by several factors, including the intestinal bacterial microbiota of sand flies.

METHODS: In this work, we carried out a metagenomic study of the intestinal microbiota of Ny. umbratilis populations from MAN and RPE. Ny. umbratilis females were collected in forested areas, sand fly midguts were dissected, DNA was extracted, and the 16 S rRNA gene sequenced to identify the bacterial composition of the microbiota.

RESULTS: In total, 16 phyla, 33 classes, 49 orders, 93 families, and 112 genera of bacteria were identified. The phylum Proteobacteria was the most frequent (85.9%) in both localities, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes with, 9.9%, 4.9%, and 4.4%, respectively. In MAN, 84 genera were identified and 79 in RPE, with MAN having a greater richness compared with RPE. Among these, the genera Rickettsia, Prevotella, Porphyromonas, Peptostreptococcus, and Caulobacter were the most prevalent in MAN, and the genera Rickettsia, Prevotella, Cryocola, Porphyromonas, and Caulobacter were the most prevalent in RPE.

CONCLUSIONS: Bacterial microbiota from MAN insects presents a greater diversity in relation to the RPE insects. Some of the identified bacteria have the potential to be used in alternative transmission control approaches as the development of transgenic vectors, and also, bacteria found exclusively in MAN sand flies may be candidates for a future transmission control approach to combat leishmaniasis in the Amazon region.},
}

Animals
*Psychodidae/microbiology/parasitology
Brazil
Female
*Leishmania guyanensis/physiology
*Insect Vectors/microbiology/parasitology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Microbiota
Humans

@article {pmid40829558,
year = {2025},
author = {Huang, WC and Spang, A},
title = {DPANN archaea.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R791-R794},
doi = {10.1016/j.cub.2025.06.038},
pmid = {40829558},
issn = {1879-0445},
mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; },
abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.},
}

*Archaea/genetics/physiology/classification/metabolism
*Symbiosis
Phylogeny
*Genome, Archaeal
Biological Evolution

@article {pmid40829433,
year = {2025},
author = {Chen, W and He, Y and Xiang, Y and Xie, L},
title = {Porous filter balls alternating internal structure of aerobic composting to drive rapid stabilization and efficient metabolic collaboration.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115082},
doi = {10.1016/j.wasman.2025.115082},
pmid = {40829433},
issn = {1879-2456},
abstract = {Co-composting of food waste and agricultural residues offers a promising biotechnological solution for organic solid waste management, where oxygen availability critically governs efficiency. This study evaluated the impact of polypropylene-based porous filter balls (PFB) on composting performance. The results demonstrated that PFB addition elevated peak temperature by 10.1 % and reduced oxygen content by 11.2-55.3 % compared to the control (CK), indicating enhanced oxygen utilization through construction of transport channels. Meanwhile, PFB treatment accelerated organic matter and crude fiber degradation, shortening maturation time by 14 days while improving end-product quality. Three-dimensional excitation emission matrix analysis confirmed enhanced humification, and physical characterization revealed a more porous structure with greater soil amendment potential. Microbial analysis showed that PFB addition enriched organic-degrading taxa (e.g., Aeribacillus) and strengthened metabolic cooperation. Metagenomic analysis further revealed upregulation of key pathways including dissimilatory nitrate reduction to ammonium, glycolysis, fatty acid metabolism, tricarboxylic acid cycle and aromatic amino acid biosynthesis, collectively improving nitrogen retention, degradation efficiency and humification. This study establishes PFB treatment as an effective oxygen-management strategy for enhancing composting efficiency and product quality.},
}

@article {pmid40829401,
year = {2025},
author = {Zhang, J and Chen, J and Wang, C and Wang, P and Feng, B and Gao, H and Chen, D},
title = {Nitrate input enriched the antibiotic resistance genes in lake sediments by shaping co-host community and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139580},
doi = {10.1016/j.jhazmat.2025.139580},
pmid = {40829401},
issn = {1873-3336},
abstract = {The impact of various non-antibiotic factors on antibiotic resistance has garnered widespread attention. However, there has been little investigation into whether the coexistence of nutrients with antibiotic resistance genes (ARGs) in aquatic ecosystems contributes to the increasing abundance of ARGs. We employed a microcosm experiment and metagenomic analysis to investigate the impact of nitrate on ARG profiles in lake sediments. Our results revealed that increased nitrate input correspondingly elevated the abundance of sediment ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and nitrate reduction genes (NRGs). Among the metagenome-assembled genomes (MAGs) harboring ARGs found by binning analysis, nitrate inputs increased the abundance of 78.4 % ARG-carried MAGs, especially in genera Nitrosomonas and Sulfuriomonas. All MAGs carrying ARGs simultaneously encoded NRGs, suggesting that ARG-NRG co-hosts are important factors for ARG proliferation. Co-localization and Pearson's correlation analyses suggested that nitrate input most likely accelerated the acquisition of ARGs by particular bacterial taxa via horizontal gene transfer (HGT). Genes involved in HGT, including those related to reactive oxygen species production, membrane permeability, ATP synthesis, and pili synthesis, were also upregulated by nitrate input, thus potentially enhancing ARG transfer. Based on the partial least squares path modeling analysis, abundances of genes involved in HGT (r = 0.43) and ARG-NRG co-hosts (r = 0.41) had the highest direct positive impact on the ARG abundance. Our study suggests the increased nitrate levels may drive the dissemination of antibiotic resistance, consequently affecting human health.},
}

@article {pmid40829219,
year = {2025},
author = {Jing, J and Wang, T and Guo, X and Huang, P and Li, C and Qu, Y},
title = {Continuous exogenous bioaugmented remediation of petroleum-contaminated soil: Ecological effects, microbial communities, and mechanisms.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127007},
doi = {10.1016/j.jenvman.2025.127007},
pmid = {40829219},
issn = {1095-8630},
abstract = {The exogenous bioaugmentation technique is a widely employed strategy for remediating petroleum-contaminated soil. However, sustaining exogenous functional bacteria over extended periods in complex petroleum-contaminated environments is challenging, leading to reduced efficacy, and the interaction mechanisms with indigenous microorganisms remain poorly understood. This study utilized the previously developed petroleum-degrading bacterial agent ECT in a continuous bioaugmentation (C-Bio) approach for soil remediation. The outcomes were compared with those from a disposable bioaugmentation (D-Bio) and a control group (CG). After a 200-day remediation period, the C-Bio approach achieved a simulated petroleum degradation rate of 99.42 %. Concurrently, assessments of soil physicochemical properties, enzyme activities, and plant growth demonstrated that C-Bio resulted in favorable ecological restoration. Metagenomic analysis confirmed the successful colonization of the three exogenous bacteria in the C-Bio system. Network analysis revealed that this approach facilitated the directional succession of soil microbial communities, with the newly dominant indigenous bacteria forming cooperative or symbiotic relationships with the exogenous strains. Together, they synergistically degrade alkanes via terminal oxidation pathways and aromatic hydrocarbons through salicylic acid and phthalic acid pathways, leading to effective remediation of petroleum-contaminated soil. This study offers theoretical insights and empirical evidence supporting the development of continuous bioaugmentation processes for the remediation of petroleum-contaminated soils.},
}

@article {pmid40828642,
year = {2025},
author = {Davies, RG and Wood, LA and Hengist, A and O'Donovan, C and Barton, W and Crispie, F and Walhin, JP and Valdivia-Garcia, MA and Garcia-Perez, I and Frost, G and O'Sullivan, O and Cotter, PD and Gonzalez, JT and Betts, JA and Koumanov, F and Thompson, D},
title = {Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP287424},
pmid = {40828642},
issn = {1469-7793},
support = {MR/P002927/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Metabolic health improvements in response to exercise and energy restriction may be mediated by the gut microbiome, yet causal evidence in humans remains limited. We used a 3-week exercise and energy restriction intervention to examine changes to the gut microbiome in otherwise healthy sedentary men and postmenopausal women with overweight/obesity. Intervention participants (n = 18) reduced habitual energy intake by 5000 kcal/week and expended 2000 kcal/week in addition to habitual physical activity through treadmill walking at 70% V̇O2Peak. Control participants (n = 12) maintained their usual lifestyle. Participants underwent dual-energy X-ray absorptiometry (DEXA), and samples of faeces, fasted venous blood, subcutaneous adipose tissue and skeletal muscle were collected. Faecal DNA was sequenced and profiled using shotgun metagenomics, Kraken2/Bracken and Human Microbiome Project Unified Metabolic Analysis Network 2 (HUMAnN2). The intervention significantly reduced body mass (mean Δ ± SD: -2.6 ± 1.5 kg), fat mass (-1.5 ± 1.3 kg), fasted insulin (-23.5 ± 38.1 pmol/l), leptin (-10.6 ± 7.3 ng/ml) and total cholesterol (-0.70 ± 0.42 mmol/l) concentrations, and also improved insulin sensitivity (HOMA2%S (homeostatic model of assessment)). Despite these significant metabolic changes the gut microbiome was unchanged in terms of α and β diversity and relative abundance. Thus, despite clinically meaningful improvements in body composition and metabolic health, we found no evidence for changes to the gut microbiome. In conclusion early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome. KEY POINTS: Changes to the gut microbiome could contribute to metabolic improvements associated with weight loss in humans, but there have been limited attempts to address this question using robust randomised controlled trials (RCTs). We used a parallel-group RCT to examine whether a 3-week combined energy intake restriction and vigorous-intensity exercise intervention in people with overweight and obesity was temporally associated with changes to gut microbiome taxonomic composition and functional potential, short-chain fatty acid concentrations and expression of genes related to host-microbiome interactions in skeletal muscle and subcutaneous adipose tissue. We found that the human gut microbiome remains unchanged in the face of an intensive energy intake restriction and vigorous exercise intervention that significantly improved body composition and metabolic health in people with overweight/obesity. These findings indicate that early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome.},
}

