@article {pmid40671255,
year = {2025},
author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F},
title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251346781},
doi = {10.1177/00220345251346781},
pmid = {40671255},
issn = {1544-0591},
abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.},
}

@article {pmid40671160,
year = {2025},
author = {Wang, S and Kong, F and Zhang, X and Dai, D and Li, C and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Disruption of hindgut microbiome homeostasis promotes postpartum energy metabolism disorders in dairy ruminants by inhibiting acetate-mediated hepatic AMPK-PPARA axis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {167},
pmid = {40671160},
issn = {2049-2618},
support = {32130100//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Cattle ; *Energy Metabolism ; *AMP-Activated Protein Kinases/metabolism ; *Liver/metabolism ; Homeostasis ; *Postpartum Period/metabolism ; *PPAR alpha/metabolism/genetics ; *Acetates/metabolism ; 3-Hydroxybutyric Acid/blood ; Ruminants/microbiology ; },
abstract = {BACKGROUND: Postpartum energy metabolism disorders pose a significant challenge to the health and productivity of dairy ruminants, yet their underlying pathogenesis remains poorly understood. The critical role of the gut microbiota in regulating host metabolic processes via the "gut-liver axis" has garnered increasing attention, but its specific mechanisms in dairy ruminant energy metabolism disorders are still unclear. This study uses dairy cows as a model and employs a large-scale case-control analysis to systematically investigate the pathophysiological basis of postpartum energy metabolism disorders through the lens of the "gut-liver axis."

RESULTS: Postpartum energy metabolism disorders in dairy cows are characterized by elevated blood β-hydroxybutyrate (BHB) and aspartate aminotransferase (AST) levels, and hepatic steatosis. A random forest model based on gut microbiota effectively predicts disease occurrence (AUC = 0.74). Multi-omics (metagenomics, metabolomics, and transcriptomics) analysis further identified key microbes, including Faecousia species (sp017465625 and sp017380435), Methanosphaera species (sp016282985), and Bifidobacterium globosum. These microbes regulate acetate concentration in the gut, which is significantly correlated with key genes in the hepatic PPAR and PI3K-AKT pathways, as well as with blood BHB levels. Primary hepatocyte culture experiments further confirmed that sodium acetate effectively inhibits hepatic fat deposition induced by mixed fatty acids through the hepatic AMPK-PPARA axis and reduces the production of BHB in the culture medium.

CONCLUSION: This study demonstrates that key gut microbes and their metabolic product (acetate) inhibit the occurrence of metabolic disorders through the hepatic AMPK-PPARA axis. These findings provide new insights and potential therapeutic targets for understanding and mitigating postpartum metabolic disorders in dairy ruminants. Video Abstract.},
}

Animals
Female
*Gastrointestinal Microbiome/physiology
Cattle
*Energy Metabolism
*AMP-Activated Protein Kinases/metabolism
*Liver/metabolism
Homeostasis
*Postpartum Period/metabolism
*PPAR alpha/metabolism/genetics
*Acetates/metabolism
3-Hydroxybutyric Acid/blood
Ruminants/microbiology

@article {pmid40670871,
year = {2025},
author = {Chen, YC and Liao, PH and Chen, YW and Yen, DH and How, CK and Chang, CM},
title = {Optimization of Metagenomic Next-Generation Sequencing Workflow with a Novel Host Depletion Method for Enhanced Pathogen Detection.},
journal = {Molecular diagnosis & therapy},
volume = {},
number = {},
pages = {},
pmid = {40670871},
issn = {1179-2000},
support = {Grant No T21006//Taipei Veterans General Hospital/ ; },
abstract = {INTRODUCTION: Sepsis is a critical condition requiring timely and accurate pathogen identification. Traditional blood cultures are slow and often yield low sensitivity. Metagenomic next-generation sequencing (mNGS) offers broad and rapid pathogen detection but is hindered by excessive human DNA background in blood samples. This study evaluated a novel Zwitterionic Interface Ultra-Self-assemble Coating (ZISC)-based filtration device designed to deplete host cells and enhance microbial DNA recovery for improved mNGS diagnostics.

METHODS: We assessed the novel filter's performance in depleting white blood cells (WBCs) while preserving microbial integrity using spiked blood samples. Comparisons were made with other host depletion techniques, including differential lysis and CpG-methylated DNA removal. Analytical sensitivity was tested using spiked microbial communities at varying genome equivalents (GEs). Clinical validation involved eight blood culture-positive sepsis patient samples, processed with and without filtration, for both genomic DNA (gDNA) and cell-free DNA (cfDNA)-based mNGS. All libraries were sequenced on a NovaSeq600 with at least 10 million reads per sample.

RESULTS: The novel filter achieved > 99% WBC removal across various blood volumes and allowed unimpeded passage of bacteria and viruses. Compared to other depletion methods, the novel filtration was more efficient, less labor-intensive, and preserved microbial reads. mNGS with filtered gDNA detected all expected pathogens in 100% (8/8) of clinical samples, with an average microbial read count of 9351 reads per million (RPM), over tenfold higher than unfiltered samples (925 RPM). In contrast, cfDNA-based mNGS showed inconsistent sensitivity and was not significantly enhanced by filtration (1251-1488 RPM). Finally, the novel filtration did not alter the microbial composition, making it suitable for accurate pathogen profiling.

CONCLUSION: The workflow with the novel host depletion method significantly enhanced the analytical sensitivity of gDNA-based mNGS by reducing the host DNA background and enriching microbial content. This approach improved diagnostic yield in sepsis and may be a valuable tool for further clinical infectious disease diagnostics.},
}

@article {pmid40670853,
year = {2025},
author = {Lu, L and Chen, Y and Leng, M and He, S and Liu, Q and Zou, S and Liu, Y and Fan, F},
title = {Overcoming the Diagnostic Challenges in Cutaneous Cryptococcosis Caused by Cryptococcus neoformans: A Case Study Utilizing Metagenomic Next-Generation Sequencing.},
journal = {Mycopathologia},
volume = {190},
number = {4},
pages = {64},
pmid = {40670853},
issn = {1573-0832},
mesh = {Humans ; *Cryptococcosis/diagnosis/microbiology/pathology ; *Cryptococcus neoformans/genetics/isolation & purification ; *Dermatomycoses/diagnosis/microbiology/pathology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Molecular Diagnostic Techniques/methods ; },
abstract = {Cryptococcosis, a rare deep fungal infection, primarily affects immunocompromised individuals and carries a high mortality risk when hematogenously disseminated to the central nervous system (CNS). Cutaneous cryptococcosis poses diagnostic challenges due to its diverse and nonspecific dermatological manifestations. Traditional diagnostic methods, including mycological examination, culture, and histopathology, are time-consuming and require specialized expertise, often leading to misdiagnosis. Metagenomic next-generation sequencing (mNGS), an advanced molecular tool, enables rapid and unbiased pathogen identification. Here, we present the first documented case of cutaneous cryptococcosis diagnosed via mNGS, demonstrating its pivotal role in guiding timely treatment despite negative initial conventional tests.},
}

Humans
*Cryptococcosis/diagnosis/microbiology/pathology
*Cryptococcus neoformans/genetics/isolation & purification
*Dermatomycoses/diagnosis/microbiology/pathology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Molecular Diagnostic Techniques/methods

@article {pmid40670710,
year = {2025},
author = {Woodcroft, BJ and Aroney, STN and Zhao, R and Cunningham, M and Mitchell, JAM and Nurdiansyah, R and Blackall, L and Tyson, GW},
title = {Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40670710},
issn = {1546-1696},
support = {FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; n/a//Google/ ; n/a//Amazon Web Services (AWS)/ ; },
abstract = {Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present 'SingleM', which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website 'Sandpiper' collates microbial community profiles from 248,559 publicly available metagenomes.},
}

@article {pmid40670379,
year = {2025},
author = {Shi, W and Lv, M and Wang, R and Saleem, M and Wang, L and Li, M and Wang, B and Lin, R and Xu, B and Yang, C and Ning, T and Zhou, B and Gao, Z},
title = {Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {134},
pmid = {40670379},
issn = {2055-5008},
support = {2024M751875//China Postdoctoral Science Foundation/ ; 42407427//National Natural Science Foundation of China/ ; 42377309//National Natural Science Foundation of China/ ; 2023YFD20014003//Shandong Provincial "811" Project of First-class Discipline Construction, the National Key R&D Program of China/ ; 2023BCF01015//Key R&D Program of Ningxia Hui Autonomous Region of China/ ; M2023-07//State Key Natural Science Foundations of China Laboratory of Microbial Technology Open Projects Fund/ ; SDAIT-16-01//Potato Innovation Program for the Chief Expert of Shandong Province/ ; 2021CXGC010804//Shandong Province Key R&D Program/ ; },
mesh = {*Solanum tuberosum/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Soil/chemistry ; },
abstract = {The assembly mechanisms of soil microbiome during plant disease progression remain incomplete. This study linked potato common scab (PCS) severity to destabilized soil microbiome dynamics in potato geocausphere soil (GS) through integrated metagenomic analysis and culture-based experiments. Across four Shandong fields, PCS-infected GS exhibited an 11.66% reduction in bacterial α-diversity (Shannon index) and elevated stochastic community assembly. Bacterial community structure explained 39.28% (GS) and 15.96% (bulk soil) of PCS variance, outperforming pathogen abundance contributions (14.39% GS, 7.33% BS). Two microbial interaction patterns emerged in GS: 1) synchronized shifts between pathogens and beneficial taxa as PCS intensified; 2) stochastic assembly governing entire communities but deterministic processes dominating specialized subgroups. These results propose a microbial stability framework connecting soil microbiome structural rules to plant disease progression, emphasizing community-level dynamics over pathogen-centric explanations.},
}

*Solanum tuberosum/microbiology
*Soil Microbiology
*Plant Diseases/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Soil/chemistry

@article {pmid40670173,
year = {2025},
author = {Ai, S and Gao, D and Zhai, Z and Wang, S and Xue, Y and Liu, Z and Yan, X},
title = {[Effect mechanism of electroacupuncture on diabetic peripheral neuropathy in rats based on gut microbiota and metabolomics].},
journal = {Zhongguo zhen jiu = Chinese acupuncture & moxibustion},
volume = {45},
number = {7},
pages = {945-956},
doi = {10.13703/j.0255-2930.20250225-k0005},
pmid = {40670173},
issn = {0255-2930},
mesh = {Animals ; *Electroacupuncture ; Male ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/therapy/metabolism/microbiology ; Rats, Sprague-Dawley ; Rats ; Metabolomics ; Humans ; Acupuncture Points ; },
abstract = {OBJECTIVE: To explore the effect mechanism of electroacupuncture (EA) for ameliorating diabetic peripheral neuropathy (DPN) based on the analysis of gut microbiota and metabolomics.

METHODS: Thirty SPF-grade male SD rats were randomly divided into a normal group, a model group, and an EA group, with 10 rats in each one. Except in the normal group, the intraperitoneally injection with streptozotocin was used to induce diabetes mellitus model in the rest groups. In the EA group, acupuncture was delivered at bilateral "Zusanli" (ST36), "Sanyinjiao" (SP6), "Pishu" (BL20) and "Shenshu" (BL23), and electric stimulation was attached to "Zusanli" (ST36)-"Sanyinjiao" (SP6) and "Pishu" (BL20)-"Shenshu" (BL23), on the same side, with continuous wave and a frequency of 2 Hz, for 10 min in each intervention. The intervention measure of each group was delivered once every 2 days, 3 times a week, for 8 consecutive weeks. Body weight, random blood glucose (RBG), thermal withdrawal latency (TWL), and mechanical withdrawal threshold (MWT) before intervention, and in 4 and 8 weeks of intervention, separately, as well as sensory nerve conduction velocity (SCV) and motor nerve conduction velocity (MCV) of the sciatic nerve after intervention were measured. Metagenomic sequencing (MS) was used to analyze gut microbiota and screen for differential species. Liquid chromatography-mass spectrometry (LC-MS) was employed to detect the differential metabolites in plasma, and the metabolic pathway enrichment analysis was performed on the differential metabolites. Spearman correlation analysis was adopted to assess the relationship between gut microbiota and metabolomics.

RESULTS: After 4 and 8 weeks of intervention, when compared with the model group, the EA group showed the increase in body weight, TWL, MWT (P<0.01), and the decrease in RBG (P<0.01). Compared with the normal group, SCV and MCV, as well as Chao1 index were dropped in the model group (P<0.01), and those were elevated in the EA group when compared with those in the model group (P<0.01). The dominant bacterial phyla of each group were Firmicutes (F) and Bacteroidota (B), the ratio of them (F/B) in the model group was lower than that of the normal group (P<0.05), and F/B in the EA group was higher when compared with that in the model group (P<0.05). In comparison with the normal group, the relative abundance increased in Prevotella, Segatella, Prevotella-hominis and Segatella-copri (P<0.05); and it decreased in Ligilactobacillus, Eubacterium, Pseudoflavonifractor, Ligilactobacillus-murinus (P<0.05) in the model group. Compared with the model group, the relevant abundance of the above mentioned gut bacteria was all ameliorated in the EA group (P<0.05, P<0.01). Among the three groups, 120 differential metabolites were identified and enriched in 28 key metabolic pathways, such as glycerophospholipid and linoleic acid, of which, glycerophospholipid was the most significantly affected pathway in EA intervention. Spearman correlation analysis showed that 6 phosphatidylcholine metabolites were significantly positively correlated with Pseudoflavonifractor and were negatively with Prevotella, Segatella, Prevotella-hominis, Segatella-copri; 5 phosphatidylethanolamine metabolites were significantly negatively correlated with Pseudoflavonifractor and positively correlated with Prevotella, Segatella, Prevotella-hominis, Segatella-copri.

CONCLUSION: EA may regulate metabolic pathways such as glycerophospholipid, modulate specific gut microbiota such as Pseudoflavonifractor, Prevotella, and Segatella, and the co-expressed differential metabolites like phosphatidylcholine and phosphatidylethanolamine, thereby reducing blood glucose and protecting nerve function, so as to relieve the symptoms of DPN of rats.},
}

Animals
*Electroacupuncture
Male
*Gastrointestinal Microbiome
*Diabetic Neuropathies/therapy/metabolism/microbiology
Rats, Sprague-Dawley
Rats
Metabolomics
Humans
Acupuncture Points

@article {pmid40669737,
year = {2025},
author = {Li, W and Wang, H and Li, J and Lv, G},
title = {Unraveling the interaction of iron oxide and microorganisms with internal iron cycling in Arid desert riparian forest.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122354},
doi = {10.1016/j.envres.2025.122354},
pmid = {40669737},
issn = {1096-0953},
abstract = {Iron (Fe) is crucial for the normal growth and development of plant roots. In arid desert soils, the low availability of Fe poses a significant nutritional obstacle to the growth and development of desert riparian forests. However, the characteristics and mechanisms of microbial Fe cycling in desert riparian forests ecosystems are poorly understood. This study used metagenomics to assess the responses and driving mechanisms of key microbial functional genes associated with Fe cycle in the rhizosphere and bulk soils along a drought stress gradient (mild, moderate, and severe) in a desert riparian forest in northwest China. Generally, the rhizosphere effect lowers soil pH while increasing the availability of Fe-related nutrients. Genes involved in Fe uptake (mbt, pch, ccm) and Fe-Mn transport (sit) were significantly higher in the rhizosphere than in bulk soils (P < 0.001). Genes involved in Fe transport (tro, sit) were significantly higher under severe drought stress (S) than under the mild drought stress (Mi) gradient (P < 0.05). In the Fe cycle network, the complexity of Fe cycling genes and the co-occurrence network increased gradually with an increase in drought stress. Enrichment of Actinomycetes involved in the Fe cycle is a conservative response of plants to drought stress. Iron oxide (Fed, Fep) is the main composition of soil Fe in desert riparian forests, and on the drought stress gradient, Fep is the key influencing factor of Fe cycling where microbes participate, while soil pH plays a leading role in the rhizosphere environment. Our findings highlight that the rhizosphere effect, akin to a magnetic effect, transfers Fe from the bulk soil to the rhizosphere, particularly enhancing Fe absorption and transport. This rapid Fe redox cycle and transport help mitigate Fe deficiency in arid desert forests.},
}

@article {pmid40669611,
year = {2025},
author = {Song, S and Li, F and Zhao, B and Xu, Y and Liu, Z and Liu, J and Hou, Q and Chen, J and Chen, M and Liu, Z and Zhou, M and Wu, X and Wang, X},
title = {Sparfloxacin ameliorates DSS-induced ulcerative colitis by suppressing cellular senescence, JAK/NF-κB signaling pathway and modulation of the gut microbiota-metabolite axis.},
journal = {Biochemical pharmacology},
volume = {241},
number = {},
pages = {117167},
doi = {10.1016/j.bcp.2025.117167},
pmid = {40669611},
issn = {1873-2968},
abstract = {The progression of ulcerative colitis (UC) involves immune dysregulation, intestinal barrier dysfunction, and microbial dysbiosis while existing targeted therapies present challenges, including adverse effects and economic burdens. UC is characterized by persistent intestinal inflammation, manifesting as abdominal pain, hematochezia, and malnutrition. Prolonged uncontrolled inflammation may lead to colorectal cancer or severe complications, significantly impairing quality of life. Recent studies have revealed a significant correlation between pathological accumulation of senescent cells and UC pathogenesis, suggesting anti-senescence therapeutics as potential interventions. In this study, we identified sparfloxacin (SPA), a fluoroquinolone antibiotic, through high-throughput screening as an effective senolytic agent that markedly alleviates DSS-induced murine colitis. Mechanistically, combining cellular and animal experiments with transcriptomic, untargeted metabolomic, and metagenomic analyses, we demonstrated sparfloxacin's tripartite therapeutic effects: ① Senescence inhibition via downregulation of p16/p21 expression; ② Effective suppression of aberrant JAK/NF-κB signaling activation with a concomitant reduction in pro-inflammatory cytokines (TNF-α, IL-6); ③ Gut microbiota remodeling characterized by increased probiotic abundance and elevated levels of beneficial metabolites. This study for the first time elucidates the molecular mechanism whereby SPA ameliorates UC through coordinated multi-target actions involving senescence inhibition, anti-inflammatory effects, and microbiome restoration. Our findings not only expand the clinical applications of fluoroquinolones but also provide a theoretical foundation for developing integrated UC treatment strategies targeting cellular senescence.},
}

@article {pmid40669466,
year = {2025},
author = {Ghiotto, G and Xirostylidou, A and Gaspari, M and Kougias, PG and Campanaro, S and Treu, L},
title = {Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100949},
doi = {10.1016/j.xgen.2025.100949},
pmid = {40669466},
issn = {2666-979X},
abstract = {Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.},
}

@article {pmid40669445,
year = {2025},
author = {Omary, L and Canfora, EE and Puhlmann, ML and Gavriilidou, A and Rijnaarts, I and Holst, JJ and Op den Kamp-Bruls, YMH and de Vos, WM and Blaak, EE},
title = {Intrinsic chicory root fibers modulate colonic microbial butyrate-producing pathways and improve insulin sensitivity in individuals with obesity.},
journal = {Cell reports. Medicine},
volume = {6},
number = {7},
pages = {102237},
doi = {10.1016/j.xcrm.2025.102237},
pmid = {40669445},
issn = {2666-3791},
mesh = {Humans ; *Insulin Resistance ; *Butyrates/metabolism ; *Obesity/microbiology/metabolism/diet therapy ; Male ; *Dietary Fiber ; *Gastrointestinal Microbiome/drug effects ; *Plant Roots/chemistry/metabolism ; Middle Aged ; *Cichorium intybus/chemistry ; Female ; *Colon/microbiology/metabolism ; Adult ; Diabetes Mellitus, Type 2 ; Triglycerides/blood ; },
abstract = {Type 2 diabetes and obesity have become major public health concerns. Growing evidence suggests that increased dietary fiber intake, through its interaction with the gut microbiota, may help prevent these diseases. Here, we demonstrate in a 12-week randomized, placebo-controlled trial in individuals at risk for type 2 diabetes that intake of an intrinsic fiber product, consisting of entire plant cells, tended to improve peripheral insulin sensitivity (p = 0.085), increased whole-body insulin sensitivity (p = 0.032), reduced circulating triglycerides (p = 0.049), and tended to reduce intrahepatic lipid content (p = 0.063), along with an increased proportion of small adipocytes (p = 0.008). Phylogenetic and metagenomic analysis revealed that these outcomes coincided with increased levels of fiber-degrading Bifidobacterium spp. and butyrate-producing Anaerostipes spp. and a functional shift toward a distal butyrogenic trophic chain while the best responding individuals had increased levels of pectin degraders that may produce propionate. Our findings demonstrate the pivotal role of slowly fermented, intrinsic plant cell fibers in improving cardiometabolic health. This study was registered at ClinicalTrials.gov (NCT04714944).},
}

Humans
*Insulin Resistance
*Butyrates/metabolism
*Obesity/microbiology/metabolism/diet therapy
Male
*Dietary Fiber
*Gastrointestinal Microbiome/drug effects
*Plant Roots/chemistry/metabolism
Middle Aged
*Cichorium intybus/chemistry
Female
*Colon/microbiology/metabolism
Adult
Diabetes Mellitus, Type 2
Triglycerides/blood

@article {pmid40669347,
year = {2025},
author = {Yu, H and Lv, W and Ding, D and Hu, N and Zhang, H and Chen, M and Wang, C and Yan, Q and Deng, Y and He, Z and Carlson, HK and Hu, R},
title = {Arsenite-oxidizing chemolithooautotrophic prokaryotes underpin inorganic carbon fixation and arsenic detoxification in deep underground uranium mining layers.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139213},
doi = {10.1016/j.jhazmat.2025.139213},
pmid = {40669347},
issn = {1873-3336},
abstract = {Acid in-situ leach uranium (U) mining layers (ML) characterized by anaerobic, oligotrophic conditions, high arsenic (As) concentration, represent an unique but poorly characterized microbial habitat. Herein, autotrophic microbial metabolisms and arsenic detoxification strategies in underground ML (depth >111 m) were revealed through 16S rRNA gene amplicon sequencing and metagenomic analysis. Dissolved organic matter (DOM) content in ML after acid in-situ leach mining was significantly higher than that in non-mining layers (NML). Compared with NML, the arsenite (As(III)) content in ML showed a decreasing trend, while the As(V) content correspondingly increased significantly. As(III) and DOM showed significant positive effects on the diversity of bacterial communities in ML and NML. The genes involved in Calvin Benson Bassham (CBB) pathway and monosaccharide decomposition dominated the DOM dynamics in ML and NML. Notably, metabolic pathway analyses demonstrated that microbial As(III) anaerobic oxidation by coupling with nitrate reduction favors CO2 fixation driven by CBB pathway, reducing As toxicity and enhancing DOM content in ML. Chemolithoautotrophs utilize multiple survival strategies (e.g., nitrate assimilation, metals efflux) in ML. These findings reveal that chemolithoautotropic microbial As(III) oxidation contributes to CO2 fixation and As detoxification in ML, broadening our horizons of As and carbon cycling in deep underground mining environments.},
}

@article {pmid40669246,
year = {2025},
author = {Liu, S and Chen, Q and Dong, C and Qiu, X and Li, W and Tang, K},
title = {Impact of coastal deoxygenation on antibiotic resistance gene profiles in size-fractionated bacterial communities.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118445},
doi = {10.1016/j.marpolbul.2025.118445},
pmid = {40669246},
issn = {1879-3363},
abstract = {Oxygen loss disrupts marine ecosystems, threatening biodiversity and causing mass mortality of marine life. Antibiotic resistance genes (ARGs) pose a significant threat to human health by promoting the spread of resistant pathogens, making infections harder to treat and increasing mortality risks. However, the interplay between deoxygenation and ARG dynamics remains poorly understood. In this study, we employed time-series metagenomics to investigate the responses of ARG profiles in free-living (FL) and particle-associated (PA) fraction to oxygen loss during a 22-day summer deoxygenation event in the East China Sea. In total, we identified 1,186 ARG subtypes and 2,279 mobile genetic element (MGE) subtypes. The most dominant resistance classes of antibiotics were multidrug (23.5%), followed by tetracycline (15%), macrolide-lincosamide-streptogramin (13.4%), peptide (10.3%), glycopeptide (8.7%), aminoglycoside (7.3%), and beta-lactam (4.9%). We found that ARG richness in FL fraction increased with declining oxygen levels, particularly for beta-lactam and multidrug class, while no significant relationship was observed in the PA fraction. Although the total relative abundance of ARGs in both fraction showed no significant oxygen dependence, beta-lactam and multidrug resistance genes in FL fraction significantly increased with oxygen loss. Co-occurrence network analysis revealed stronger positive associations between ARGs and MGEs in the FL fraction, suggesting enhanced gene transfer among environmental bacteria. Furthermore, neutral community model analysis indicated that stochastic processes also played an interactive role in shaping ARG composition dynamics in both bacterial fractions. Our findings provide evidence that coastal deoxygenation preferentially enriches high-risk ARGs (e.g., beta-lactamase genes) in FL bacteria through MGE-mediated transfer, highlighting escalating antibiotic resistance risks that threaten both ecosystem and human health under climate warming. This study offers a framework for size-fractionated ARG monitoring and targeted mitigation strategies in coastal ecosystems.},
}