@article {pmid40828272,
year = {2025},
author = {Guiglielmoni, N},
title = {De novo Genome Assembly Using Long Reads and Chromosome Conformation Capture.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {1-27},
pmid = {40828272},
issn = {1940-6029},
abstract = {The field of genome assembly merely exists as long as sequencers are not able to yield chromosome-level error-less sequencing reads for all species. It consists in reconstituting the original genome sequence from sequencing reads, with a final number of fragments matching the expected number of chromosomes. This process has been facilitated by the availability of longer and more accurate reads. At the incipit of genome assembly, Sanger sequencing reads Sanger et al (Proc Natl Acad Sci 74(12)spiepr A3B2 twbch ":":spiepr A3B2 twbch5463-5467, 1977) were already used to yield initial assemblies of different species, including the first human genome assembly International Human Genome Sequencing Consortium (Nature 409(6822):860-921, 2001). The higher throughput of second-generation sequencing, often called next-generation sequencing, democratized assemblies for a wider variety of species but brought assembly difficulties as the large datasets of short reads required long computational time, large memory resources, and yielded highly fragmented assemblies, with fragment numbers far over the expected number of chromosomes Metzker (Nat Rev Genet 11(1):31-46, 2010). Third-generation sequencing introduced long reads through the technologies of Oxford Nanopore Deamer et al(Nat Biotechnol 34(5):518-524, 2016) and Pacific BioSciences (PacBio) Eid et al (Science 323(5910):133-138, 2009). Long reads can reach several tens of kilobase, and up to hundreds of thousands of base pairs; although these reads initially had a low accuracy, recent developments to decrease the error rate below 1% Sereika et al (Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. bioRxiv, 2021); Wenger et al (Nat Biotechnol 37(October):1155-1162, 2019) have additionally reduced the complexity of genome assembly.Chromosome-level assemblies have become a standard in genome assembly publications: they can be used for synteny analysis, finding chromosomal rearrangements, they have more complete gene sets, a better resolution of repetitive content, and fewer contaminants. The availability of long reads and Hi-C and the decreasing cost of sequencing have brought about many high-quality insect genome assemblies, with currently 6,194 assemblies published on GenBank (accessed on 20.11.2024). Some remarkable efforts have been put toward Lepidoptera genomes, for which 188 chromosome-level assemblies were generated by the Darwin Tree of Life Wright et al (Nat Ecol Evol 8(4):777-790, 2024). At a smaller scale, a highly contiguous assembly was obtained for the ant Camponotus pennsylvanicus using Nanopore reads with a budget of only 1000$.Traditionally, genome assemblies are collapsed, meaning that sets of homologous chromosomes are represented by a single consensus sequence Guiglielmoni et al (BMC Bioinf 22(1):303, 2021). This approach is most adequate for low-heterozygosity genomes, and variants are documented a posteriori. Along the advent of high-accuracy long reads, phased assemblies, in which all haplotypes are included, are becoming more common.The assembly process typically involves multiple steps to tackle the challenges posed by the characteristics of the genome: ploidy, heterozygosity, repetitiveness… Reads may need to be preprocessed to remove adapters, select the longest and/or most accurate reads, or correct them to further improve accuracy. The most essential part lies, of course, in the assembly step. Reads are overlapped to build an assembly graph, and ad hoc algorithms are applied to find a path giving the most faithful representation of the genome. Assemblers yield a set of contiguous sequences or contigs. The output should then be evaluated to decide whether the assembly has reached the highest contiguity, completeness, and correctness, and if not, which steps should be performed subsequently to increase quality.},
}

@article {pmid40828164,
year = {2025},
author = {Pang, J and Wong, JCC and Wulandari, SM and Tay, M and Karlsson, EA and Oktaria, V and Nisar, I and Alam, M and Murni, IK and Amir, A and Ishtiaq, F and Tong, Z and Kitajima, M and Nolan, M and Mak, ST and Maurer-Stroh, S and Smith, GJ and de Alwis, R and Boucher, YF and Ng, LC and Pronyk, PM},
title = {Wastewater surveillance for early pathogen detection in Asia.},
journal = {International journal of environmental health research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/09603123.2025.2544736},
pmid = {40828164},
issn = {1369-1619},
abstract = {Wastewater surveillance (WS) has emerged as an important population-based surveillance tool for early pathogen detection to inform timely public health action. Despite global guidance to initiate WS programming in Asia, the priorities and needs in Asia remain poorly understood. To address this gap, we conducted a cross-sectional assessment of WS efforts in Asia. An institutional survey recorded 89 separate projects among 45 institutions in 19 countries in Asia. Financing for WS was equally split between domestic and external resources. Most projects were research-oriented, with one-fifth embedded within national surveillance systems. Influents from urban wastewater treatment plants were the most common sampling sources identified, with either monthly or weekly sampling frequencies. Most efforts were single-pathogen focused, with SARS-CoV-2, antimicrobial resistance (AMR) bacteria, enterovirus, influenza and poliovirus being the top five pathogens assessed. Despite challenges including limited funding and government support, there has been substantial recent progress on the adoption of WS across Asia. Opportunities to enhance sustainability and scale will depend upon efforts to document public health use cases, support national planning and budgeting, develop tailored protocols and regional guidance, and advance innovative multi-pathogen approaches that leverage innovations including pathogen genomics to advance cost-efficient WS systems for public health impact.},
}

@article {pmid40827925,
year = {2025},
author = {Caffrey, EB and Olm, MR and Kothe, CI and Wastyk, HC and Evans, JD and Sonnenburg, JL},
title = {MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014125},
doi = {10.1128/msystems.00141-25},
pmid = {40827925},
issn = {2379-5077},
abstract = {Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes. Using this primary database of metagenome-assembled genomes and relevant deposited genomes of prokaryotes, eukaryotes, and common food-relevant substrates, we investigated 89 fermented food samples. We present a streamlined high-confidence characterization of microbial diversity in fermented food, identifying previously undiscovered genomes and facilitating strain-level tracking across food environments. The easy and robust functionality of the workflow has significant implications for advancing food safety, promoting desired microbial communities, and increasing sustainability in food production.IMPORTANCEFermented foods have microbial communities that influence food safety, flavor, and human health. Microbial Food DataBase (MiFoDB), an alignment-based sequencing workflow and database, addresses the limitations of existing tools by enabling strain-level resolution, identifying novel genomes, and providing functional insights into microbial communities. Applying MiFoDB to fermented food samples, we demonstrate its ability to uncover novel species, track microbial strains across substrates, and integrate functional annotations. Additionally, the outlined workflow is highly customizable and can be used to generate alignment-based databases for other microbial ecosystems. This work highlights the importance of fermentation-specific workflows for studying microbial food ecosystems, advancing food safety, sustainability, and innovation in fermented food research.},
}

@article {pmid40827884,
year = {2025},
author = {Liu, H and Sun, J and Si, J and Liao, Y and Bai, J and Li, X and Wang, L and Cai, K and Ni, W and Zhou, P and Hu, S},
title = {Unexplored diversity and potential functions of extra-chromosomal elements.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0017525},
doi = {10.1128/msystems.00175-25},
pmid = {40827884},
issn = {2379-5077},
abstract = {In addition to the main chromosome, approximately 10% bacterial genomes have one or more large secondary replicons, including a unique type of replicon known as "chromid," which has plasmid-type replication and partition systems but carries core genes. Their nucleotide composition of chromids is very similar to that of their related chromosomes. However, the distribution, characteristics, functions, and origins of these chromids remain unclear. In this study, we established a workflow to identify chromids from complete bacterial genomes and screened 36,322 complete bacterial genomes, resulting in the identification of 1,104 bacterial genomes with chromids as secondary replicons. These chromid-carrying bacteria belong to eight phyla and 73 genera, exhibiting diversity and a wide global distribution. We analyzed the characteristics of chromids and found that their average size is larger than that of "megaplasmids" and that multi-chromid bacteria exist. Furthermore, chromids encode genes related to bacterial respiratory chain enzyme complexes and antiviral systems, expanding bacterial metabolic capabilities and enhancing their antiviral defenses. In addition, we developed an automated identification program, Chromid-Finder, for identifying chromid sequences in metagenomic data, which has demonstrated outstanding performance. To demonstrate its application, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome. We found that the distribution of chromid-carrying bacteria in the human gut is closely associated with host age, health status, and geographic location. Species with chromids exhibit unique functional capabilities, showing good separation at the phylum level.IMPORTANCEIn this study, we have developed a workflow to identify chromids from complete bacterial genomes. We utilized this workflow to search for chromids in the latest NCBI RefSeq databases, to map the distribution of bacteria carrying chromids, to identify the characteristics of bacterial chromids, to discuss their origins, and to investigate their roles in bacterial life. To address the growing volume of metagenomic data, we developed a high-performance automated identification program, Chromid-Finder, designed to identify chromids and their corresponding bacterial main chromosomes within extensive metagenomic data sets. Using this tool, we analyzed 92,143 metagenome-assembled genomes (MAGs) from the human gut microbiome.},
}

@article {pmid40827869,
year = {2025},
author = {Allen, JM},
title = {Rediscovering the wild: MiFoDB brings fermented food microbiomes into focus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0059925},
doi = {10.1128/msystems.00599-25},
pmid = {40827869},
issn = {2379-5077},
abstract = {Fermented foods have sustained human societies for thousands of years, with their microbial communities subtly shaping flavor, nutrient preservation, and health. Yet despite this long-standing relationship, much of the microbial complexity within fermented foods remains unresolved. In recent work, Caffrey et al. (E. B. Caffrey, M. R. Olm, C. I. Kothe, H. C. Wastyk, et al., mSystems 10:e00141-25, 2025, https://doi.org/10.1128/msystems.00141-25) put forth a new tool, MiFoDB, a metagenomic workflow that offers a promising alternative for advancing food microbiome science. By enabling strain-level resolution, functional gene annotation, and microbial tracking across substrates and time, MiFoDB provides a clearer view into the ecological and functional landscape of the fermented food microbiota. This work also bridges gaps between food and human microbiome research and brings us closer to a mechanistic understanding of how fermented foods influence health, helping transform ancient dietary practices into actionable and targeted nutritional strategies for improving human health and well-being.},
}

@article {pmid40827364,
year = {2025},
author = {McShea, HS and Viens, RA and Olagunju, BO and Giner, JL and Welander, PV},
title = {The evolutionary history and modern diversity of triterpenoid cyclases.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf203},
pmid = {40827364},
issn = {1537-1719},
abstract = {Cyclic terpenoids are a class of lipid compounds containing immense structural and functional diversity, with many cyclic triterpenoids acting as regulators of the physical properties and spatial organization of lipid membranes. Cyclic terpenoids are also readily preserved as terpane fossils, such as steranes and hopanes, forming a rich record of the evolution of life on Earth. Formation of the multiple ring structure of all cyclic terpenoids is catalyzed by terpenoid cyclase enzymes, among which are whole clades of proteins - many from environmental metagenomes and uncultured organisms - whose substrates and products are completely unknown. We investigate the function of these divergent cyclases through biochemical assays, and the evolutionary processes that produced them by testing and applying a variety of evolutionary models. We find deep divergence between the diterpenoid cyclases and triterpenoid cyclases, with other clades branching between the two, rooting the triterpenoid cyclase subtree, between squalene-hopene cyclases and sterol cyclases. Through a simple test of evolutionary rate shifts, we find an elevated evolutionary rate in the enzyme active site on the squalene-hopene cyclase stem, potentially indicative of positive selection. Finally, by testing the activity of divergent cyclases for a variety of substrates, we find a group of early-branching sterol cyclases from bacteria that synthesize arborinols, two of which produce the molecular precursor to a Permian "orphan biomarker." Together, our data present an evolutionary framework for triterpenoid cyclases that can inform both the biochemical potential of these proteins and their products' occurrence in the geological record.},
}

@article {pmid40827090,
year = {2025},
author = {Mulligan, C and Gold, DA},
title = {A Reassessment of the Coprostane Biomarker in the Ediacaran With Implications for Dickinsonia.},
journal = {Geobiology},
volume = {23},
number = {4},
pages = {e70029},
doi = {10.1111/gbi.70029},
pmid = {40827090},
issn = {1472-4669},
support = {2044871//National Science Foundation/ ; },
abstract = {The discovery of cholestane in animal fossils from the Ediacaran (571-541 million years ago) has generated much excitement, but it is not the only interesting biomarker recovered. Coprostane, a geologically stable form of coprostanol, has also been found in Ediacaran rocks. This is surprising, since coprostanol is typically used in modern settings as an environmental biomarker for humans and other mammals, who produce the compound with help from bacteria in their gut. The prevailing hypothesis is that an abundance of coprostane in some Ediacaran fossils-particularly Dickinsonia-represents the degradation of the organism's cholesterol by bacteria in the microbial mat, comparable to what is seen in modern vertebrate corpses as they decompose. However, this hypothesis assumes coprostanol-producing bacteria were absent in the guts of Ediacaran organisms, and to date no one has tested whether such bacteria exist in modern invertebrates. In this study, we assembled 115 metagenomes to look for evidence of coprostanol-producing enzymes in invertebrate microbiomes. Ultimately, we did not find any evidence for the enzyme in any invertebrate microbiomes, supporting the hypothesis that coprostane is not a gut biomarker for Ediacaran animals. However, a reassessment of coprostane/cholestane ratios shows Dickinsonia was unique in coprostanol enrichment, with ratio levels comparable to waste polluted marine waters and modern vertebrate feces. While we cannot rule out the possibility of contamination, we prefer a novel interpretation of the coprostane signature in dickinsoniomorph fossils, where the elevated level of coprostanol comes from digestion of the microbial mat and concentration of the biologically inert compound. If correct, the elevated coprostanol signal provides new insights into the feeding strategy of these enigmatic animals.},
}

@article {pmid40826422,
year = {2025},
author = {Johnston, CM and Gunalan, V and Baagøe, HJ and Fomsgaard, AS and Polacek, C and Rasmussen, M and Lohse, L and Rasmussen, TB},
title = {Characterization of a MERS-related betacoronavirus in Danish brown long-eared bats (Plecotus auritus).},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {283},
pmid = {40826422},
issn = {1743-422X},
support = {101102733//EU4Health program (DURABLE)/ ; 101102733//EU4Health program (DURABLE)/ ; 101102733//EU4Health program (DURABLE)/ ; 101102733//EU4Health program (DURABLE)/ ; 101102733//EU4Health program (DURABLE)/ ; },
abstract = {BACKGROUND: Bats are recognized as natural reservoir hosts for numerous viruses and are believed to be the evolutionary origin of alpha- and beta-coronaviruses (CoVs), such as SARS-CoV, SARS-CoV-2, and possibly MERS-CoV. MERS-related beta-CoVs have been identified in bat species from Africa, America, Asia, and Europe. In this study, we describe the first detection and characterization of a MERS-related beta-CoV in Danish brown long-eared bats (Plecotus auritus).

METHODS: Fecal samples collected through a national surveillance program were screened using pan-CoV RT-qPCRs. Positive samples underwent ORF1b sequencing, microarray analysis and Illumina MiSeq sequencing, followed by metagenomic assembly of full-length genomes. A global phylogenetic tree was used to determine placement within the Coronaviridae family and local maximum likelihood phylogenetic analysis clarified subgroup placement. The receptor-binding potential of the spike protein to human DPP4, ACE2, and bat ACE2 orthologs was assessed through phylogenetic analysis of the receptor-binding domain (RBD), alongside homology modeling and structural analysis.

RESULTS: Three samples tested positive for CoVs. One sample from a Soprano pipistrelle (Pipistrellus pygmaeus) was identified as alpha-CoV by ORF1b sequencing. The remaining two samples, obtained from a colony of Plecotus auritus, were identified as beta-CoVs, and separate microarray results indicated the presence of a MERS-related CoV. Full genomes were successfully assembled using a metagenomic approach. Phylogenetic analysis placed them within the merbecoviruses, forming a distinct clade with viruses detected in Vespertilionidae bats from Western Europe and East Asia. Analysis of the RBD placed them within the HKU25 clade. Structural modeling suggested hydrogen bonding patterns between the RBD and human/bat ACE2 orthologs or human DPP4, similar to known in vitro complexes, indicating potential receptor binding.

CONCLUSION: This is the first report of MERS-related beta-CoVs in bats from Denmark. Phylogenetic analyses reveal that these novel viruses belong to the HKU25 clade, a clade with known ACE2 receptor preference. Experimental validation is needed to confirm the receptor-binding potential, as additional interactions at the RBD-receptor interface may differ from previously described bat-merbecoviruses. Continued surveillance is crucial to identify potential intermediate hosts and assess interspecies transmission risk, with focus on the spike protein, receptor specificity, and binding affinity.},
}

@article {pmid40826150,
year = {2025},
author = {Dang, HT and Phung, TTB and Tran, DM and Bui, ATP and Vu, YH and Luong, MT and Nguyen, HM and Trinh, HT and Vo, HTN and Nguyen, TTT and Nguyen, AH and Tung, PD and Tran, LH and Van Nguyen, AT},
title = {High-dose multi-strain Bacillus probiotics enhance treatment and reduce antibiotic usage in children with persistent diarrhea through immune and microbiota modulation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30231},
pmid = {40826150},
issn = {2045-2322},
support = {ANABIO/RG-2022-06//ANABIO R&D Ltd. Company, Viet Nam/ ; },
abstract = {Persistent diarrhea remains medical challenge to date regarding both its etiology and therapeutic interventions. Here, we conducted a randomized, double-blind, controlled clinical trial to evaluate the effectiveness of high-dose multi-strain Bacillus spore probiotics (LiveSpo DIA30) containing B. subtilis, B. clausii, and B. coagulans at 5 billion CFU/5 mL ampoule, in the supportive treatment of persistent diarrhea in children. Our findings revealed a significant 3-day shorter recovery period, 1.60-fold enhanced efficacy, and a 9.47-fold increase in odds (all p-values < 0.0001) for effectively resolving diarrhea by day 5 with the Bacillus spores. Notably, the group receiving LiveSpo DIA30 (Dia30 group) experienced a reduction in antibiotic treatment duration by 2 days compared to the Control group, equivalent to a 25% decrease in antibiotic usage. After 5 days of treatment, LiveSpo DIA30 demonstrated significant reductions in elevated blood pro-inflammatory cytokines, including IL-17 (26.62%; p = 0.0178), IL-23 (25.13%; p = 0.0256), TNF-α (19.09%; p = 0.038), and in fecal sIgA (24.24%; p = 0.0433). Analysis of 16S rRNA metagenome revealed that Dia30 group exhibited a notable increase in density of Actinomycetota and Bacillota phylum, along with Actinomycetaceae, Lactobacillaceae, and Streptococaceae families. Lacticaseibacillus rhamnosus, a beneficial gut species, was not detectable at day 0 but reached a density of 0.91% (p = 0.015) in Dia30 group by day 5. Additionally, Dia30 group showed a significant reduction in density of the Proteobacteria phylum, Enterobacteriaceae family, and harmful species Escherichia fergusoni (682.8-fold; p = 0.011). In conclusion, this clinical trial presents robust clinical evidence, supported by laboratory testing data, demonstrating the efficacy of multi-strain and high-concentration Bacillus spore probiotics in rapidly alleviating symptoms and reducing antibiotic usage in children with persistent diarrhea. This is archived by improving the native gut microbiota and modulating immunological responses.Trial registration: ClinicalTrials.gov, Identifier No: NCT05812820, 14/4/2023.},
}

@article {pmid40781499,
year = {2025},
author = {Kumari, J and Uthaman, A and Bose, S and Kundu, A and Sharma, V and Dutta, S and Dhar, A and Roy, S and Srinivasan, R and Pande, S and Vinothkumar, KR and Gayathri, P and Palani, S},
title = {Distinct filament morphology and membrane tethering features of the dual FtsZ paralogs in Odinarchaeota.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40781499},
issn = {1460-2075},
support = {IA/I/21/1/505633//Wellcome Trust DBT India Alliance (India Alliance)/ ; IA/S/23/1/506755//Wellcome Trust DBT India Alliance (India Alliance)/ ; IA/I/20/1/504921//Wellcome Trust DBT India Alliance (India Alliance)/ ; BT/INF/22/SP33046/2019//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; DBT/PR12422/MED/31/287/2014//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; SRG/2021/001600//DST | Science and Engineering Research Board (SERB)/ ; STARS2/2023-1015//Ministry of Education STARS grant/ ; RTI 4006//Department of Atomic Energy, Government of India (DAE)/ ; },
abstract = {The Asgard phylum has emerged as a model to study eukaryogenesis because of their close relatedness with the eukaryotes. In this study, we use FtsZ proteins from a member of the class Odinarchaeia as representatives to investigate the probable origin, evolution, and assembly of the FtsZ/tubulin protein superfamily in Asgard archaea. We performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the anchor OdinSepF via OdinFtsZ2's C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting. Our findings highlight the diversity of FtsZ proteins in the archaeal phylum Asgardarchaeota, providing valuable insights into the evolution and differentiation of tubulin-family proteins.},
}

@article {pmid40778433,
year = {2025},
author = {Li, W and Pan, S and Qian, J and Xia, Y and Han, G and Liu, J and Wang, Y and Peng, L and Huang, S and Chen, Y and Xie, Y and Xu, J and Zhang, W and Zhou, C},
title = {Comparisons of blood, upper respiratory tract and gut viromes from patients with lung cancer and healthy persons.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70075},
pmid = {40778433},
issn = {1097-0215},
support = {TZKY20230204//Clinical Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; TZKY20230305//Key Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; 24142202800//Shanghai Science and Technology Innovation Action Plan/ ; 82341106//National Natural Science Foundation of China/ ; },
abstract = {Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics. Significant differences in viral diversity and composition were observed between cancer and healthy groups, with lower similarities in blood, respiratory, and gut viromes. Notably, LUSC and LUAD groups showed high similarity, with LUAD exhibiting the most diverse virome. In blood, Anelloviridae dominated in cancer patients, while Retroviridae was more abundant in specific subgroups. The upper respiratory tract virome in cancer patients was enriched with Siphoviridae and Myoviridae, contrasting with Retroviridae in healthy individuals. Gut viromes were dominated by Podoviridae and Virgaviridae in cancer patients, with Virgaviridae showing higher abundance compared to healthy controls. Alpha and beta diversity analyses indicated significant differences in blood and respiratory viromes but not in gut viromes. STAMP and LEfSe analyses identified Anelloviridae and Siphoviridae as potential biomarkers for lung cancer. Additionally, 242 anelloviruses with complete ORF1 were isolated, revealing high genetic diversity. These findings highlight distinct virome profiles in lung cancer patients, offering insights into potential diagnostic and therapeutic targets.},
}