@article {pmid40669229,
year = {2025},
author = {Liu, S and Zhang, Y and Cui, Y and Du, W and Li, Y and Xiong, Z and Wang, J and Wu, Z and Yuan, J and Liu, W},
title = {Close interactions between prokaryotes and plasmids or viruses highlight a pivotal role of horizontal gene transfer in shaping antibiotic/metal(loid) resistome and their prokaryotic supercarriers in untreated hospital sewage.},
journal = {Water research},
volume = {286},
number = {},
pages = {124178},
doi = {10.1016/j.watres.2025.124178},
pmid = {40669229},
issn = {1879-2448},
abstract = {Unveiling horizontal gene transfer (HGT) of antibiotic (ARGs) and metal(loid) resistance genes (MRGs) in hospital sewage is critical for surveilling antimicrobial resistance (AMR) mobility that poses huge threats to public health. Using metagenomic shotgun sequencing, we provided an integrate insight into AMR characters and the relevant HGT in untreated sewage from one of the world's largest comprehensive hospitals from Oct 2022 to Aug 2023. We uncovered higher richness and diversity of ARGs or MRGs than mobile genetic elements (MGEs), while MGEs exhibited the highest abundance, suggesting great HGT potentials. Higher number of ARG, MRG, and MGE subtypes and abundances of putative human pathogens were found in autumn-winter than in spring-summer. ARG- and MGE-carrying prokaryotes outcompeted non-carriers in abundances, and multi-ARG and MGE carriers outcompeted single ones. Resistome supercarriers occupying 25 % of prokaryotic abundance harbored higher functional diversity and more metabolic capacity than other prokaryotes, which could be related to more predicted HGT events. Notably, 30 %, 22 %, and 40 % of prokaryote-carrying ARGs, MRGs, and MGEs were associated with HGTs. Diversity variation of plasmids as a critical contributor to HGT was positively correlated with those of prokaryotes and ARGs or MRGs. Plasmids carrying high-risk ARGs (e.g., multidrug and tetracycline types) showed higher abundances than prokaryotes and viruses. Most bacterial taxa may undergo high levels of active viral replication (phylum-specific virus/host abundance ratios >12). Hundreds of virulent viruses could lyse abundant ARG or MRG supercarriers and hosts of multidrug, multi-metals, and As resistome, whilst one temperate virus infecting multiple Azonexus supercarriers may contribute the HGT of Hg resistome. We found the dominance of stochasticity in assembling of ARGs/MGEs rather than prokaryotes or viruses, which was likely owed to functional redundancy led by HGT. Overall, this study sheds lights on a pivotal role of HGT in driving microbial community and functionality, and provides a guidance for the optimization of the treatment strategies particularly on MGEs.},
}

@article {pmid40669186,
year = {2025},
author = {Liu, Y and Song, X and Hou, X and Xiao, Y and Wang, Y and Cao, X},
title = {Dual regulation of microbial denitrification and methane mitigation with manganese-humic chelates.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126514},
doi = {10.1016/j.jenvman.2025.126514},
pmid = {40669186},
issn = {1095-8630},
abstract = {Methane emissions pose a significant environmental threat, as they contribute significantly to global climate change. During the conventional denitrification process, the demand for exogenous organic carbon and anoxic conditions can favor methanogenesis. The incorporation of transition metal manganese may supplant organic carbon as electron donor in conventional denitrification procedures, which may impede methanogenesis theoretically. The study explored the inhibitory effects of manganese, introduced as manganese-humus chelates (Mn-HA), on methanogenesis in manganese-driven nitrification and denitrification sludge. By Gompertz model fitting and Metagenomic analysis, a significant reduction in methanogenesis was observed, which is manifested by an extended methanogenic lag time λ and a diminished potential methanogenic content Pm. In the nitrogen removal experiment, Mn[2+] may substitute for COD in manganese autotrophic denitrification, resulting in the removal of nitrate. The generated high-valence manganese may replace part of the dissolved oxygen (DO) for manganese-mediated ammonia oxidation (Mnammox), leading to the removal of more ammonium.},
}

@article {pmid40668900,
year = {2025},
author = {Alvarez Mulett, S and Molina Garcia, S and Abu Saleh, O and Wolf, MJ and Rodning, AA and Wengenack, NL and Norgan, AP and Patel, R},
title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid: First Year Experience at a Tertiary Referral Hospital.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf390},
pmid = {40668900},
issn = {1537-6591},
abstract = {BACKGROUND: Central nervous system (CNS) infections are significant causes of morbidity and mortality, especially when diagnosis is delayed. Traditional cerebrospinal fluid (CSF) diagnostic methods for CNS infections have limited sensitivity. Metagenomic next-generation sequencing of cerebrospinal fluid (MSCSF) is a newer diagnostic tool capable of detecting a broad range of pathogens in a single assay.

METHODS: This retrospective cohort study evaluated the first-year experience with MSCSF at Mayo Clinic (Rochester, Minnesota). 422 tests performed during calendar year 2024 on adult patients at Mayo Clinic facilities and those tested through Mayo Clinic Laboratories were analyzed, with a subcohort analysis of the 210 Mayo Clinic patients performed to define patient characteristics associated with positive results and clinical outcomes.

RESULTS: The sensitivity of MSCSF for detecting neuroinfection in the subcohort was 64%, with 43% of confirmed neuroinfections diagnosed by MSCSF only. Subjects who were immunosuppressed (OR: 3.5, p =0.008) and those with a high pretest probability of CNS infection (OR: 20.1, p <0.001) were more likely to have positive results. Also, those who tested positive were more likely to die within the ensuing 30 days than those who tested negative (OR: 5.2, p =0.001).

CONCLUSIONS: MSCSF can be a valuable tool for diagnosing CNS infection but should not be used indiscriminately. It appears to be most beneficial when there is a high clinical suspicion of CNS infection and conventional diagnostics, and available molecular tests yield negative results. Its integration into clinical practice should be guided by diagnostic stewardship to maximize cost-effectiveness and clinical utility.},
}

@article {pmid40668828,
year = {2025},
author = {Fang, L and Lakshmanan, P and Zhang, H and Deng, Y and Xiao, R and Wen, T and Ma, B and Ge, T and Müller, C and Zhang, J and Chen, X and Zhu, Y and Su, X},
title = {Ciprofloxacin-driven purifying selection on viral genomes accelerates soil N2O production.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {29},
pages = {e2503199122},
doi = {10.1073/pnas.2503199122},
pmid = {40668828},
issn = {1091-6490},
support = {U20A2047//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFD1901402//MOST | National Key Research and Development Program of China (NKPs)/ ; CYB22127//Foundation of Graduate Research and Innovation in Chongqing/ ; SWU-KQ22054//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Ciprofloxacin/pharmacology ; *Nitrous Oxide/metabolism ; *Soil Microbiology ; *Genome, Viral/drug effects ; Denitrification/drug effects ; Soil/chemistry ; Selection, Genetic/drug effects ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Viruses are ubiquitous regulators of microbial dynamics and may thus greatly influence global microbial-driven greenhouse gas emissions. Anthropogenic stressors, such as chemical contamination, are likely to amplify these viral contributions; however, their global significance and underlying mechanisms remain elusive. Utilizing [15]N tracing, metagenomics, and laboratory assays, we explore soil viral communities and their evolutionary potential under the stress from antibiotic ciprofloxacin (CIP), focusing on their roles in regulating nitrogen cycling and N2O production. Through isolation and reinoculation of soil viruses, we demonstrate that CIP stimulates soil denitrification-derived N2O production, with 18 to 29% of the increase attributed to viral activity. Under CIP stress, soil viruses shift toward a lysogenic lifestyle, promoting mutualism with denitrifiers by horizontally transferring viral denitrification-related auxiliary metabolic genes (AMGs). The observed synonymous mutations in these AMGs, driven by CIP, suggest enhanced purifying selection, likely optimizing codon usage to align with host preferences. This optimization likely enhances the expression of denitrifying AMGs and increases N2O production. This study provides insights into the overlooked role of viral dynamics and genomic mutations in modulating N2O production under stressful environments, highlighting their evolutionary significance and impact on biogeochemical cycles in the Anthropocene.},
}

*Ciprofloxacin/pharmacology
*Nitrous Oxide/metabolism
*Soil Microbiology
*Genome, Viral/drug effects
Denitrification/drug effects
Soil/chemistry
Selection, Genetic/drug effects
Anti-Bacterial Agents/pharmacology

@article {pmid40668000,
year = {2025},
author = {Jiang, D and Hurst, JH and Mohamed, G and Kelly, MS and Roper, J and Surana, NK},
title = {Decreased Microbiota-Driven Tyrosine Metabolism Is Associated With Symptomatic COVID-19 in Children.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf325},
pmid = {40668000},
issn = {1537-6613},
abstract = {BACKGROUND: The gut microbiota has been implicated in driving coronavirus disease 2019 (COVID-19) disease severity, but the underlying mechanisms remain unknown. We investigated the relationship between the gut microbiota and development of symptomatic COVID-19 in children.

METHODS: We prospectively collected stool and plasma samples from 229 children who were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including 45 COVID-19 negative, 57 with asymptomatic COVID-19, and 127 with symptomatic COVID-19. We performed shotgun metagenomic sequencing on the stool samples to characterize the microbial taxa and functional profiles. Plasma cytokine levels were measured in SARS-CoV-2-infected individuals.

RESULTS: Children with symptomatic COVID-19 had reduced microbial biodiversity and decreased functional capacity for several metabolic pathways, including a reduction in the tyrosine biosynthesis pathway, as compared to SARS-CoV-2-uninfected children or those with asymptomatic infection. The abundance of the tyrosine biosynthesis pathway was associated with plasma levels of interferon alpha (IFN-α), which were lower in children with symptomatic COVID-19.

CONCLUSIONS: Our findings highlight a relationship between the ability of the gut microbiota to metabolize tyrosine and the development of COVID-19 symptoms in children. More generally, our study suggests that the gut microbiota may help protect against more severe forms of COVID-19, potentially by modulating IFN-α.},
}

@article {pmid40667647,
year = {2025},
author = {Yan, C and Li, XN and Peng, ZL and Wu, W and Wang, Z and Zhu, ZR and Liu, JC and Wang, Y and Ren, JL and Zhang, ZY and Li, JT},
title = {Hologenomics Reveals Specialized Dietary Adaptations in the Mengla Snail-Eating Snake.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e09999},
doi = {10.1002/advs.202509999},
pmid = {40667647},
issn = {2198-3844},
support = {2024NSFSC1181//Sichuan Science and Technology Program/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 32325011//National Natural Science Foundation of China/ ; 32220103004//National Natural Science Foundation of China/ ; 32370449//National Natural Science Foundation of China/ ; 32300351//National Natural Science Foundation of China/ ; },
abstract = {Serpents, as highly adaptable vertebrates, provide robust models for studying the mechanisms of dietary specialization. Using an integrative multi-omics approach, encompassing host genomic, transcriptomic, proteomic, gut metagenomic, and enzymatic analyses, the mechanisms underlying dietary adaptations in the Mengla snail-eating snake (Pareas menglaensis), a species specialized in consuming snails is investigated. Adaptations supporting this diet included evolution of infralabial glands secreting toxin homologs and digestive enzymes, facilitating molluscan predation and digestion. This specialization has driven adaptive evolution in the host genome and shaped the gut microbiota, addressing both nutritional challenges (e.g., lipid deficiency) and digestive requirements (e.g., mucus degradation) associated with snail consumption. Notably, the functional convergence in microbial gene functions between reptiles and mammals highlights parallel evolutionary pathways in dietary specialization. These findings elucidate the genomic foundations of dietary specialization in P. menglaensis, offering broader insights into evolutionary adaptation within a holobiome framework.},
}