@article {pmid40739342,
year = {2025},
author = {Ruffolo, JA and Nayfach, S and Gallagher, J and Bhatnagar, A and Beazer, J and Hussain, R and Russ, J and Yip, J and Hill, E and Pacesa, M and Meeske, AJ and Cameron, P and Madani, A},
title = {Design of highly functional genome editors by modelling CRISPR-Cas sequences.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40739342},
issn = {1476-4687},
abstract = {Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native environments, such as human cells[1]. Artificial-intelligence-enabled design provides a powerful alternative with the potential to bypass evolutionary constraints and generate editors with optimal properties. Here, using large language models[2] trained on biological diversity at scale, we demonstrate successful precision editing of the human genome with a programmable gene editor designed with artificial intelligence. To achieve this goal, we curated a dataset of more than 1 million CRISPR operons through systematic mining of 26 terabases of assembled genomes and metagenomes. We demonstrate the capacity of our models by generating 4.8× the number of protein clusters across CRISPR-Cas families found in nature and tailoring single-guide RNA sequences for Cas9-like effector proteins. Several of the generated gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector, while being 400 mutations away in sequence. Finally, we demonstrate that an artificial-intelligence-generated gene editor, denoted as OpenCRISPR-1, exhibits compatibility with base editing. We release OpenCRISPR-1 to facilitate broad, ethical use across research and commercial applications.},
}

@article {pmid40254701,
year = {2025},
author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K},
title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40254701},
issn = {1867-1314},
abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.},
}

@article {pmid39966546,
year = {2025},
author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and Mihula, M and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M},
title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.},
journal = {Pediatric research},
volume = {97},
number = {7},
pages = {2267-2271},
pmid = {39966546},
issn = {1530-0447},
mesh = {Humans ; Female ; *Milk, Human/immunology/chemistry ; Pregnancy ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects ; *Immunoglobulin A/metabolism ; Case-Control Studies ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Translational Research, Biomedical ; *Microbiota/drug effects ; Adult ; *Prenatal Exposure Delayed Effects ; },
abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

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

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

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

IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.},
}

Humans
Female
*Milk, Human/immunology/chemistry
Pregnancy
Infant, Newborn
*Anti-Bacterial Agents/adverse effects
*Immunoglobulin A/metabolism
Case-Control Studies
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
Translational Research, Biomedical
*Microbiota/drug effects
Adult
*Prenatal Exposure Delayed Effects

@article {pmid39794073,
year = {2025},
author = {Kitsios, GD and Morris, A},
title = {Blurred Lines on the Dysbiosis Spectrum: Pneumocystis Colonization vs Infection by Metagenomics.},
journal = {Chest},
volume = {167},
number = {1},
pages = {3-5},
doi = {10.1016/j.chest.2024.08.038},
pmid = {39794073},
issn = {1931-3543},
support = {R03 HL162655/HL/NHLBI NIH HHS/United States ; },
}

@article {pmid39273328,
year = {2024},
author = {Zhu, N and Qian, Y and Song, L and Yu, Q and Sheng, H and Li, Y and Zhu, X},
title = {Regulating Leaf Photosynthesis and Soil Microorganisms through Controlled-Release Nitrogen Fertilizer Can Effectively Alleviate the Stress of Elevated Ambient Ozone on Winter Wheat.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273328},
issn = {1422-0067},
support = {BE2022312//Special Technology Innovation Fund of Carbon Neutrality in Jiangsu Province/ ; },
mesh = {*Fertilizers ; *Triticum/growth & development/metabolism/microbiology/drug effects ; *Photosynthesis/drug effects ; *Soil Microbiology ; *Plant Leaves/drug effects/metabolism ; *Nitrogen/metabolism ; *Ozone/pharmacology ; Stress, Physiological ; Soil/chemistry ; Bacteria/drug effects/metabolism/genetics ; },
abstract = {The mitigation mechanisms of a kind of controlled-release nitrogen fertilizer (sulfur-coated controlled-release nitrogen fertilizer, SCNF) in response to O3 stress on a winter wheat (Triticum aestivum L.) variety (Nongmai-88) were studied in crop physiology and soil biology through the ozone-free-air controlled enrichment (O3-FACE) simulation platform and soil microbial metagenomics. The results showed that SCNF could not delay the O3-induced leaf senescence of winter wheat but could enhance the leaf size and photosynthetic function of flag leaves, increase the accumulation of nutrient elements, and lay the foundation for yield by regulating the release rate of nitrogen (N). By regulating the soil environment, SCNF could maintain the diversity and stability of soil bacterial and archaeal communities, but there was no obvious interaction with the soil fungal community. By alleviating the inhibition effects of O3 on N-cycling-related genes (ko00910) of soil microorganisms, SCNF improved the activities of related enzymes and might have great potential in improving soil N retention. The results demonstrated the ability of SCNF to improve leaf photosynthetic function and increase crop yield under O3-polluted conditions in the farmland ecosystem, which may become an effective nitrogen fertilizer management measure to cope with the elevated ambient O3 and achieve sustainable production.},
}

*Fertilizers
*Triticum/growth & development/metabolism/microbiology/drug effects
*Photosynthesis/drug effects
*Soil Microbiology
*Plant Leaves/drug effects/metabolism
*Nitrogen/metabolism
*Ozone/pharmacology
Stress, Physiological
Soil/chemistry
Bacteria/drug effects/metabolism/genetics

@article {pmid35685890,
year = {2022},
author = {Lamichhane, S and Siljander, H and Salonen, M and Ruohtula, T and Virtanen, SM and Ilonen, J and Hyötyläinen, T and Knip, M and Orešič, M},
title = {Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {859627},
pmid = {35685890},
issn = {2296-861X},
abstract = {BACKGROUND: Current evidence suggests that the composition of infant formula (IF) affects the gut microbiome, intestinal function, and immune responses during infancy. However, the impact of IF on circulating lipid profiles in infants is still poorly understood. The objectives of this study were to (1) investigate how extensively hydrolyzed IF impacts serum lipidome compared to conventional formula and (2) to associate changes in circulatory lipids with gastrointestinal biomarkers including intestinal permeability.

METHODS: In a randomized, double-blind controlled nutritional intervention study (n = 73), we applied mass spectrometry-based lipidomics to analyze serum lipids in infants who were fed extensively hydrolyzed formula (HF) or conventional, regular formula (RF). Serum samples were collected at 3, 9, and 12 months of age. Child's growth (weight and length) and intestinal functional markers, including lactulose mannitol (LM) ratio, fecal calprotectin, and fecal beta-defensin, were also measured at given time points. At 3 months of age, stool samples were analyzed by shotgun metagenomics.

RESULTS: Concentrations of sphingomyelins were higher in the HF group as compared to the RF group. Triacylglycerols (TGs) containing saturated and monounsaturated fatty acyl chains were found in higher levels in the HF group at 3 months, but downregulated at 9 and 12 months of age. LM ratio was lower in the HF group at 9 months of age. In the RF group, the LM ratio was positively associated with ether-linked lipids. Such an association was, however, not observed in the HF group.

CONCLUSION: Our study suggests that HF intervention changes the circulating lipidome, including those lipids previously found to be associated with progression to islet autoimmunity or overt T1D.

CLINICAL TRIAL REGISTRATION: [Clinicaltrials.gov], identifier [NCT01735123].},
}

@article {pmid32564244,
year = {2020},
author = {Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Laitinen, K},
title = {GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {16},
number = {7},
pages = {76},
pmid = {32564244},
issn = {1573-3890},
mesh = {Acetylglucosamine/blood ; Adult ; Biomarkers/blood ; C-Reactive Protein/metabolism ; Cardiovascular Diseases/blood/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; Female ; Fibrinogen/metabolism ; Gastrointestinal Microbiome/*physiology ; Glycoproteins/blood ; Haptoglobins/metabolism ; Humans ; Inflammation/blood/*metabolism ; Metabolomics/methods ; Obesity/blood/metabolism ; Pregnancy ; Serum Amyloid A Protein/metabolism ; },
abstract = {INTRODUCTION: Gut microbiota is, along with adipose tissue, recognized as a source for many metabolic and inflammatory disturbances that may contribute to the individual's state of health.

OBJECTIVES: We investigated in cross-sectional setting the feasibility of utilizing GlycA, a novel low grade inflammatory marker, and traditional low grade inflammatory marker, high sensitivity CRP (hsCRP), in reflecting serum metabolomics status and gut microbiome diversity.

METHODS: Fasting serum samples of overweight/obese pregnant women (n = 335, gestational weeks: mean 13.8) were analysed for hsCRP by immunoassay, GlycA and metabolomics status by NMR metabolomics and faecal samples for gut microbiome diversity by metagenomics. The benefits of GlycA as a metabolic marker were investigated against hsCRP.

RESULTS: The GlycA concentration correlated with more of the metabolomics markers (144 out of 157), than hsCRP (55 out of 157) (FDR < 0.05). The results remained essentially the same when potential confounding factors known to associate with GlycA and hsCRP levels were taken into account (P < 0.05). This was attributable to the detected correlations between GlycA and the constituents and concentrations of several sized VLDL-particles and branched chain amino acids, which were statistically non-significant with regard to hsCRP. GlycA, but not hsCRP, correlated inversely with gut microbiome diversity.

CONCLUSION: GlycA is a superior marker than hsCRP in assessing the metabolomic profile and gut microbiome diversity. It is proposed that GlycA may act as a novel marker that reflects both the gut microbiome and adipose tissue originated metabolic aberrations; this proposal will need to be verified with regard to clinical outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT01922791, August 14, 2013.},
}

Acetylglucosamine/blood
Adult
Biomarkers/blood
C-Reactive Protein/metabolism
Cardiovascular Diseases/blood/metabolism
Cross-Sectional Studies
Feces/chemistry
Female
Fibrinogen/metabolism
Gastrointestinal Microbiome/*physiology
Glycoproteins/blood
Haptoglobins/metabolism
Humans
Inflammation/blood/*metabolism
Metabolomics/methods
Obesity/blood/metabolism
Pregnancy
Serum Amyloid A Protein/metabolism

@article {pmid40825968,
year = {2025},
author = {Ahmed, S and Emon, MI and Moumi, NA and Huang, L and Zhou, D and Vikesland, P and Pruden, A and Zhang, L},
title = {ProtAlign-ARG: antibiotic resistance gene characterization integrating protein language models and alignment-based scoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30174},
pmid = {40825968},
issn = {2045-2322},
support = {2319522//National Science Foundation (NSF)/ ; 2004751//National Science Foundation (NSF)/ ; },
abstract = {The evolution and spread of antibiotic resistance pose a global health challenge. Whole genome and metagenomic sequencing offer a promising approach to monitoring the spread, but typical alignment-based approaches for antibiotic resistance gene (ARG) detection are inherently limited in the ability to detect new variants. Large protein language models could present a powerful alternative but are limited by databases available for training. Here we introduce ProtAlign-ARG, a novel hybrid model combining a pre-trained protein language model and an alignment scoring-based model to expand the capacity for ARG detection from DNA sequencing data. ProtAlign-ARG learns from vast unannotated protein sequences, utilizing raw protein language model embeddings to improve the accuracy of ARG classification. In instances where the model lacks confidence, ProtAlign-ARG employs an alignment-based scoring method, incorporating bit scores and e-values to classify ARGs according to their corresponding classes of antibiotics. ProtAlign-ARG demonstrated remarkable accuracy in identifying and classifying ARGs, particularly excelling in recall compared to existing ARG identification and classification tools. We also extended ProtAlign-ARG to predict the functionality and mobility of ARGs, highlighting the model's robustness in various predictive tasks. A comprehensive comparison of ProtAlign-ARG with both the alignment-based scoring model and the pre-trained protein language model demonstrated the superior performance of ProtAlign-ARG.},
}

@article {pmid40825877,
year = {2025},
author = {Xu, Y and Liu, Y and Leng, Y and Qian, J and Yang, Q and Zhu, J and Li, G and Peng, Y},
title = {Signature of oral microbial dysbiosis in different periodontitis risk levels.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {186},
pmid = {40825877},
issn = {1432-0614},
support = {XDYC-YLWS-2023-0048//Xingdian Talents Support Program/ ; 202401AU070088//Natural Science Foundation of Yunnan Province/ ; EYQ2024001//National Key Clinical Specialty Development Project of Pediatric Dentistry Division of China/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202401AY070001-365//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; },
abstract = {Individuals categorized into distinct periodontitis risk levels often demonstrate substantial disparities not only in the likelihood of developing periodontitis but also in the rate at which the disease progresses. However, the oral microbial communities and their functional characteristics corresponding to different periodontitis risk levels remain to be further explored. Therefore, 52 subjects with periodontitis were selected and categorized into different periodontitis risk groups based on the periodontal risk calculator (PRC). Unstimulated saliva was collected, and metagenomics sequencing was performed to compare microbial diversity, taxonomy, and functional annotation among groups. There was no significant difference in species richness and evenness between the very high risk group and the high risk group, but beta diversity increased in the former group. A higher abundance of Filifactor alocis, Streptococcus cristatus, Klebsiella pneumoniae, and Streptococcus anginosus was attributed to the very high risk group, while Pseudopropionibacterium propionicum and Abiotrophia defectiva were found in higher abundance in the high risk group. Functional annotation revealed that biosynthesis of amino acids (lysine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; valine, leucine, and isoleucine biosynthesis), citrate cycle (TCA cycle), carbon fixation pathways in prokaryotes, oxidative phosphorylation, lipopolysaccharide biosynthesis, fatty acid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, pantothenate and CoA biosynthesis, and glutathione metabolism were enriched in the very high risk group. The combined results indicate that the periodontal pathogens associated with a higher risk of periodontitis and the regulation of their related functional pathways increase the risk and likelihood of periodontitis development. KEY POINTS : • There were differences in microbial diversity among different periodontitis risk-level groups. • Some previously overlooked species and pathogenic pathways were linked to periodontitis risk differences. • Combining PRC with metagenomic sequencing revealed more potential pathogens.},
}

@article {pmid40825855,
year = {2025},
author = {Gopaulchan, D and Moore, C and Ali, N and Sukha, D and Florez González, SL and Herrera Rocha, FE and Yang, N and Lim, M and Dew, TP and González Barrios, AF and Umaharan, P and Salt, DE and Castrillo, G},
title = {A defined microbial community reproduces attributes of fine flavour chocolate fermentation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40825855},
issn = {2058-5276},
support = {133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; 133788//Innovate UK/ ; },
abstract = {Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.},
}

@article {pmid40825829,
year = {2025},
author = {Du, S and Wu, Z and Wu, Y and Yang, M and Deng, C and Zhang, Y and Chen, F and Zhang, Z and Zhao, Y},
title = {Marine Autographiviridae phages exhibit high genetic diversity and global-scale biogeographic patterns.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1240},
pmid = {40825829},
issn = {2399-3642},
support = {42276144//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42206096//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Marine viral communities harbor an astounding diversity of phages infecting diverse marine bacteria. The double-stranded DNA phage family Autographiviridae is among the most abundant phage families in the ocean. However, the current understanding of marine Autographiviridae phages is predominantly derived from isolates infecting cyanobacteria, SAR11, and Roseobacter. To achieve a more comprehensive understanding of the diversity, ecological traits, and functional profiles of this phage family, we recovered 1253 complete marine Autographiviridae uncultivated viral genomes (UViGs). Comparative genomic analysis showed that marine-derived Autographiviridae phages display genome synteny and share a conserved core of seven genes. The core gene-based phylogenomic analysis classified them into 14 groups, 6 of which were previously undescribed. These groups varied in G + C content, genome size, and presence of specific genes. Metagenomic recruitment analysis demonstrated that Autographiviridae phages are globally distributed and enriched in the upper ocean layers of tropical and temperate zones. The differential distribution patterns among these groups mirror the ecological niches of their potential hosts, emphasizing the top-down control these phages exert on their host populations. Collectively, our study substantially expands knowledge regarding the diversity, potential hosts, functional capacity, and ecological distribution of Autographiviridae phages in the ocean, emphasizing their ecological implications in marine environments.},
}

@article {pmid40825816,
year = {2025},
author = {Kaushal, M and Kolombia, YA and Alakonya, AE and Masso, C},
title = {Comparing soil microbial diversity in smallholder plantain backyard gardens and main farms in Western and Central Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30220},
pmid = {40825816},
issn = {2045-2322},
support = {HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; },
abstract = {In sub-Saharan Africa (SSA), plantains (Musa spp.) are a staple crop and a vital source of income for smallholder farmers. Despite their importance, the microbial diversity of soils in plantain-growing agroecologies remains poorly understood-particularly how it may influence plant performance and resilience through soil-plant interactions. In this study, we used Illumina MiSeq-based 16S rDNA sequencing to characterize bacterial communities in the rhizosphere of plantains cultivated under two distinct agroecological settings: Backyard gardens and main farms. Analyses of alpha and beta diversity (Sobs, Chao1, ACE, Shannon-Wiener, and Simpson indices; P < 0.05) revealed significant differences in species richness and community structure between the two agroecologies. Actinobacteria (55%) emerged as the dominant phylum, followed by Proteobacteria (21%) and Acidobacteria (15%). Beneficial genera such as Bacillus, Streptomyces, Bradyrhizobium, and Paenibacillus were also detected. Functional predictions based on COG and KEGG databases indicated notable differences in microbial functional potential between the two settings. These results suggest that agroecological context and habitat type strongly influence rhizosphere microbial diversity, with important implications for enhancing plant-microbe interactions and supporting crop resilience in SSA's resource-limited smallholder systems.},
}

@article {pmid40825794,
year = {2025},
author = {Ahirwar, A and Khan, MJ and Khandelwal, P and Singh, G and Harish, and Vinayak, V and Ghangrekar, MM},
title = {Bioelectromics of a photosynthetic microalgae assisted microbial fuel cell for wastewater treatment and value added production.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30196},
pmid = {40825794},
issn = {2045-2322},
support = {PPMB 7133/2020//Indo-French Centre for the Promotion of Advanced Research/ ; SR/NM/NT-1090/2014(G)//Department of science and Technology Nanomission/ ; },
abstract = {Power generation and recovery of value-added products using microalgae, Haematococcus lacustris is tested in a dual chamber photosynthetic microalgae-assisted microbial fuel cell (PMA-MFCt1). The microalgal cells in conical flask act as control. The performance was compared to another, test PMA-MFCt2. The control MFC in second test had electrode wires not connected (PMA-MFCnw). The PMA-MFCt1 set had microalgal catholytic media replenished unlike in PMA-MFCt2. A comparative PMA0-MFC, was used without microalgae and only water as catholyte. The results demonstrated maximum power density (PDmax) of 33.76 mW m[-2] in PMA-MFCt1, 15.36 mW m[-2] in PMA-MFCt2 and 8.05 mW m[-2] in PMA0-MFC. The non replenishment of catholytic media in PMA-MFCt2 set resulted in nutrient limitations, poor photosynthesis, and disrupted redox reactions. Further lowest PDmax in PMA0-MFC proves that microalgae are excellent source of free nascent oxygen required for redox reaction. Taxonomic identity of microbes at the anode via 16 S rRNA showed the dominance of catalytic microbes mainly Proteobacteria. The different kinds of carotenoids from microalgae were estimated by UV-Vis and liquid chromatography-mass spectrometry (LC-MS) analysis. The microalgal growth, evaluated in terms of biomass dry weight (DW), was 118 mg L[-1], after 40 days of PMA-MFCt1 operation, which was lesser than in control (conical flask) 123 mg L[-1]. The pigments including total chlorophyll (a + b), and total carotenoids were 699.7 µg g[-1] and 224.6 µg g[-1], respectively, on day 16. Microalgal performance in PMA-MFCt2 and its control (PMA-MFCnw) was 10% and 32.52% inferior than in PMA-MFCt1 and its control. The continuous replenishment of media in PMA-MFCt1 maintained microalgal cells in continuous state of multiplication and photosynthesis resulting into higher bioelectricity generation and bioproducts than PMA-MFCt2, and PMA-MFCnw.},
}

@article {pmid40825471,
year = {2025},
author = {Suzuki, H and Moriguchi, K and Shintani, M and Suzuki, M and Nojiri, H},
title = {Insights from public database sequences related to the replication initiation protein TrfA of the IncP-1 plasmid RK2.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102756},
doi = {10.1016/j.plasmid.2025.102756},
pmid = {40825471},
issn = {1095-9890},
abstract = {Replicon typing identifies sequences similar to known DNA replication initiators and is widely used to detect specific plasmid groups (e.g., IncP-1) in genome and metagenome sequencing data. However, the characteristics of these homologous sequences in public databases have not been systematically assessed, making it difficult to determine whether detecting a specific replicon type reliably indicates the presence of a particular plasmid group. Here, we conducted amino acid sequence alignments to identify sequences similar to the replication initiation protein TrfA of the IncP-1 plasmid RK2 in the NCBI non-redundant (nr) database. In the nr nucleotide database, TrfA-matched nucleotide sequences were found across diverse taxonomic groups and replicons, including complete and partial plasmids and chromosomes. In total, 76 protein sequences from the reference plasmid RK2 were screened against the nucleotide sequences of the trfA-harboring plasmids to identify candidate IncP-1 plasmids. TrfA-related proteins, originating from bacterial chromosomes, plasmids, and phages, were selected from the nr amino acid database and used to infer phylogenetic trees. Our phylogenetic analyses reveal that TrfA homologs have diverged through vertical inheritance within IncP-1 and horizontal gene transfer across replicons and taxa. These findings caution against overreliance on single-gene replicon typing to infer plasmid group identity from sequence data.},
}