@article {pmid40667600,
year = {2025},
author = {Chen, X and Wu, L and Wu, R and Dong, J},
title = {A Pulmonary Abscess Caused by Porphyromonas gingivalis Infection: A Case Report and Literature Review.},
journal = {The clinical respiratory journal},
volume = {19},
number = {7},
pages = {e70099},
pmid = {40667600},
issn = {1752-699X},
mesh = {Humans ; Male ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Bacteroidaceae Infections/diagnosis/microbiology/complications/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing/methods ; *Lung Abscess/microbiology/diagnosis/drug therapy ; Periodontitis/microbiology/diagnosis ; *Porphyromonas gingivalis/isolation & purification/genetics ; Tomography, X-Ray Computed/methods ; },
abstract = {Lung abscess is a common disease in respiratory medicine, which is a suppurative lesion caused by various pathogens, and microbiological examination is crucial for the treatment of lung abscess. Due to the widespread use of antibiotics, it is difficult to obtain reliable microbiological evidence through routine tests. There are various pathogens present in the oral cavity, and periodontitis is a risk factor for the formation of lung abscess. Enhancing understanding of lung abscesses caused by Porphyromonas gingivalis and the importance of accurately interpreting NGS reports. This article will present a case report of a lung abscess related to oral bacteria (Porphyromonas gingivalis). The patient was initially treated with empirical anti-infective therapy, which was ineffective, and despite multiple sputum cultures and bronchoalveolar lavage fluid analysis using metagenomic next-generation sequencing (mNGS), the pathogen could not be identified clearly. However, based on the significant presence of oral bacteria in the NGS of the bronchoalveolar lavage fluid, which guided the examination to discover periodontitis. Subsequently, a percutaneous lung tissue biopsy was performed for NGS testing, which further suggested Porphyromonas gingivalis as the pathogenic bacterium. This article summarizes the clinical manifestations, imaging findings, and characteristics of the pathogenic microorganisms in this case of lung abscess, reviews relevant literature to enhance the understanding of lung abscess caused by Porphyromonas gingivalis. It also confirms the importance of careful analysis of background bacteria in bronchoalveolar lavage fluid NGS based on objective risk factors, and highlights that combining patient clinical features with multisample NGS examination can promptly clarify the microbiology.},
}

Humans
Male
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Bacteroidaceae Infections/diagnosis/microbiology/complications/drug therapy
Bronchoalveolar Lavage Fluid/microbiology
High-Throughput Nucleotide Sequencing/methods
*Lung Abscess/microbiology/diagnosis/drug therapy
Periodontitis/microbiology/diagnosis
*Porphyromonas gingivalis/isolation & purification/genetics
Tomography, X-Ray Computed/methods

@article {pmid40667514,
year = {2025},
author = {Chen, J and Pang, Z and Qin, C and Huang, Z and Chen, Y},
title = {Metagenomic Next-Generation Sequencing Unravels Talaromyces Marneffei-Induced Bone Destruction in an HIV-Negative Woman: A Case Report with Fatal Outcome.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3481-3486},
pmid = {40667514},
issn = {1178-6973},
abstract = {INTRODUCTION: Talaromycosis is an opportunistic fungal disease caused by Talaromyces marneffei (TM), a significant pathogen predominantly affecting immunocompromised individuals, especially those with HIV infection. Although traditionally regarded as an HIV-associated infection, increasing cases have been reported among HIV-negative patients.

CASE PRESENTATION: This report details a case of a 36-year-old HIV-negative woman infected with Talaromyces marneffei. The patient presented with bone destruction and was diagnosed through metagenomic next-generation sequencing (mNGS). Despite receiving antifungal, anti-inflammatory, and symptomatic treatment, the infection remained uncontrolled, ultimately progressing to multi-organ failure and resulting in death.

CONCLUSION: Bone damage due to Talaromyces marneffei infection is very uncommon in HIV-negative patients. Thus, healthcare providers should be alert for possible skeletal lesions linked to this infection. Early diagnosis and appropriate antimicrobial treatment are vital for the patient's prognosis.},
}

@article {pmid40667420,
year = {2025},
author = {Orejudo, M and Gómez, MJ and Riestra, S and Rivero, M and Gutiérrez, A and Rodríguez-Lago, I and Fernández-Salazar, L and Ceballos, D and Benítez, JM and Aguas, M and Bastón-Rey, I and Bermejo, F and Casanova, MJ and Lorente-Poyatos, RH and Ber, Y and Ginard, D and Esteve, M and de Francisco, R and García, MJ and Francés, R and Rodríguez, A and Alcaide Suárez, N and Guerra Del Río, E and Soto, P and Nos, P and Barreiro-de Acosta, M and Guerra, I and Hervías Cruz, D and Domínguez Cajal, M and Royo, V and Aceituno, M and Aldars-García, L and Garre, A and Ramírez, C and Soleto, I and Schuppe-Koistinen, I and Engstrand, L and Baldán-Martín, M and Sánchez-Cabo, F and Gisbert, JP and Chaparro, M},
title = {Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595884},
pmid = {40667420},
issn = {2235-2988},
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Crohn Disease/microbiology ; Colitis, Ulcerative/microbiology ; Young Adult ; Aged ; Computational Biology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; },
abstract = {INTRODUCTION: Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-naïve IBD patients.

METHODS: Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis.

RESULTS: A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial diversity to HC, which was unaffected by disease activity. Taxonomic abundance analysis revealed a tendency towards a higher relative abundance of Escherichia coli and a lower relative abundance of Faecalibacterium prausnitzii in IBD patients compared to HC. However, the most significant differences in these patients compared to HC were observed in less abundant species, such as Toxoplasma gondii, Gemella morbillorum, and several species of the Adlercreutzia genera. Functional analysis in these patients highlighted changes in carbohydrate and nucleotide pathways.

DISCUSSION: Our data suggest that newly diagnosed CD patients show significant microbiota composition disparities compared to UC patients and HC. Microbiota differences in these patients are linked to dysbiosis, characterized by a reduction in beneficial genera such as Gemella and Adlercreutzia, and a rise in pathogenic species.},
}

Humans
*Feces/microbiology
*Metagenomics/methods
Female
Male
Adult
Middle Aged
*Inflammatory Bowel Diseases/microbiology/diagnosis
Dysbiosis/microbiology
*Gastrointestinal Microbiome
Crohn Disease/microbiology
Colitis, Ulcerative/microbiology
Young Adult
Aged
Computational Biology
Bacteria/classification/genetics/isolation & purification
Biodiversity

@article {pmid40667084,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Precision Prediction of Microbial Ecosystem Impact on Host Metabolism Using Genome-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.661827},
pmid = {40667084},
issn = {2692-8205},
abstract = {Microbes drive ecosystem function through their physical interactions and metabolic transformations. However, since microbiomes are ecologically and metabolically interconnected, it is challenging to predict emergent ecosystem responses once the microbiome is disturbed. While it is widely acknowledged that mammalian gut dysbiosis influences host metabolism, mechanistic links that predict these effects are understudied. This study employs a genome-resolved eco-systems biology approach, using a high-resolution 'spinal cord-gut axis' model system and dataset, to predict how dysbiotic gut metabolism impacts overall mammalian health. By scaling and combining temporally resolved network analytics and consensus statistical methods, key microbial species were identified that predict overall host physiology and presumably control the gut ecosystem. In silico validation by pathway-centric functional analyses and comparative genomics revealed that key bacteria, sometimes exclusively, encode functions linking microbial and host metabolisms. Notably, spinal-mediated disturbances in the ecosystem shifted gut microbial nitrogen metabolism from urease-to amino acid-dependent pathways, with patterns that varied by host sex and bacterial species. Overall, this research challenges the traditional paradigm that only the host maintains whole-body nitrogen balance and instead invokes the microbiome as an environmentally-sensitive regulatory organ that can dictate health or disease by influencing mammalian whole-body elemental balance.},
}

@article {pmid40666980,
year = {2025},
author = {Markey, L and Qu, EB and Mendall, C and Finzel, A and Materna, A and Lieberman, TD},
title = {Microbiome diversity of low biomass skin sites is captured by metagenomics but not 16S amplicon sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.24.661265},
pmid = {40666980},
issn = {2692-8205},
abstract = {UNLABELLED: Established workflows for microbiome analysis work well for high microbial biomass samples, like stool, but often fail to accurately define microbial communities when applied to low microbial biomass samples. Here, we systemically compare microbiome analysis methods -16S rRNA sequencing, shallow metagenomics, and qPCR PMP™ panels-as well as extraction methods across skin swab samples and mock community dilutions. While extraction method minimally impacted results, with no significant signal for method-specific contamination or bias, we observed critical differences in inferred composition across analysis methods for low biomass samples. Metagenomic sequencing and qPCR revealed concordant, diverse microbial communities on low biomass leg skin samples, whereas 16S amplicon sequencing exhibited extreme bias toward the most abundant taxon. Both qPCR and metagenomics showed that female genital tract bacteria dominated the leg skin microbiome in about half of female subjects. Metagenomics also enabled sub-species analysis, which demonstrated that individuals have consistent within-species diversity across high-biomass forehead and low-biomass leg skin sites. This work illustrates that shallow metagenomics provides the necessary sensitivity and taxonomic resolution to characterize species and strain-level diversity in extremely low biomass samples, opening possibilities for microbiome discovery in previously unexplored niches.

IMPORTANCE: Despite the importance of the skin microbiome in health and disease, there have been far fewer studies characterizing the microbiome of skin compared to that of the gut. In part, this is because microbiome methods were initially developed for bacteria-rich samples like stool and these methods perform poorly on bacteria-poor samples like skin swabs. The perceived difficulty of getting reliable data from such low biomass sites has limited the scope and types of analyses performed. Here we demonstrate that shotgun, whole-genome, metagenomic sequencing recovers the full input from even very dilute control community samples, and reveals a highly diverse population even on very low biomass skin sites. We describe a streamlined sample processing and analysis pipeline which can be applied broadly to characterize low biomass microbiome samples and reveal new host-microbiome interactions.},
}

@article {pmid40666886,
year = {2025},
author = {Li, X and Trepka, KR and Song, F and Kyaw, TS and Turnbaugh, PJ and Abate, AR},
title = {Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.18.660470},
pmid = {40666886},
issn = {2692-8205},
abstract = {Microbial communities encompass diverse bacteria, archaea, and eukaryotes that play vital roles in ecosystems and host health. Comprehensive analysis of these communities requires accurate, quantitative, and cross-domain profiling, yet current sequencing methods-metagenome shotgun sequencing (MGS) and ribosomal RNA (rRNA) amplicon sequencing-struggle to achieve these goals in a single assay. MGS provides broad functional insights but suffers from high cost, computational burden, and reliance on incomplete reference databases. rRNA amplicon sequencing, while more taxonomically targeted, typically profiles either prokaryotes or eukaryotes separately, depending on the chosen primer sets, and thus lacks simultaneous cross-domain resolution. To address these limitations, we developed PAMA-seq, a droplet-digital multiplex PCR technique. PAMA-seq partitions DNA sample from microbial communities into nanoliter droplets, each containing a single template molecule, and independently amplifies both the 16 S and 18 S rRNA genes, resulting in uniform amplification efficiency and accurate quantification. We validated PAMA-seq on a synthetic microbial community, a stool sample from a patient with colorectal cancer, and a coastal seawater sample. The method provided stable, cross-domain taxonomic profiles at sequencing depths as low as 10 [4] reads-one to two orders of magnitude fewer than comparable shotgun metagenomics approaches-while significantly reducing variability between replicates. By combining comprehensive domain coverage with low sequencing depth requirements, PAMA-seq offers an efficient, cost-effective, and scalable method for monitoring microbial communities across diverse ecosystems, from clinical samples to global marine environments.},
}

@article {pmid40666868,
year = {2025},
author = {Yang, Y and Wang, T and Huang, D and Wang, XW and Weiss, ST and Korzenik, J and Liu, YY},
title = {Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656232},
pmid = {40666868},
issn = {2692-8205},
abstract = {Microbial communities are essential for sustaining ecosystem functions in diverse environments, including the human gut. Phages interact dynamically with their prokaryotic hosts and play a crucial role in shaping the structure and function of microbial communities. Previous approaches for inferring phage-host interactions (PHIs) from metagenomic data are constrained by low sensitivity and the inability to accurately capture ecological relationships. To overcome these limitations, we developed PHILM (P hage- H ost Interaction L earning from M etagenomic profiles), a deep learning framework that predicts PHIs directly from the taxonomic profiles of metagenomic data. We validated PHILM on both synthetic datasets generated by ecological models and real-world data, finding that it consistently outperformed the co-abundance-based approach for inferring PHIs. When applied to a large-scale metagenomic dataset comprising 7,016 stool samples from healthy individuals, PHILM identified 90% more genus-level PHIs than the traditional assembly-based approach. In a longitudinal dataset tracking PHI dynamics, PHILM's latent representations recapitulated microbial succession patterns originally described using taxonomic abundances. Furthermore, we demonstrated that PHILM's latent representations served as more discriminative features than taxonomic abundance-based features for disease classifications. In summary, PHILM represents a novel computational framework for predicting phage-host interactions from metagenomic data, offering valuable insights for both microbiome science and translational medicine.},
}

@article {pmid40666800,
year = {2025},
author = {Weiss, SL and Bbosa, N and Orf, GS and Berg, MG and Ssemwanga, D and Kalungi, S and Balinandi, S and Mata, M and Bosa, HK and Nabirye, SE and Buule, J and Lutalo, T and Havron, A and Downing, R and Rodgers, MA and Averhoff, F and Cloherty, GA and Kaleebu, P},
title = {A novel post-mortem pathogen discovery program detects an outbreak of Echovirus E7: Uganda, 2022-2023.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1557576},
pmid = {40666800},
issn = {1664-302X},
abstract = {OBJECTIVES: Utilizing post-mortem examination for routine monitoring of infectious diseases and pandemic preparedness is a common-sense, yet uncommon, public health measure. Here, we established a novel mortuary surveillance program in Uganda that leverages the unbiased nature of metagenomic next-generation sequencing (mNGS) to detect pathogens in recently deceased individuals.