@article {pmid40825123,
year = {2025},
author = {Park, JD and Lee, SR and Dhennezel, C and Taylor, N and Dame, A and Kadoki, M and Pishchany, G and Graham, DB and Xavier, RJ and Seyedsayamdost, MR},
title = {Elucidating the role of Campylobacter concisus-derived indole metabolites in gut inflammation and immune modulation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {34},
pages = {e2514071122},
doi = {10.1073/pnas.2514071122},
pmid = {40825123},
issn = {1091-6490},
support = {2023A004123//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; },
abstract = {The gut microbiota plays a pivotal role in maintaining human health with dysbiosis linked to a variety of diseases. Metagenome sequencing and robust statistical analysis have linked specific strains, including the gut bacterium Campylobacter concisus, to Crohn's disease and ulcerative colitis, together known as inflammatory bowel disease (IBD). However, the roles of this and other strains in disease progression remain to be investigated. Herein, we assess the contribution of C. concisus secondary metabolites to inflammation. Through untargeted metabolomics, we identified a diverse array of nineteen indole-containing metabolites produced by C. concisus, including trisindoline, previously isolated from a marine bacterium. Collectively, these metabolites modulate inflammatory responses by significantly inducing the release of proinflammatory cytokines interleukin (IL)-1β, IL-6, IL-8, and MCP-1. The metabolites act through the aromatic hydrocarbon receptor arylhydrocarbon receptor and in vivo intravital imaging revealed a marked increase in the recruitment and activation of immune cells, specifically neutrophils and macrophages, following the administration of trisindoline. Several indole metabolites also exhibited antimicrobial activity against commensal strains that facilitate a proper immune response. Our study provides a possible rationale for the association of C. concisus with IBD and underscores the complex interplay between gut bacteria and host immunity. The identification of indole-derived secondary metabolites as key modulators of inflammation offers new avenues for therapeutic intervention.},
}

@article {pmid40824903,
year = {2025},
author = {Flinkstrom, Z and Bryson, SJ and Pelivano, B and Candry, P and Hunt, KA and Winkler, MH},
title = {Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330380},
doi = {10.1371/journal.pone.0330380},
pmid = {40824903},
issn = {1932-6203},
abstract = {Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.},
}

@article {pmid40824425,
year = {2025},
author = {İstanbullugil, FR and Sanli, K and Ozturk, T and Keskin, BC and Düyşöbayeva, A and Risvanli, A and Acaröz, U and Acaröz, DA and Salykov, R and Sahin, M},
title = {Koumiss Microbiome: Investigation of the Microbial Composition and Functional Potential of a Unique Beverage of Fermented Milk Produced at Kyrgyz Mountains.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40824425},
issn = {1867-1314},
support = {KTMU-BAP-2023.FB.15//KTMU Scientific Research Projects Unit/ ; },
abstract = {This study aims to investigate the microbial composition of koumiss made via traditional methods in Kyrgyz mountain pastures. We collected koumiss samples produced in plastic (P), wood (T), and leather (D) containers at household settings. These samples were subjected to shotgun metagenomic sequencing. As a result of the metagenome analyses, we identified a diversity of bacteria, yeasts, bacteriophages, and archaea in koumiss produced within different containers. Koumiss' microbial community was predominantly composed of lactic acid bacteria (LAB), particularly Lactobacillus helveticus and Lactococcus lactis. Additional LAB species such as Lactobacillus kefiranofaciens, Lactococcus raffinolactis, Lactiplantibacillus plantarum, and Lactococcus cremoris, as well as non-LAB taxa such as Kluyvera intermedia, Raoultella planticola, and Hafnia alvei were also identified as part of the koumiss microbiota. Nonetheless, the opportunistic pathogen, Enterobacter hormaechei, was among the detected species. The most abundant yeast species was identified as Brettanomyces bruxellensis. Other yeast species involving Monosporozyma unispora, Monosporozyma servazzii, and Yarrowia lipolytica were also detected within the metagenome. Despite the type of container material not significantly affecting the microbial diversity, Bifidobacterium spp. and bacteriophages were identified at higher levels in plastic containers. We detected various antimicrobial resistance genes and gene clusters that produce bioactive compounds within koumiss samples. This study highlights koumiss' rich microbial composition and its potential health impacts. It underscores the importance of effectively utilizing metagenomic and bioinformatics methods for better comprehension of the microbiota of koumiss.},
}

@article {pmid40824084,
year = {2025},
author = {Li, J and Liang, L and Ye, J and Miao, Y and Zhao, K and Tian, Y and Li, X and Li, X and Chen, X and Wen, B and He, Y and Chen, B and Qin, L and Wang, Y and Fu, X},
title = {Gastric microbiota transplantation enhanced the eradication of refractory Helicobacter pylori infection by modulating the gastric microbiota: a pilot study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0326324},
doi = {10.1128/spectrum.03263-24},
pmid = {40824084},
issn = {2165-0497},
abstract = {UNLABELLED: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. In this study, we investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. We performed a metagenomic analysis of the microecological systems across different regions of the stomach, including the gastric fluid (GF), the gastric mucus layer (GML), and the gastric mucosa (GM). We initiated a clinical GMT intervention by transplanting microbial communities from healthy individuals' GML into patients exhibiting refractory H. pylori infection and chronic atrophic gastritis. Our findings demonstrated significant disparities in species richness among the GF, GML, and GM, with the GML exhibiting the highest diversity of unique microbial genera. H. pylori infection primarily influenced the relative species abundance within the GML community, without altering its fundamental composition. Clinically, GMT was well-tolerated by all recipients and showed substantial synergistic efficacy against refractory H. pylori infection, achieving a 100% eradication rate in all patients, and significantly alleviating symptoms in individuals with H. pylori-positive atrophic gastritis (P < 0.05). Compared with the gastric microbiota of H. pylori-negative patients, the gastric microbiota of H. pylori-positive patients treated with GMT exhibited closer alignment with those of healthy donors. In conclusion, GMT utilizing GML enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis through modulating the gastric microbiota.

IMPORTANCE: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. We investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. GMT significantly enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis. GMT demonstrated improvements in the cure rate of refractory H. pylori infection, potentially offering a new clinical treatment approach. This finding provides new insights and a potential therapeutic direction for treating dysbiosis related chronic gastric diseases.},
}

@article {pmid40823826,
year = {2025},
author = {Sadler, MC and Wietz, M and Mino, S and Morris, RM},
title = {Genomic diversity and adaptation in Arctic marine bacteria.},
journal = {mBio},
volume = {},
number = {},
pages = {e0155525},
doi = {10.1128/mbio.01555-25},
pmid = {40823826},
issn = {2150-7511},
abstract = {Arctic marine bacteria experience seasonal changes in temperature, salinity, light, and sea ice cover. Time-series and metagenomic studies have identified spatiotemporal patterns in Arctic microbial communities, but a lack of complete genomes has limited efforts to identify the extent of genomic diversity in Arctic populations. We cultured and sequenced the complete genomes of 34 Arctic marine bacteria to identify patterns of gene gain, loss, and rearrangement that structure genomes and underlie adaptations to Arctic conditions. We found that the most abundant lineage in the Arctic (SAR11) is comprised of diverse species and subspecies, each encoding 50-150 unique genes. Half of the 16 SAR11 genomes harbor a genomic island with the potential to enhance survival in the Arctic by utilizing the osmoprotectant and potential methyl donor glycine betaine. We also cultured and sequenced four species representing an uncultured family of Pseudomonadales, four subspecies of Pseudothioglobus (SUP05), a genus of high GC Puniceispirillales (SAR116), and a family of low GC SAR116. Time-series 16S rRNA amplicon data indicate that this culture collection represents up to 60% of the marine bacterial community in Arctic waters. Their genomes provide insights into the evolutionary processes that underlie bacterial diversity and adaptation to Arctic waters.IMPORTANCEGenetic diversity has limited efforts to assemble and compare whole genomes from natural populations of marine bacteria. We developed a cultivation-based population genomics approach to culture and sequence the complete genomes of bacteria from the Arctic Ocean. Cultures and closed genomes obtained in this study represent previously uncultured families, genera, and species from the most abundant lineages of bacteria in the Arctic. We report patterns of gene gain, loss, rearrangement, and adaptation in the dominant lineage (SAR11), as well as the size, composition, and structure of genomes from several other groups of marine bacteria. This work demonstrates the potential for cultivation-based high-throughput genomics to enhance understanding of the processes underlying genomic diversity and adaptation.},
}

@article {pmid40823805,
year = {2025},
author = {Kim, L and Lavrinienko, A and Sebechlebska, Z and Stoltenberg, S and Bokulich, NA},
title = {Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.},
journal = {Nucleic acids research},
volume = {53},
number = {15},
pages = {},
doi = {10.1093/nar/gkaf777},
pmid = {40823805},
issn = {1362-4962},
support = {2020-2024//ETH Domain's Open Research Data (ORD)/ ; 2021-362//ETH Domain's Open Research Data (ORD)/ ; //Strategic Focus Area "Personalized Health and Related Technologies (PHRT)/ ; //ETH Zurich/ ; //ETH Read and Publish OA/ ; },
abstract = {Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (i) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (ii) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and case studies of soil and gut microbiota (n = 370), we found nearly half do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements and (ii) the lack of consistent metadata reporting. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate data reuse, supporting best practices that make microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).},
}

@article {pmid40823537,
year = {2025},
author = {Subramanian, P and Romero-Soto, HN and Stern, DB and Maxwell, GL and Levy, S and Hourigan, SK},
title = {Delivery mode impacts gut bacteriophage colonization during infancy.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {40823537},
issn = {2993-3935},
abstract = {Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory outcomes. Although gut bacteriophages can alter the gut microbiome and host responses, little is known about how delivery mode impacts bacteriophage colonization over time. Therefore, we conducted shotgun metagenomic sequencing on serial stool samples from infants from birth to 24 months of age. 60% of infants were born by vaginal delivery. 94% of the DNA viral sequences identified were bacteriophages. Virome alpha diversity was increased in vaginally delivered infants at 2 months (p=0.004). Beta diversity differed by delivery mode up to 12 months when stratified by peripartum antibiotic use (p<0.05). Predicted bacteriophage hosts differed by delivery mode (Q <0.1) up to 24 months. Moreover, predicted bacteriophage functional genes differed by delivery mode up to 24 months. There was a higher abundance of viral auxiliary metabolic genes associated with host responses in vaginal delivery at early timepoints. Clear differences in bacteriophage composition and function by delivery mode were seen in early life. Given that bacteriophages are known to affect immune responses, our results suggest that future investigation into how delivery mode leads to adverse inflammatory outcomes should also include the potential role of bacteriophages and transkingdom interactions.},
}

@article {pmid40822586,
year = {2025},
author = {Dharmalingam, D and Semalaiyappan, J and Thirumal, S and Kuttiatt, VS},
title = {Unveiling Facklamia: detection of an emerging microbe in the skin microbiome of patients with filarial lymphedema.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1624288},
pmid = {40822586},
issn = {2235-2988},
abstract = {Facklamia is an emerging pathogen in human beings and only a few clinical cases were reported in the literature. We detected the presence of this unusual microbe among the skin flora of three patients with filarial lymphedema in a 16S rRNA-based metagenomic study on the skin microbiome. To our knowledge, this is the first report of detection of this microbe in patients affected with filarial lymphedema. Further investigations are required to elucidate the role of Facklamia in secondary skin and soft tissue infection of filarial lymphedema patients.},
}

@article {pmid40822578,
year = {2025},
author = {Wu, X and Zhu, H and Hu, Y and Zhang, L and Huang, L},
title = {Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1610523},
pmid = {40822578},
issn = {2235-2988},
abstract = {INTRODUCTION: Helicobacter pylori is a globally prevalent gastric pathogen associated with chronic gastritis, peptic ulcers, and gastric cancer. Its interaction with the gut microbiome (GM), a dynamic microbial community within the gastrointestinal tract, plays a critical role in modulating host immune responses and disease progression. This study aimed to investigate the complex interactions between H. pylori infection and the GM and to evaluate how microbiome alterations relate to clinical outcomes such as gastritis, ulcers, and gastric cancer.