METHODS: Between October 2022 and December 2023, specimens and patient metadata were collected from 2,607 individuals across five mortuary sites around Kampala. Specimens were pre-screened for hemorrhagic fever viruses by RT-qPCR and a subset (n = 134) of RT-qPCR negatives were sequenced by mNGS.

RESULTS: A variety of DNA (herpes, parvovirus, bufavirus) and RNA (Saffold, Salivirus, HAV) viruses, vectored (Bartonella, Rickettsia) and nosocomial (Enterobacter, Klebsiella) bacterial infections, and potentially lethal respiratory pathogens (e.g., Cryptococcus neoformans, Corynebacterium diphtheria) were detected. A localized outbreak of Enterovirus B (EV-B), specifically a recombinant Echovirus E7, was observed in Kampala. An epidemiologic assessment indicated that most identified pathogens were acquired via direct and/or indirect contact (e.g., fecal-oral, fomites) and that other modes of transmission (e.g., food-borne, insect-vectored) played a less significant role.

CONCLUSION: Integration of mortuary surveillance, coupled with mNGS, into public health systems represents a powerful strategy for identifying unrecognized outbreaks and monitoring the (re-) emergence of infectious diseases.},
}

@article {pmid40666679,
year = {2025},
author = {Lei, S and Wang, J and Zhang, M and Huang, J and Liu, Y and Long, Y and Xing, Y and Yu, Z},
title = {The Succession of Cervical Canal Microbiota in Endometrial Cancer and Cervical Cancer: A Clinical Metagenomics Study.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {2039-2050},
pmid = {40666679},
issn = {1179-1411},
abstract = {OBJECTIVE: To define stage-specific cervical canal microbiota signatures across the continuum of gynecologic malignancies from benign endometrial cancer (BE)/cervical cancer precancerous lesions (CIN) to endometrial cancer (EC)/cervical cancers (CC), and to evaluate their potential as diagnostic biomarkers and therapeutic targets.

METHODS: In the observational study, metagenomic sequencing was employed to investigate the cervical canal microbiota of 45 patients, including BE, EC, CIN, and CC. Specimen collection was performed by an experienced physician. All samples were sequenced utilizing the shotgun approach. The microbial statistical analyses were conducted using R.

RESULTS: Compared to the non-cancerous group (BE and CIN), the index related to microbial community stability decreases significantly and the incidence of cervical canal dysbiosis increases in the cancerous group (EC and CC). Microbial diversity exhibited significant differences between BE and EC, CIN and CC, as well as cancerous and non-cancerous groups. At the species level, some species were significantly decreased (eg, Lactobacillus iners) and increased (eg, Staphylococcus haemolyticus, Pasteurella multocida, Pseudomonas putida, and other opportunistic pathogen) in the cancerous group.

CONCLUSION: The cervical canal represents a distinct microbial niche, with its dysbiotic progression reflecting the trajectory of oncogenic transformation. The progression from non-cancerous to cancerous states is characterized by the replacement of the vaginal microbial community, which is dominated by Lactobacillus iners, with a gradual shift towards opportunistic pathogen. Disease diagnosis and complementary therapies focused on lactobacilli and hallmark opportunistic pathogen may offer new insights for precision oncology.},
}

@article {pmid40666309,
year = {2025},
author = {Geraldini, DB and Bittar, C and Possebon, FS and Gismene, C and Mariutti, RB and da Costa, VG and Campos, GRF and Beltrão, RC and Neto, GG and Lofego, AC and Nogueira, ML and Arni, RK and Junior, JPA and de Freitas Calmon, M and Rahal, P},
title = {Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf045},
pmid = {40666309},
issn = {2057-1577},
abstract = {Ticks are obligate hematophagous arthropods that can transmit pathogens and are important vectors of diseases affecting wild and domestic animals, as well as humans, thus representing a serious risk to public health. Despite the growing concern about arboviruses, our understanding of tick-borne viruses remains limited compared to those transmitted by mosquitoes. We performed metagenomic analysis, focusing on the virome of ticks collected from wild animals in the countryside of the state of São Paulo, Brazil. The experimental analysis highlighted important molecular evidence of a potential new virus from the Jingmenvirus group in ticks collected from wild animals. The four pools that were positive included Amblyomma sculptum and A. nodosum ticks, collected from Myrmecophaga tridactyla, Callithrix penicillata, and Cerdocyon thous. These data suggest that it is a new member of the Jingmenvirus group, which we propose to be named Rio Preto tick virus (RPTV). In addition, the RPTV genome was analysed in silico, and proteins with high homology to those of the Jingmenvirus group were identified. Here, we report the identification of a potentially novel virus found in ticks from wild animals in southeastern Brazil. This study contributes to the epidemiological surveillance of the region and helps to understand the potential risks of the emergence of zoonoses, which can impact human health, in addition to the potential impacts on the fauna.},
}

@article {pmid40666308,
year = {2025},
author = {Ng, DYM and Sun, W and Sit, THC and Brackman, CJ and Tse, ACN and Bui, CHT and Tang, AWY and Wong, ANC and Tsang, ATL and Koo, JCT and Cheng, SMS and Peiris, M and Samborskiy, DV and Gorbalenya, AE and Chin, AWH and Poon, LLM},
title = {Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in the Deltacoronavirus.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf049},
pmid = {40666308},
issn = {2057-1577},
abstract = {Migratory birds may carry emerging viruses over long distances. Regular surveillance and metagenomic analysis were employed to explore the diversity of avian coronaviruses at Hong Kong's Mai Po Wetland. We tested a total of 3239 samples collected from 2018 to 2024, among which the prevalence rate of viruses of the genus Gammacoronavirus (64.4%) was higher than that of Deltacoronavirus (35.6%). The host species were identified for 79.8% of the coronavirus-positive samples. Two deltacoronaviruses with full-genome sequences and one nearly complete gammacoronavirus genome were identified in faecal samples of three bird species. We also predicted putative transcriptional regulatory sequences and 3CLpro and PLpro cleavage sites for these viruses. Results from our phylogenetic analysis and pairwise amino acid identity comparisons, using the International Committee on Taxonomy of Viruses classification criteria based on the DEmARC framework, indicate that black-faced spoonbill coronavirus (BSCoV, strain MP22-1474) prototypes a new subgenus. Great cormorant coronavirus (GCCoV, strain MP18-1070) and falcated duck coronavirus (FDCoV, strain MP22-196) belong to two previously known species while diverging most profoundly from known viruses of these species. Two recombination events may have contributed to the evolution of FDCoV MP22-196 in genome regions from ORF1b to the S gene and from the M gene to the N gene. The cophylogenetic analysis between avian hosts and coronaviruses provides evidence for a strong linkage between viruses of the genus Gammacoronavirus and the birds of order Anseriformes. This study highlights the importance of ongoing surveillance for coronaviruses in wild migratory birds.},
}

@article {pmid40665424,
year = {2025},
author = {Yvenou, S and Le Moigne, M and Rouxel, O and Aubé, J and Trouche, B and Cathalot, C and Rinnert, E and Philippon, X and Chéron, S and Boissier, A and Guyader, V and Germain, Y and Godfroy, A and Roussel, EG and Alain, K},
title = {Sulfur-rich deposits associated with the deep submarine volcano Fani Maoré support broad microbial sulfur cycling communities.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {166},
pmid = {40665424},
issn = {2049-2618},
support = {ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-22-CE02-0001//French National Research Agency for the project MISD (with the Pole Mer Bretagne Atlantique label)/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; ANR-17-EURE-0015//ISblue project, Interdisciplinary graduate school for the blue planet/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; Sino-French IRP 1211 MicrobSea//CNRS-INEE/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; doi: 10.18715/MAYOTTE.REVOSIMA//REVOSIMA/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; FR000063751 //876//TOTAL ENERGIES/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; 20/1001730//IFREMER/ ; },
mesh = {*Sulfur/metabolism/analysis ; *Volcanic Eruptions/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; *Geologic Sediments/microbiology/chemistry ; Indian Ocean ; Metagenomics/methods ; Seawater/microbiology/chemistry ; Metagenome ; },
abstract = {BACKGROUND: In 2018, the island of Mayotte located in the western Indian ocean, has experienced a seismo-volcanic crisis linked to the birth of an impressive intraplate submarine volcano at the east of the island. This volcano, named Fani Maoré, which has not yet been the subject of microbiological studies, triggered the largest submarine eruptive event ever recorded. Close to the volcano's summit is a singular meter-size structure containing abundant native sulfur mineralizations. While a wide variety of ecosystems, with more or less well documented microbial communities, are found in active volcanoes on the ocean floor, knowledge on microbial communities hosted in habitats such as sulfur-rich intraplate volcanoes, that are not located on hotspots, remains limited. Genome-resolved metagenomics, culture-based functional approaches, geochemical and mineralogical analyses were combined to characterize the geological and physico-chemical constraints of the environment surrounding the yellow deposit part of this hotspot volcano and the composition and functions of its microbial community.

RESULTS: Geological and geochemical analyses indicated that this volcanic habitat had high concentrations in various sulfur species, including native sulfur, hydrogen sulfide and sulfate. Twenty-three Metagenome Assembled Genomes (MAGs) belonging to 8 different bacterial phyla, mainly Pseudomonadota, Bacteroidota and Campylobacterota, were reconstructed from the sulfur-rich deposit and analyzed. The vast majority of MAGs encoded genes for complete sulfur cycling metabolic pathways, in particular sulfur oxidation. Estimation of the cultivable microbial fraction revealed a diversity of microorganisms, with high growth rates for sulfur reduction, sulfate reduction with dihydrogen, and sulfur oxidation. Sulfur compound (S[0], SO3[2-] and S2O3[2-]) disproportionation was also observed in cultures. The versatile genus Sulfurimonas was prevalent in culture at 6 and 20 °C, in the presence of different sulfur redox couples.

CONCLUSIONS: Microbial communities, including taxa commonly found in ridge hydrothermal systems, were composed of autotrophic, heterotrophic or mixotrophic taxa using a large range of electron donors and acceptors to fuel their catabolism, particularly sulfur compounds in all common oxidation states. They had the genetic potential and physiological capacity to carry out all the metabolic reactions of the microbial sulfur cycle using the abiotic sulfur compounds present in their habitat. Representatives of the Sulfurimonas genus were among the main chemoautotrophs, since they predominated in eleven different temperature-redox pair culture combinations. Based on the observations, a conceptual model was proposed to describe the interactions in this sulfur-rich deposit that may occur between the microorganisms, the physico-chemical conditions and the sulfur compounds supplied by the environment. Video Abstract.},
}

*Sulfur/metabolism/analysis
*Volcanic Eruptions/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
*Geologic Sediments/microbiology/chemistry
Indian Ocean
Metagenomics/methods
Seawater/microbiology/chemistry
Metagenome

@article {pmid40665409,
year = {2025},
author = {Lyu, L and Fan, Y and Vogt, JK and Clos-Garcia, M and Bonnefond, A and Pedersen, HK and Dutta, A and Koivula, R and Sharma, S and Allin, KH and Brorsson, C and Cederberg, H and Chabanova, E and De Masi, F and Dermitzakis, E and Elders, PJ and Blom, MT and Hollander, M and Eriksen, R and Forgie, I and Frost, G and Giordano, GN and Grallert, H and Haid, M and Hansen, TH and Jablonka, B and Kokkola, T and Mahajan, A and Mari, A and McDonald, TJ and Musholt, PB and Pavo, I and Prehn, C and Ridderstråle, M and Ruetten, H and Hart, LM' and Schwenk, JM and Stankevic, E and Thomsen, HS and Vangipurapu, J and Vestergaard, H and Viñuela, A and Walker, M and Hansen, T and Linneberg, A and Nielsen, HB and Brunak, S and McCarthy, MI and Froguel, P and Adamski, J and Franks, PW and Laakso, M and Beulens, JWJ and Pearson, E and Pedersen, O},
title = {The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {78},
pmid = {40665409},
issn = {1756-994X},
support = {FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; FP7/2007-2013//European Union's Seventh Framework Programme/ ; },
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics ; Blood Glucose ; Europe ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Glucose Tolerance Test ; Metagenomics ; *Prediabetic State/microbiology/metabolism ; Prospective Studies ; },
abstract = {BACKGROUND: Previous case-control studies have reported aberrations of the gut microbiota in individuals with prediabetes. The primary objective of the present study was to explore the dynamics of the gut microbiota of individuals with prediabetes over 4 years with a secondary aim of relating microbiota dynamics to temporal changes of metabolic phenotypes.

METHODS: The study included 486 European patients with prediabetes. Gut microbiota profiling was conducted using shotgun metagenomic sequencing and the same bioinformatics pipelines at study baseline and after 4 years. The same phenotyping protocols and core laboratory analyses were applied at the two timepoints. Phenotyping included anthropometrics and measurement of fasting plasma glucose and insulin levels, mean plasma glucose and insulin under an oral glucose tolerance test (OGTT), 2-h plasma glucose after an OGTT, oral glucose insulin sensitivity index, Matsuda insulin sensitivity index, body mass index, waist circumference, and systolic and diastolic blood pressure. Measures of the dynamics of bacterial microbiota were related to concomitant changes in markers of host metabolism.

RESULTS: Over 4 years, significant declines in richness were observed in gut bacterial and viral species and microbial pathways accompanied by significant changes in the relative abundance and the genetic composition of multiple bacterial species. Additionally, bacterial-viral interactions diminished over time. Despite the overall reduction in bacterial richness and microbial pathway richness, 80 dominant core bacterial species and 78 core microbial pathways were identified at both timepoints in 99% of the individuals, representing a resilient component of the gut microbiota. Over the same period, individuals with prediabetes exhibited a significant increase in glycemia and insulinemia alongside a significant decline in insulin sensitivity. Estimates of the gut bacterial microbiota dynamics were significantly correlated with temporal impairments in host metabolic health.

CONCLUSIONS: In this 4-year prospective study of European patients with prediabetes, the gut microbiota exhibited major changes in taxonomic composition, bacterial species genetics, and microbial functional potentials, many of which paralleled an aggravation of host metabolism. Whether the temporal gut microbiota changes represent an adaptation to the progression of metabolic abnormalities or actively contribute to these in prediabetes cases remains unsettled.

TRIAL REGISTRATION: The Diabetes Research on Patient Stratification (DIRECT) study, an exploratory observational study initiated on October 15, 2012, was registered on ClinicalTrials.gov under the number NCT03814915.},
}

Adult
Aged
Female
Humans
Male
Middle Aged
Bacteria/classification/genetics
Blood Glucose
Europe
Follow-Up Studies
*Gastrointestinal Microbiome
Glucose Tolerance Test
Metagenomics
*Prediabetic State/microbiology/metabolism
Prospective Studies

@article {pmid40665121,
year = {2025},
author = {Balasubramaniyan, M and Veeran, Y},
title = {Unravelling Evolutionary and Ecological Insights of Foraminifera by Using Next Generation Sequencing: A Review.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40665121},
issn = {1573-4927},
abstract = {Next-generation sequencing (NGS) has transformed our understanding of foraminifera biology by revealing cryptic diversity, clarifying phylogenetic relationships, and elucidating adaptive mechanisms previously inaccessible through morphological studies alone. This review delves into the potential of NGS in uncovering the secrets of foraminifera. We examine the current state of knowledge, recent breakthroughs, and future directions in applying NGS to foraminiferal research. Specifically, this study highlights how NGS enhances our understanding of foraminiferal taxonomy, adaptation to environmental changes, and functional genomics. Additionally, this review explores the potential of NGS to elucidate the genetic basis of foraminiferal shell formation, symbiotic relationships, and their responses to environmental stressors. We also address challenges and limitations associated with foraminiferal NGS, such as genome assembly complexities, intra-species heterogeneity, and sampling biases. Overall, this review aims to promote further research and collaboration in foraminiferal genomics, ultimately enhancing knowledge of these ecologically significant organisms and their contributions to marine ecosystems and paleoenvironments.},
}

@article {pmid40665020,
year = {2025},
author = {Liu, Y and Zhang, H and Cao, L and Fu, L and Lian, C and Guo, Y and Zhong, Z and Seim, I and Wang, M and Li, C},
title = {Methane filtration and metabolic cooperation of microbial communities in cold seep water columns from South China Sea.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1052},
pmid = {40665020},
issn = {2399-3642},
support = {42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; China ; *Seawater/microbiology ; *Bacteria/metabolism/genetics/classification ; *Microbiota ; Metagenome ; *Water Microbiology ; Oceans and Seas ; Metagenomics ; },
abstract = {Microbes in cold seep water columns are essential for methane sequestration and biogeochemical cycling, yet their structures and ecological functions, particularly at the bottom water interface (BWI), are poorly understood. Here, we performed metagenomic analyses to explore the microbial biodiversity and functions at the F-site cold seep in the South China Sea. Functional stratification revealed that photosynthetic autotrophs dominate surface zones, heterotrophs are prevalent in mesopelagic zones, and chemosynthetic bacteria are abundant at the BWI. We obtained 377 metagenome-assembled-genomes (MAGs) and constructed genome-scale metabolic models to unveil metabolic interactions facilitating the coupling of carbon, nitrogen, and sulfur among microbes, particularly at the BWI. Notably, methanotrophic bacteria with diverse metabolic capabilities distributed from the BWI zone to the deep mesopelagic regions, highlighting the broader influence of methane. In conclusion, our findings reveal a high degree of heterogeneity in the composition and function of microorganisms across the F-site cold seep water column. Our study also sheds light on the ecological interactions and environmental gradients that shape these microbial communities.},
}

*Methane/metabolism
China
*Seawater/microbiology
*Bacteria/metabolism/genetics/classification
*Microbiota
Metagenome
*Water Microbiology
Oceans and Seas
Metagenomics

@article {pmid40664945,
year = {2025},
author = {Jiang, W and Xi, R and Zhou, J and Pei, Y and Huang, P and Liu, M},
title = {16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1234},
pmid = {40664945},
issn = {2052-4463},
mesh = {Animals ; *Goats/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Metagenome ; Fetus/microbiology ; },
abstract = {The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90 ± 10 gestational days) and metagenomics (3 7-day-old goat kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.},
}

Animals
*Goats/microbiology
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
Metagenomics
*Metagenome
Fetus/microbiology

@article {pmid40664768,
year = {2025},
author = {Lema, NK and Gemeda, MT and Woldesemayat, AA},
title = {Secondary metabolite biosynthetic gene clusters and microbial diversity as predicted by shotgun metagenomic sequencing approach in hospitals and pharmaceutical industry wastes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25500},
pmid = {40664768},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Drug Industry ; *Multigene Family ; *Bacteria/genetics/classification/metabolism ; *Secondary Metabolism/genetics ; Metagenome ; Hospitals ; Biosynthetic Pathways/genetics ; Archaea/genetics ; },
abstract = {Hospital and pharmaceutical industry wastes harbor a diverse microbial community influenced by their complex chemical composition, including antibiotic-rich compounds originating from soil microorganisms. This study employs a shotgun metagenomic approach to comprehensively characterize the microbial composition of hospital and Pharmaceutical industry wastes for the first time in Ethiopia. Metagenomic DNA was extracted and used to construct a whole-genome shotgun library, which was subsequently sequenced using the Illumina HiSeq1500 platform. Taxonomic analysis revealed that bacteria were the predominant domain across all samples, followed by eukaryotes and archaea. Among the bacterial phyla, Pseudomonadota was the most prevalent in both hospital and pharmaceutical waste samples. At the genus level, Pseudomonas and Pedobacter were the most abundant taxa, followed by Flavobacterium and Streptomyces. Notably, Streptomyces exhibited higher-than-expected abundance in the waste metagenome, suggesting a potential adaptive response to environmental stressors. Across all samples, Pedobacter and Pseudomonas were consistently the most dominant bacterial genera. Functional analysis using gene ontology (GO) annotations highlighted the predominance of metabolic and biosynthetic processes. Further investigation revealed an enrichment of ATP-binding cassette (ABC) transporter protein families and winged-helix protein domains, both of which are linked to antibiotic resistance, metabolite translocation, and antibiotic biosynthesis regulation. KEGG pathway analysis identified key biosynthetic pathways, including terpenoid and polyketide biosynthesis, as well as beta-lactam antibiotic production. Additionally, antiSMASH analysis detected multiple biosynthetic gene clusters (BGCs), including those encoding terpenes, bacteriocins, and non-ribosomal peptide synthetases. Overall, this study underscores the adaptive potential of microorganisms inhabiting industrial waste environments, highlighting their genomic capacity to produce bioactive secondary metabolites in response to toxic compounds. These findings provide valuable insights into microbial resilience and the potential for biotechnological applications in bioremediation and drug discovery.},
}

*Metagenomics/methods
*Drug Industry
*Multigene Family
*Bacteria/genetics/classification/metabolism
*Secondary Metabolism/genetics
Metagenome
Hospitals
Biosynthetic Pathways/genetics
Archaea/genetics

@article {pmid40663936,
year = {2025},
author = {Wang, Z and Rong, XL and Dai, CX and Wang, Q and Lu, LF and Zhang, WT and Zhang, L and Chen, QQ and Liu, EH},
title = {Fucoidan alleviates renal fibrosis in mice via Akkermansia muciniphila-mediated suppression of NEU1-TLR4-NFκB signaling axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {157060},
doi = {10.1016/j.phymed.2025.157060},
pmid = {40663936},
issn = {1618-095X},
abstract = {BACKGROUND: Fucoidan, a bioactive sulfated polysaccharide, is renowned for its extensive range of biological activities, including anticancer activity, antioxidative properties, immune activation and has demonstrated supportive therapeutic effects in treating kidney ailments. However, the underlying mechanism related to renal fibrosis remains not fully understood.

PURPOSE: The aim of this study was to elucidate the protective effects and mechanism of FPS against renal fibrosis with a focus on gut-kidney axis.

METHODS: We established renal fibrosis models in mice using unilateral ureteral obstruction (UUO), folic acid (FA) challenge, or a microbiota-depleted, with continuous oral administration of FPS, Akkermansia muciniphila (AKK), or acetate at specified doses and intervals. Simultaneously, we examined the impact of FPS on epithelial mesenchymal transformation in cultured HK-2 and investigated the associated mechanisms.

RESULTS: In this study, we demonstrate that fucoidan administration reduces renal collagen deposition, inflammation, epithelial mesenchymal transformation and improves renal function in mouse models of renal fibrosis induced by UUO or FA. Metagenomics analysis showed that fucoidan significantly increases the abundance of AKK by promoting its growth in UUO-induced renal fibrosis. Oral administration of live AKK alleviates renal fibrosis in UUO and FA mouse models. Using oral antibiotic-treated mice, we found that the effect of fucoidan on renal fibrosis was weakened. Gas chromatography-mass spectrometry (GC-MS/MS) study results show that AKK produces the short-chain fatty acids (acetate), which protects against renal fibrosis by suppressing NEU1-TLR4-NFκB-mediated inflammation in the kidney.