METHODS: A meta-analysis was conducted using publicly available 16S rRNA and shotgun metagenomic datasets. Microbiome composition differences were assessed using differential abundance analysis, alpha- and beta-diversity metrics, and principal component analysis (PCA). Random forest models were employed to predict the clinical outcomes based on microbiome and clinical data. Hyperparameter tuning and cross-validation were applied to ensure model robustness.

RESULTS: The analysis revealed significant microbial shifts associated with H. pylori infection, including enrichment of Proteobacteria, Fusobacterium spp., and Prevotella spp., and depletion of beneficial taxa like Lactobacillus spp. and Faecalibacterium prausnitzii. Microbial diversity declined progressively with disease severity. Predictive models demonstrated high accuracy (89.3%) in classifying the disease states and identifying key microbial biomarkers such as Fusobacterium spp. and Bacteroides fragilis with strong predictive power.

DISCUSSION: This study highlights the critical role of GM dysbiosis in H. pylori-related disease progression. The identified microbial signatures and predictive models offer promising tools for early diagnosis, risk stratification, and personalized treatment of H. pylori-associated gastrointestinal disorders. Future integration of multi-omics data may further unravel the microbial mechanisms and support microbiome-based precision medicine.},
}

@article {pmid40822389,
year = {2025},
author = {Jaarsma, AH and Sipes, K and Zervas, A and Feord, HK and Campuzano Jiménez, F and Thøgersen, MS and Benning, LG and Tranter, M and Anesio, AM},
title = {The encoded and expressed biosynthetic potential of Greenland Ice Sheet microbes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620548},
pmid = {40822389},
issn = {1664-302X},
abstract = {Supraglacial habitats of the Greenland Ice Sheet (GrIS) harbor active microbial communities. Microbes produce a plethora of natural products, which hold great promise in biotechnology. Understudied environments such as the Greenland Ice Sheet are therefore of interest for the discovery of unknown biosynthetic gene clusters (BGCs) that encode these compounds. Though many applications of these natural products have been identified, little is known about their ecological function for the producer itself. Some hints exist toward roles in competition and environmental adaptation, yet confirmation of the expression of these BGCs in the natural environment is often lacking. Here, we investigated the expression of BGCs in supraglacial habitats of the GrIS. Using total RNA sequencing, we conducted a seasonal study to analyze metatranscriptomes of ice and cryoconite habitats over a 21-day period during the ablation season. Genome mining on metagenomic contigs identified BGCs within ice and cryoconite metagenomes, after which the metatranscriptomes were mapped to them. Our study identified a majority of previously unknown BGCs, 59% of which are actively expressed in situ, with relatively stable expression levels throughout the melting season. The 10 most highly expressed BGCs in ice were of eukaryotic origin, whereas in cryoconite, the 10 most highly expressed BGCs were prokaryote-derived. Among these was biosynthetic machinery for the production of carotenoids, terpenes, beta-lactones, and modified peptides, and their producers are likely ecosystem engineers of the supraglacial habitats, such as glacier ice or snow algae, and cyanobacteria. These findings highlight the significant, yet mostly unexplored, biosynthetic capabilities of GrIS supraglacial microbes, and suggest an active role of these BGCs in community ecology.},
}

@article {pmid40821992,
year = {2025},
author = {Zhou, J and Tian, Y and Yang, M and Hao, T and Ma, J and Wang, S},
title = {RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19849},
pmid = {40821992},
issn = {2167-8359},
abstract = {BACKGROUND: The capacity of metagenomic sequencing-based diagnostics to fully identify infections have made them useful instruments in clinical practice. We introduce an interactive platform that runs on a local server-class hardware resource and implements a number of open-source programs.

RESULTS: RpNGS integrates an interactive tabular interface for the management of experimental processes, patient metadata, and automated sequencing analysis. This technology optimizes clinical reporting by autonomously generating standardized reports in Word format. We have utilized the platform on an artificial microbial community reference panel and several clinical metagenomics datasets from public databases to demonstrate the efficacy of this workflow.

CONCLUSIONS: RpNGS is an innovative, user-friendly standalone application designed to store laboratory data (including reagents, primers, contaminants and run configurations), manage clinical metadata, process FASTQ files and produce analytical and comparative reports (including Word documents) that can be readily reviewed and certified. Its interactive interface necessitates no programming expertise, rendering it an invaluable instrument for clinical metagenomic pathogen identification.},
}

@article {pmid40821988,
year = {2025},
author = {Koehler, SI and Middlebrook, EA and Hovde, BT and Hanschen, ER},
title = {Use ATCCfinder to identify commercially available American Type Culture Collection strains based on sequence queries.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19832},
pmid = {40821988},
issn = {2167-8359},
abstract = {Microbiology research was conducted for decades before widespread availability of sequencing resources and large culture collection sequence repositories, making it challenging to efficiently identify and validate strains used in historical studies. Similarly, finding commercially available microbe strains similar to strains of interest, or containing target genes of interest found during metagenomic experiments is challenging. Despite tremendous advances in sequencing data availability, database curation, and sequence-searching software capabilities, identifying commercially available microbe strains from sequence data remains complicated and tedious. The American Type Culture Collection (ATCC) is an organization selling a wide variety of microbes, uniquely providing strain-level taxonomy classification and associated sequenced reference genomes for over four thousand isolates, with more being added regularly. As researchers purchase and sequence isolates from ATCC, many sequences derived from ATCC isolates are deposited on public databases such as NCBI-Genome. Sequences uploaded to public databases will vary in laboratory, bioinformatics, and metadata quality and can also contain mutations derived from cultivation which are not representative of ATCC stocks. Using ATCC-sourced reference genomes ensures consistent quality and analysis methodologies are implemented to accurately represent strain sequences. Currently, ATCC does not provide methods to search for sequence similarity between many query sequences and ATCC genomes. While NCBI-BLAST could be used to search for queries against GenBank, with results filtered for "ATCC" tags, search result quality varies and requires time-consuming sorting. Here we present the software ATCCfinder (GitHub: https://github.com/lanl/ATCCfinder, Zenodo: https://doi.org/10.5281/zenodo.15178103), utilizing ATCC application interface software (API) to generate query-able databases from ATCC genome resources. The algorithm generates databases of the four ATCC data types: strain-specific genome assembly sequence data (sequence), information about how each strain was collected (metadata, catalogue), and structural/functional information about genome assemblies (annotation). Once ATCC sequences are retrieved by ATCCfinder, nucleotide queries are compared against ATCC reference genomes via sequence alignment tool minimap2, with results parsed and analyzed to produce summaries describing ATCC-available strain homologous sequence matches. ATCCfinder identifies and downloads new ATCC references, allowing users to maintain an updated target search database. ATCCfinder efficiently accesses, queries, and summarizes ATCC resources, identifying purchasable strains homologous to historical sequences, functional genes, operons, and other genetic components.},
}

@article {pmid40821356,
year = {2025},
author = {Qi, S and Wang, S and Xia, Y and Chen, S and Lu, H},
title = {Identification of human pathogens in soil by virulence gene-based machine learning method.},
journal = {Eco-Environment & Health},
volume = {4},
number = {3},
pages = {100171},
pmid = {40821356},
issn = {2772-9850},
abstract = {Soils are important reservoirs of human pathogenic bacteria that can spread to humans through various pathways. Metagenomics enables high-throughput pathogen identification by mapping sequencing reads to known pathogen genomes. However, this approach has several limitations, e.g., sequence assembly is time-consuming, and reliance on reference databases may overlook potential pathogens lacking close genomic matches. Here, we developed a novel, virulence factor (VF) based machine learning method using the K-Nearest Neighbors model (VF-KNN) for identifying human pathogenic bacteria from soil metagenomes. Through learning the VF features of pathogenic and non-pathogenic bacteria, VF-KNN could achieve the desired performance in soil pathogen identification (AUC: 0.95, Accuracy: 0.85). Model prediction accuracy (0.95) was further validated using 61 pathogenic strains isolated from soil. For the top 15 most frequent soil pathogens, the prediction accuracy was >0.90 at 0.4X-1.0X genome coverage. VFs contributing significantly to pathogen identification were associated with regulation, effector delivery, motility, etc. By using VF-KNN, the averaged abundance of total potential pathogens in topsoils across China was 0.44% (n = 336), predominantly concentrated in the eastern coastal provinces. Compared with the conventional method based on a predefined pathogen list, VF-KNN identified 28% more potential pathogenic species, including some newly reported but not in the predefined list (e.g., Mycolicibacterium cosmeticum). Agricultural land exhibited significantly higher pathogen abundance and diversity than the other land types. This newly developed VF-KNN method is applicable for pathogen identification in broader environments.},
}

@article {pmid40821031,
year = {2025},
author = {He, Z and Kong, J and Su, Q and Lin, J},
title = {Application value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid in pathogen detection and diagnostic efficiency of acute exacerbation of bronchiectasis.},
journal = {American journal of translational research},
volume = {17},
number = {7},
pages = {4912-4925},
pmid = {40821031},
issn = {1943-8141},
abstract = {OBJECTIVE: To investigate pathogen detection performance and diagnostic efficacy of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in patients with acute exacerbation of bronchiectasis (AE-bronchiectasis).

METHODS: A retrospective analysis was conducted on 78 patients with AE-bronchiectasis admitted to the First Affiliated Hospital of Guangxi Medical University from March 2020 to December 2023. Pathogen detection rates and diagnostic efficacy of conventional culture detection and BALF mNGS group were compared. Seventy-six patients diagnosed as positive by the gold standard were further stratified by bronchiectasis severity index (BSI) into mild-to-moderate and severe groups to analyze differences in pathogen profiles.

RESULTS: Compared to conventional culture, mNGS showed significantly higher detection rates for bacteria, fungi, and mycobacteria (all P<0.05), notably Pseudomonas aeruginosa, Aspergillus fumigatus, and Mycobacterium tuberculosis (all P<0.05). In addition, mNGS exhibited superior diagnostic accuracy (94.87%) and sensitivity (94.74%) compared to conventional culture (P<0.05), with a higher area under the ROC curve (AUC=0.974). BSI stratification showed that the detection rates of fungi and viruses were higher in the severe group than those in the mild-to-moderate group, while the detection rate of bacteria was slightly lower than that in the mild-to-moderate group. The detection rate of Pseudomonas aeruginosa in the severe group (51.06%) was significantly higher than that in the mild-to-moderate group (27.59%), while the detection rate of human herpesvirus 7 was significantly higher in the mild-to-moderate group (24.14%) compared to the severe group (4.26%) (all P<0.05).