CONCLUSION: Our findings establish a novel gut-kidney axis wherein fucoidan ameliorates renal fibrosis through AKK-mediated acetate production and subsequent NEU1-TLR4-NFκB pathway inhibition.},
}

@article {pmid40663918,
year = {2025},
author = {Vishwakarma, YK and Bhardwaj, N and Ram, K and Gogoi, MM and Banerjee, T and Mohanty, M and Singh, RS},
title = {Bioaerosol emissions from solid waste processing facilities at urban environment and their impact on human health.},
journal = {The Science of the total environment},
volume = {994},
number = {},
pages = {180049},
doi = {10.1016/j.scitotenv.2025.180049},
pmid = {40663918},
issn = {1879-1026},
abstract = {Waste management is one of the challenging issues in developing countries because of indiscriminate urbanization, huge population growth coupled with insufficient technology to manage it. The processing of waste and producing manure are good techniques for solid waste management. This study shows that during waste processing such as loading and unloading, sorting, mixing and leachate treatment, several types of bioaerosols, both bacterial and fungal, are emitted to the atmosphere. Here, both fungal and bacterial bioaerosol concentration near a waste processing facility is reported with metagenomic analysis and health assessment. Average bacterial bioaerosol concentration was noted to be 2979 ± 544 CFU/m[3], whereas the fungal bioaerosol concentration was 2288 ± 1128 CFU/m[3] at the waste processing site. Size distribution shows that the concentration of bacterial bioaerosol was mostly in the finer range (0.65-1.1 μm) while the fungal concentration was highest in the coarse size (between 3.3 and 7.0 μm). The metagenomic analysis of the bacterial bioaerosol sample revealed dominance of Alcaligenaceae (22 %), Stenotrophomonas (19 %), Bacillus (14 %) whereas, Fusarium (40 %), Epicoccum (23 %), Hypocreales (15 %), Coprinopsis (8 %), Cladosporium (4 %), Sarocladium (4 %), Tourlaspora (2 %), Alternaria (2 %) and Cryptococcus (2 %) were dominant fungal species. The top two dominant genera of bacterial strain expressed resistance towards azithromycin and cefixime. In the cross-sectional health survey near the waste processing site, participants including both workers on the site and people nearby, reported symptoms of respiratory, skin and eye irritation and bad smell. This study will help to improve the waste treatment process safety protocols and the health of the population around.},
}

@article {pmid40663882,
year = {2025},
author = {Khattak, F and Galgano, S and Pearson, R and Houdijk, JGM and Short, F and Leigh, A},
title = {Enhancing key broiler welfare indicators, meat quality, and gut microbiome composition using oxygen-enriched drinking water under commercially relevant housing conditions.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105550},
doi = {10.1016/j.psj.2025.105550},
pmid = {40663882},
issn = {1525-3171},
abstract = {Water is a critical nutrient in poultry production, yet its quality, particularly dissolved oxygen (DO) content, is often overlooked. This study is the first to comprehensively evaluate the impact of oxygen-enriched drinking water on broiler welfare, breast muscle myopathies, and gut microbiome composition under commercially relevant housing conditions. A total of 840 male Ross 308 broiler chicks were randomly assigned to two treatment groups (oxygenated water vs. tap water), with 12 replicate pens per treatment. Oxygenated water was enriched to a DO level of approximately 32 mg/L, compared to around 9.5 mg/L in tap water. Birds were reared to 36 days of age. The consistently high performance of both treatment groups under controlled experimental conditions is demonstrated by final body weights and feed conversion ratios surpassing Ross 308 breed standards by approximately 19-22 % from day 24 onward. Although growth performance remained unaffected under these optimal conditions, oxygenated water significantly improved welfare indicators, including feather condition, hock burn scores, and breast cleanliness (P< 0.05). Birds on oxygenated water also showed lower abdominal fat (-12 %) and higher thigh yield (+2.6 %) without compromising breast yield. Carcass fat deposition was significantly lower (abdominal fat pad reduced by ∼12 %), and thigh yield was higher in the oxygenated water treatment (P < 0.05), although overall carcass weight and breast yield were unchanged. No major differences were detected in breast meat nutrient composition (P > 0.05). The prevalence of white striping in breast fillets was markedly reduced in birds receiving oxygenated water, 32 mg/L indicating enhanced muscle integrity (P < 0.05). Metagenomic analysis revealed that some bacterial lipid metabolism pathways where differentially abundant in oxygenated-water birds. Following up on previous knowledge suggesting the interplay between lipid metabolism and broiler welfare, these findings suggest that supplementing broiler drinking water with 32 mg/L DO levels may offer a practical, non-pharmaceutical strategy to mitigate breast muscle myopathies and improve overall animal welfare and meat quality.},
}

@article {pmid40663851,
year = {2025},
author = {Wang, P and He, D and Xiao, Z and Zhao, J and Jin, Q and Ma, X and Ma, J and Zheng, M},
title = {Dual sludge system driven NDFO-Feammox coupling: Optimization of the iron cycling network for sustainable and efficient nitrogen removal.},
journal = {Water research},
volume = {286},
number = {},
pages = {124186},
doi = {10.1016/j.watres.2025.124186},
pmid = {40663851},
issn = {1879-2448},
abstract = {This research addresses the significant reliance on carbon sources and high energy consumption in traditional biological nitrogen removal methods. It introduces sponge iron (SI) as a source of iron to drive the coupled nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) processes using activated sludge and anaerobic ammonium oxidation (Anammox) sludges. The findings indicate that supplementing with SI significantly enhances the nitrogen removal capacity of the system. The system achieved up to 87.1 ± 3.2 % removal of NH4[+]-N and 91.8 ± 2.7 % removal of NO3[-]-N. A dual-constraint mathematical model confirms that the NDFO pathway provides at least 66.1 % of the Fe(III) required for Feammox metabolism. This lays the theoretical foundation for constructing a sustainable, autotrophic iron-nitrogen cycling system under anaerobic conditions. To elucidate the mechanisms underlying the coupled nitrogen removal, batch kinetic experiments and metagenomic analyses were conducted. These analyses identified the dominance of Candidatus Brocadia in Feammox metabolism. It was also noted that Anammox genes were enriched with the addition of SI. Combined with the experimental observation of in situ Anammox activity restoration, this suggests a high degree of metabolic overlap between the Anammox and Feammox pathways. Unexpected metabolic couplings were also revealed. In particular, divergent trends in the relative abundances of gene clusters encoding Nar and Nir triggered partial NDFO metabolism, driving Candidatus Brocadia to engage in co-metabolism of Feammox and Anammox. This process diversifies nitrogen escape pathways. Further investigations showed that sustained NDFO metabolism benefited from the synergistic effects of extracellular iron oxidation, Feammox-mediated iron reduction, and iron regulatory networks. Additionally, Feammox metabolism established an iron turnover mechanism through iron storage, subsequently providing positive feedback to Feammox metabolism for high energy gain.},
}

@article {pmid40662898,
year = {2025},
author = {Budatala, JM and Purkrtova, S and Lopez Marin, MA and Appels, L and Bartáček, J},
title = {Fate of antibiotic resistance genes and resistant bacteria under various operating temperatures of sludge anaerobic digestion.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {1},
pages = {53-65},
pmid = {40662898},
issn = {0273-1223},
support = {SS01020112//Technologická Agentura České Republiky/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; Temperature ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; },
abstract = {This study investigates the impact of varying temperatures on reducing antibiotic resistance genes (ARGs) during anaerobic digestion (AD) of mixed raw sludge in wastewater treatment plants. Employing three different operating temperatures, i.e., 37, 55, and 65 °C, the research aims to identify how these conditions affect the diminution of resistant genes. The results, based on quantitative PCR analysis and metagenomic sequencing, show that higher temperatures significantly enhance the reduction of ARGs, with the most substantial decreases observed at 65 °C. This temperature-dependent reduction correlates with changes in the microbial community structure, where specific bacterial genera like Alicycliphilus, Macellibacteroides, Dokdonella, Ahniella, Thauera, and Zoogloea associated with ARGs exhibit decreased abundance at elevated temperatures. The study infers that AD at higher temperatures could be a more effective strategy in mitigating the spread of antibiotic resistance in the environment, suggesting a pivotal role of operational temperature in optimizing wastewater treatment processes for ARGs attenuation. The findings highlight the need for further research to refine AD protocols, aiming to minimize the environmental impact of antibiotic resistance dissemination.},
}

*Sewage/microbiology
Anaerobiosis
Temperature
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Waste Disposal, Fluid/methods
Anti-Bacterial Agents/pharmacology
*Genes, Bacterial

@article {pmid40662820,
year = {2025},
author = {Qu, F and Peng, C and Guan, J and Wang, D and Sun, Y and Shang, J},
title = {GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i30-i39},
doi = {10.1093/bioinformatics/btaf239},
pmid = {40662820},
issn = {1367-4811},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; },
mesh = {*Metagenomics/methods ; Monte Carlo Method ; *DNA Viruses/genetics ; *Machine Learning ; *Software ; Genome, Viral ; Metagenome ; Algorithms ; },
abstract = {MOTIVATION: Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their widespread environmental presence and critical roles in processes such as host metabolic reprogramming and nutrient cycling. Metagenomic sequencing has emerged as a powerful tool for uncovering novel NCLDVs in environmental samples. However, identifying NCLDV sequences in metagenomic data remains challenging due to their high genomic diversity, limited reference genomes, and shared regions with other microbes. Existing alignment-based and machine learning methods struggle with achieving optimal trade-offs between sensitivity and precision.

RESULTS: In this work, we present GiantHunter, a reinforcement learning-based tool for identifying NCLDVs from metagenomic data. By employing a Monte Carlo tree search strategy, GiantHunter dynamically selects representative non-NCLDV sequences as the negative training data, enabling the model to establish a robust decision boundary. Benchmarking on rigorously designed experiments shows that GiantHunter achieves high precision while maintaining competitive sensitivity, improving the F1-score by 10% and reducing computational cost by 90% compared to the second-best method. To demonstrate its real-world utility, we applied GiantHunter to 60 metagenomic datasets collected from six cities along the Yangtze River, located both upstream and downstream of the Three Gorges Dam. The results reveal significant differences in NCLDV diversity correlated with proximity to the dam, likely influenced by reduced flow velocity caused by the dam. These findings highlight GiantHunter's potential to advance our understanding of NCLDVs and their ecological roles in diverse environments.

The source code of GiantHunter is available via: https://github.com/FuchuanQu/GiantHunter.},
}

*Metagenomics/methods
Monte Carlo Method
*DNA Viruses/genetics
*Machine Learning
*Software
Genome, Viral
Metagenome
Algorithms

@article {pmid40662816,
year = {2025},
author = {Belcour, A and Megy, L and Stephant, S and Michel, C and Rad, S and Bombach, P and Dopffel, N and de Jong, H and Ropers, D},
title = {Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i49-i57},
doi = {10.1093/bioinformatics/btaf230},
pmid = {40662816},
issn = {1367-4811},
support = {//European Partnership under Joint Call 2022/ ; GA N°101069750//European Commission/ ; //Norway, France, Czech Republic, and Saxon/ ; ANR-23-CETP-0002//ANR/ ; //International Society for Computational Biology/ ; },
mesh = {*Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; Software ; Proteome/metabolism ; *Computational Biology/methods ; },
abstract = {MOTIVATION: Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as hydrogen oxidation, sulfur reduction, and carbon fixation. These functions can be directly inferred from metagenomics data, but in many environmental applications metabarcoding is still the method of choice. The reconstruction of metabolic functions from metabarcoding data and their integration into coarse-grained representations of biogeochemical cycles remains a difficult bioinformatics problem today.

RESULTS: We developed a pipeline, called Tabigecy, which exploits taxonomic affiliations to predict metabolic functions constituting biogeochemical cycles. In a first step, Tabigecy uses the tool EsMeCaTa to predict consensus proteomes from input affiliations. To optimize this process, we generated a precomputed database containing information about 2404 taxa from UniProt. The consensus proteomes are searched using bigecyhmm, a newly developed Python package relying on Hidden Markov Models to identify key enzymes involved in metabolic function of biogeochemical cycles. The metabolic functions are then projected on coarse-grained representation of the cycles. We applied Tabigecy to two salt cavern datasets and validated its predictions with microbial activity and hydrochemistry measurements performed on the samples. The results highlight the utility of the approach to investigate the impact of microbial communities on biogeochemical processes.