CONCLUSION: BALF mNGS demonstrates clear advantages over conventional methods in pathogen detection for AE-bronchiectasis, offering significantly better detection rates and diagnostic efficiency.},
}

@article {pmid40819729,
year = {2025},
author = {Nestor, D and Peker, N and Couto, N and Hiss, AN and Herbig, A and Krause, J and Rossen, JWA and Mölling, P and Sundqvist, M},
title = {Performance of shotgun metagenomics on whole blood from patients with suspected bloodstream infection: Challenges remain.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107231},
doi = {10.1016/j.mimet.2025.107231},
pmid = {40819729},
issn = {1872-8359},
abstract = {Bloodstream infections (BSI) are common, and identifying the causative organism is crucial for effective patient management. Shotgun metagenomics (SMg) has emerged as a promising diagnostic tool; however, standardized protocols are lacking. This study aimed to evaluate the use of SMg for diagnosing BSI in patients with confirmed or suspected infections, using stored samples collected at the time of blood culture (BC). DNA extraction was performed with Add-on 10 complement and SelectNA Blood Pathogen kit (Molzym) and SMg sequencing was performed on an Illumina MiSeq instrument (Illumina). The outputs from five taxonomic classification tools were compared with routine blood culture. Of the initial 51 samples (36 BCE-positive and 15 BCE-negative), 36 (71 %) were included in the taxonomic classification analysis. Fifteen samples were excluded due to a low DNA library yield (n = 8) or low sequencing output (n = 7). In two cases, SMg results matched BC findings involving one Cutibacterium acnes and one Staphylococcus aureus. These organisms could be clearly distinguished from the background level of bacterial DNA. Aside from these, SMg identified additional bacterial findings that overlapped with BC results but at low abundance making interpretation more difficult. Most SMg reads were suspected to represent contaminations, originating either from the patient or the laboratory. The output from the different taxonomic classification tools were overall similar but displayed notable differences related to their strategies for identifying bacterial findings. Based on these results, we discuss the challenges associated with SMg-based diagnosis of BSI and highlight key areas requiring further research to improve its clinical utility.},
}

@article {pmid40819522,
year = {2025},
author = {Zhang, S and Peng, F and Ma, J and Gao, B and Zhu, X and Zhang, Y and Liu, J and Peng, K and Zheng, Q and Hung, CY and Cai, C and Huang, X},
title = {Wet waste carbon source recharge improves acetoclastic methanogenesis in aged landfills.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115084},
doi = {10.1016/j.wasman.2025.115084},
pmid = {40819522},
issn = {1879-2456},
abstract = {The implementation of new waste sorting policies and "zero landfill" strategies has precipitated the premature retirement of municipal landfills and accelerated their aging, resulting in a significant decline in both the production and quality of landfill gas containing methane (CH4), thereby impeding resource utilization and exacerbating carbon emissions. Waste-derived organic matter recharge can increase the availability of landfill gas, but the underlying mechanisms and influencing factors remain unclear. In this study, waste-derived organic matter (aged landfill leachate and wet waste slurry) available at the landfill campus was used as a supplemental carbon source to infuse into an anaerobic landfill column system to investigate the effects of exogenous carbon inputs on the performance of landfill CH4 generation by using metagenomic sequencing. The results show that adding wet waste slurry and alkali-adjusted wet waste slurry increased the methane content by 50.75% and 58.31%, respectively, and significantly increased the concentration of volatile fatty acids (VFAs) in the leachate. Metagenomic sequencing revealed that wet waste slurry recharge enriched acidogenic bacteria, syntrophic bacteria, and acetoclastic methanogenic archaea and increased the expression of functional genes associated with acidification, direct interspecies electron transfer (DIET), and acetoclastic methanogenesis. A partial least squares path model (PLS-PM) revealed that functional genes and VFAs were the most important factors influencing landfill CH4 production. The results of this study provide theoretical support for the scientific management, low-carbon operation and sustainable development of aged municipal landfills.},
}

@article {pmid40819433,
year = {2025},
author = {Ma, X and Wang, L and Li, J and Chao, C and Wang, H and Li, D and Yu, W and Fan, S and Liu, C and Yu, D},
title = {Cold-season macrophyte-driven microbial modulation reduces nutrient release in eutrophic lake sediments.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126992},
doi = {10.1016/j.jenvman.2025.126992},
pmid = {40819433},
issn = {1095-8630},
abstract = {Submerged macrophyte restoration can effectively regulate internal nutrient cycling in eutrophic lake sediments, yet how cold-season macrophytes influence sediment microbial processes remain poorly understood. In this study, we conducted a field enclosure experiment combined with metagenomic sequencing using Potamogeton crispus, a cold-season submerged macrophyte, to investigate its effects on nitrogen (N) and phosphorus (P) dynamics across the sediment-water interface. The restoration of P. crispus led to marked decreases in the concentrations and sediment-to-water fluxes of bioavailable nitrogen (NH4[+], NO3[-]) and phosphorus (SRP, DGT-P). These reductions were accompanied by substantial shifts in microbial community structure and functional potential. Genes involved in nitrogen fixation and organic N metabolism were suppressed, while those related to nitrate reduction, nitrification, and nitrogen stress responses were enriched. Similarly, genes associated with phosphorus cycling exhibited increased diversity and abundance under restoration. Key microbial genes (e.g., gst, pqqB, ttdB) were strongly correlated with nutrient levels, indicating a potential role in nutrient stabilization. This study highlights the unique ecological function of cold-season macrophytes in regulating sediment biogeochemical processes and provides mechanistic insights into plant-microbe-nutrient interactions relevant to seasonally optimized lake management.},
}

@article {pmid40819273,
year = {2025},
author = {Puranik, S and Mekali, J and Damodaram, KJP},
title = {Seed Biopriming From Basics to Omics: Relieving Plants From Biotic Stress Through the Microbial Way.},
journal = {Journal of basic microbiology},
volume = {},
number = {},
pages = {e70083},
doi = {10.1002/jobm.70083},
pmid = {40819273},
issn = {1521-4028},
abstract = {From seed to harvest, cultivated crops face numerous biotic stresses, including insects, nematodes, and diseases, which significantly hinder their growth and vigor, resulting in substantial crop losses. In contrast to use of toxic agrochemicals, seed biopriming with microbial inoculants has emerged as an effective and eco-friendly alternative against pathogens and pests. Seed biopriming involves coating seeds with beneficial microorganisms that enhance protection and immunity against a variety of harmful pests and pathogens. These microbial agents colonize the seeds and establish themselves in the rhizosphere, reducing the impact of biotic stresses while fostering a healthier environment for plant growth. They are known to exhibit several mechanisms against pathogens and pests, like production of cell wall degrading enzymes, antibiosis, competition, induced systemic resistance, chelation of iron etc. Additionally, these microorganisms regulate phytohormone levels, further optimizing the physiological and metabolic characteristics of plants. This approach not only promotes robust plant growth but also enhances tolerance to deleterious bacteria, fungi, nematodes and arthropods, ensuring healthier crops. These interactions can further be well studied and expressed by using different omics approaches like metagenomics (of seed microbiome), proteomics, transcriptomics, metabolomics and differential gene expression. This review highlights the role and benefits of seed biopriming as a sustainable strategy to manage biotic stresses effectively, and the importance of omics for better understanding of complex processes during such interactions, contributing to resilient agricultural production systems and environmental sustainability.},
}

@article {pmid40819131,
year = {2025},
author = {Tang, B and Li, S and Li, X and He, J and Zhou, A and Wu, L and Xiao, X and Wang, S and Jiang, H and Jian, J and Hou, Z and Ge, Y and Lei, Y and Zhou, J and Tu, D and Lu, C and Yang, M and Yang, S},
title = {Cholecystectomy-related gut microbiota dysbiosis exacerbates colorectal tumorigenesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7638},
pmid = {40819131},
issn = {2041-1723},
support = {82030020//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172958//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Cholecystectomy represents the most prevalent biliary surgical procedure for gallbladder abnormalities. Growing evidence suggests that cholecystectomy is associated with an elevated risk of colorectal cancer. However, the underlying mechanism remains elusive. Here we show that cholecystectomy exacerbates colorectal tumorigenesis in both AOM/DSS and APC[min/+] mice models. Metagenomic sequencing and targeted metabolomics show that cholecystectomy leads to a decrease of Bifidobacterium breve (B. breve) and an increase of Ruminococcus gnavus (R. gnavus), along with increased levels of glycoursodeoxycholic acid (GUDCA) in human and tauroursodeoxycholic acid (TUDCA) in mice. Fecal microbiota transplantation, single bacterial colonization and bile acid supplementation demonstrate that cholecystectomy-related gut microbiota perturbations promote the production of TUDCA and facilitate colorectal tumorigenesis. RNA-sequencing and co-immunoprecipitation reveal that the compromised bile acid metabolism inhibits farnesoid X receptor (FXR) signaling, disrupts the FXR/β-catenin interaction, and ultimately exacerbates colorectal tumorigenesis. Significantly, FXR agonist obeticholic acid (OCA) averts cholecystectomy-related colorectal tumorigenesis. The gut microbiota holds a crucial position in cholecystectomy-induced colorectal tumorigenesis, and modulation of the gut microbiota-bile acid-FXR axis represents a promising preventive strategy.},
}

@article {pmid40817327,
year = {2025},
author = {Guo, K and Zhao, Z and Breyer, E and Baltar, F},
title = {Organic matter degradation by oceanic fungi differs between polar and non-polar waters.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7589},
pmid = {40817327},
issn = {2041-1723},
support = {OCEANIDES (P34304-B)//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; OCEANBIOPLAST (P35619-B)//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
abstract = {Recent discoveries have uncovered pelagic fungi as significant contributors to the recycling of organic matter in the ocean. However, their drivers and whether the environmental filtering on the functional role of prokaryotes also applies to pelagic fungi remain unknown. In this study, we employed the metagenomic and metatranscriptomic approaches to explore the fungi mediated organic matter degradation in the sunlit ocean. Samples were collected from the subtropical Atlantic Ocean (non-polar) to the Southern Ocean (polar), and differentiated between small (0.2 - 3 µm, SF) and large (>3 µm, LF) size fractions, to study niche partitioning in fungal communities and functions. Fungi accounted for 2-5% of eukaryotic genes and transcripts. Fungi contributed over 3% of eukaryotic carbohydrate-active enzymes (CAZymes) transcripts but less than 0.5% of protease transcripts, highlighting their specialized role in carbohydrate degradation. Non-polar and polar regions exhibited distinct fungal community composition and metabolic functions, potentially disrupting the balance of organic matter storage and cycling in these ecologically sensitive regions. Temperature emerged as a key driver of fungal CAZyme activity, revealing sensitivity to ocean warming. Our findings underscore the active role of pelagic fungi in organic matter degradation while revealing the environmental and ecological factors shaping their functional contributions across global oceanic regions.},
}