The Tabigecy pipeline is available at https://github.com/ArnaudBelcour/tabigecy. The Python package bigecyhmm and the precomputed EsMeCaTa database are also separately available at https://github.com/ArnaudBelcour/bigecyhmm and https://doi.org/10.5281/zenodo.13354073, respectively.},
}

*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
Software
Proteome/metabolism
*Computational Biology/methods

@article {pmid40662809,
year = {2025},
author = {Singh, NP and Khan, J and Patro, R},
title = {Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i237-i245},
doi = {10.1093/bioinformatics/btaf234},
pmid = {40662809},
issn = {1367-4811},
support = {R01HG009937//National Institute of Health/ ; CCF-1750472//National Science Foundation/ ; CNS-1763680//National Science Foundation/ ; 252586//National Science Foundation/ ; 2024342821//National Science Foundation/ ; //Chan Zuckerberg Initiative DAF/ ; //Silicon Valley Community Foundation/ ; //Chan Zuckerberg Initiative Foundation/ ; },
mesh = {*Single-Cell Analysis/methods ; Algorithms ; *Software ; *Genomics/methods ; *Chromatin Immunoprecipitation Sequencing/methods ; *Chromosome Mapping/methods ; *Sequence Alignment/methods ; Humans ; },
abstract = {SUMMARY: Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors." These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is 2.8 times faster than Chromap (the second fastest approach) while using only 33% of the memory required by Chromap. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger.

Alevin-fry-atac is written in Rust and C++17, and is freely-available under a BSD 3-clause license. It is integrated into piscem (https://github.com/COMBINE-lab/piscem) and alevin-fry (https://github.com/COMBINE-lab/alevin-fry), and is also supported directly as part of simpleaf (https://github.com/COMBINE-lab/simpleaf).},
}

*Single-Cell Analysis/methods
Algorithms
*Software
*Genomics/methods
*Chromatin Immunoprecipitation Sequencing/methods
*Chromosome Mapping/methods
*Sequence Alignment/methods
Humans

@article {pmid40662747,
year = {2025},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212424},
doi = {10.1128/aem.02124-24},
pmid = {40662747},
issn = {1098-5336},
abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.},
}

@article {pmid40662533,
year = {2025},
author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E},
title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.70014},
pmid = {40662533},
issn = {1098-2361},
support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G250407)./ ; },
abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.},
}

@article {pmid40661966,
year = {2025},
author = {Yao, C and Xue, X and Jia, Y and Li, M and Zhang, L and Yuan, H and Xue, H and Hu, R},
title = {Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1593581},
pmid = {40661966},
issn = {2235-2988},
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/complications/metabolism ; *Rosuvastatin Calcium/pharmacology/administration & dosage ; Mice, Inbred C57BL ; Male ; Mice ; Fatty Acids, Volatile/metabolism/analysis ; Disease Models, Animal ; Feces/microbiology/chemistry ; Metabolomics ; Metagenomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {INTRODUCTION: Insulin resistance (IR) underlies metabolic diseases such as obesity and diabetes. Statins are lipid-lowering drugs that have also been studied to improve insulin resistance, but the mechanism is not well understood. Metagenomics and metabolomics were used to analyze the main species and metabolic pathways involved in intestinal microbes while improving insulin resistance in mice with rosuvastatin in this study.

METHODS: C57BL/6J male mice fed a high-fat diet were used to establish the insulin resistance (IR) mouse model. Rosuvastatin (RSV) was then administered for 8 weeks. Metagenomics and metabolomics were utilized to analyze the microbial composition and short chain fatty acid metabolites in intestinal feces of mice.

RESULTS: It was observed that insulin-resistant mice showed significant improvement in insulin resistance following treatment with RSV. In comparison to the HFD group, specific bacterial strains were significantly increased, and the levels of butyric acid, caproic acid, and isovaleric acid among the short-chain fatty acids were notably elevated in the RSV group. Through KEGG enrichment analysis, 19 dominant strains and 15 key enzymes involved in butyric acid metabolism were identified.

CONCLUSIONS: The results suggested that IR mice might enhance insulin sensitivity by promoting butyric acid synthesis via intestinal microbes following RSV treatment.},
}

Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
*Obesity/drug therapy/complications/metabolism
*Rosuvastatin Calcium/pharmacology/administration & dosage
Mice, Inbred C57BL
Male
Mice
Fatty Acids, Volatile/metabolism/analysis
Disease Models, Animal
Feces/microbiology/chemistry
Metabolomics
Metagenomics
Bacteria/classification/genetics/drug effects

@article {pmid40661950,
year = {2025},
author = {Ma, Y and Suo, J and Sheng, S and Chen, L},
title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1622744},
pmid = {40661950},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.

METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.

RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.

CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.},
}

Animals
*Gastrointestinal Microbiome/immunology
*B7-H1 Antigen/genetics/deficiency
Mice
Mice, Knockout
*Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism
*Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism
Dysbiosis
Disease Models, Animal
Severity of Illness Index
Mice, Inbred C57BL
Dextran Sulfate
Male

@article {pmid40661024,
year = {2025},
author = {Xia, ZW and Zhao, H and Liu, TT and Li, Y and Huo, JS and Guo, X},
title = {[Research progress of childhood obesity based on genomic and epigenomic biomarkers].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {7},
pages = {1125-1130},
doi = {10.3760/cma.j.cn112150-20240729-00606},
pmid = {40661024},
issn = {0253-9624},
support = {Leading talent-01-09//Beijing Municipal Health Commission High-level Public Health Technical Talent Construction Project/ ; },
mesh = {Humans ; *Pediatric Obesity/genetics ; Child ; *Epigenomics ; Genomics ; *Epigenesis, Genetic ; Biomarkers ; },
abstract = {Obesity represents a complex, heritable condition shaped by interactions among genetic, epigenetic, metagenomic, and environmental factors. Nevertheless, the mechanistic contributions of genetic variation and epigenetic regulation to obesity pathogenesis remain incompletely elucidated. Advances in molecular profiling technologies have enabled the identification of numerous biomarkers associated with childhood obesity phenotypes. These discoveries facilitate understanding of obesity etiology and its links to chronic diseases. This review synthesizes current research on genomic and epigenomic biomarkers influencing childhood obesity susceptibility, advances our comprehension of etiological heterogeneity and intervention strategies, and offers conceptual frameworks for precision prevention based on epigenetic mechanisms.},
}

Humans
*Pediatric Obesity/genetics
Child
*Epigenomics
Genomics
*Epigenesis, Genetic
Biomarkers

@article {pmid40661021,
year = {2025},
author = {Zhen, BJ and Zhang, P and Guo, XC and Zhang, J and Zhang, Y and Gao, X and Wang, F and Li, J and Zou, L},
title = {[Genomic characterization of a case of enterovirus D68 infection in a child from Tongzhou District, Beijing City].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {7},
pages = {1108-1112},
doi = {10.3760/cma.j.cn112150-20250326-00247},
pmid = {40661021},
issn = {0253-9624},
support = {2020-2-1012//Optimization of Primer Selection and Effect Verification for Enhanced Viral Detection Using Metagenomic Next-Generation Sequencing Technology/ ; },
mesh = {Humans ; *Genome, Viral ; Phylogeny ; *Enterovirus Infections/virology ; Infant ; Male ; *Enterovirus D, Human/genetics/isolation & purification ; China ; Beijing ; Genomics ; },
abstract = {A throat swab sample from a pediatric case in Tongzhou District, Beijing was identified as enterovirus; the patient was a 1-year-and-8-month-old male sporadic case. Whole-genome sequencing revealed a viral genome length of 7 436 bp. BLAST alignment confirmed the serotype as EV-D68. Phylogenetic analysis of the whole genome indicated that this strain belongs to the B3 clade, showing closer genetic proximity to the 2018 Shanghai strain MW697453 with 99.53% whole-genome nucleotide homology. Genetic and amino acid variation analysis demonstrated that the B3 subclade to which this strain belongs exhibits a nucleotide deletion at positions 718-726, differing from deletion sites observed in other B3 clade strains. A key neuropathogenic amino acid site, T650A, was found to have undergone mutation. Recombination analysis confirmed no cross-clade recombination events in this strain. This study conducted genetic characterization of the strain's evolutionary relationship with EV-D68 strains from different regions and years in China, providing data support for formulating prevention and control measures against EV-D68 infection.},
}

Humans
*Genome, Viral
Phylogeny
*Enterovirus Infections/virology
Infant
Male
*Enterovirus D, Human/genetics/isolation & purification
China
Beijing
Genomics

@article {pmid40660868,
year = {2025},
author = {Lin, F and Liu, Q and Zhao, Y and Chen, Y and Wang, R and Miao, C and Zhang, Q},
title = {He's Yangchao Formula Ameliorates Premature Ovarian Insuf-ficiency via Remodeling Gut Microbiota to Promote Granulosa Cell Glycolysis.},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {},
number = {},
pages = {1-10},
doi = {10.3724/zdxbyxb-2024-0604},
pmid = {40660868},
issn = {1008-9292},
abstract = {OBJECTIVES: To investigate the molecular mechanism by which He's Yangchao Formula improves ovarian function in premature ovarian insufficiency (POI) mice through intestinal flora modulation.

METHODS: Forty female ICR mice (aged 6-8 weeks) were intraperitoneally injected with cyclophosphamide (150 mg/kg) to establish a POI model, while 10 untreated mice served as the blank control. Successfully modeled mice were randomly divided into four groups (n=10/group): low-dose He's Yangchao Formula (6 g crude herb/kg), high-dose He's Yangchao Formula (25 g crude herb/kg), positive control (estradiol), and model control (distilled water). Treatments were admin-istered daily by gavage for 6 weeks. Vaginal exfoliated cells were stained with Wright-Giemsa solution to monitor estrous cycles. Serum estradiol and follicle-stimulating hormone (FSH) levels were measured by ELISA. Ovarian FSH receptor (FSHR) expression was assessed by immunohistochemistry. Glycolysis-related proteins pyruvate kinase M2 (PKM2) and glucose transporter 4 (GLUT4) were analyzed by Western blotting and immuno-fluorescence. Fecal samples from blank control, model control, and high-dose groups underwent metagenomic sequencing to evaluate intestinal microbiota diversity and com-position.

RESULTS: He's Yangchao Formula restored estrous cyclicity, increased serum estradiol (P<0.05), decreased serum FSH (P<0.05), and upregulated FSHR expression in granulosa cells (P<0.05). Metagenomic analysis revealed significant structural differences in intestinal flora among blank control, model control, and high-dose groups (P<0.01). The high-dose group showed reduced abundance of conditional pathogens (e.g., Alistipes, Prevotella, Odoribacter, Blautia, Rikenella) compared to the model control (P<0.05). Functional enrichment analysis indicated involvement of glycolysis-related pathways. Concordantly, PKM2 and GLUT4 expression was downregulated in the model control but upregulated in He's Yangchao Formula groups (P<0.05).

CONCLUSIONS: He's Yangchao Formula ameliorates POI in mice by remodeling intestinal flora structure, enhancing glycolytic activity, improving ovarian sex hormone secretion, increasing granulosa cell FSHR expression, and restoring estrous cyclicity.},
}

@article {pmid40660333,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.},
journal = {Particle and fibre toxicology},
volume = {22},
number = {1},
pages = {20},
pmid = {40660333},
issn = {1743-8977},
support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth & development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; },
abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
*Air Pollution/adverse effects
Mice
Male
*Neurodevelopmental Disorders/chemically induced/microbiology
Pregnancy
*Prenatal Exposure Delayed Effects/chemically induced
*Brain/drug effects/growth & development
*Air Pollutants/toxicity
Mice, Inbred C57BL
Behavior, Animal/drug effects
*Brain-Gut Axis/drug effects

@article {pmid40660160,
year = {2025},
author = {Chae, JB and Kim, WG and Song, S and Chae, JS},
title = {Molecular characterization of ten viral pathogens causing calf diarrhea in Hanwoo (Bos Taurus coreanae) by next generation sequencing.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {464},
pmid = {40660160},
issn = {1746-6148},
support = {122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; 122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; 122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; },
abstract = {BACKGROUND: Calf diarrhea remains a significant concern in the global cattle industry, leading to considerable economic losses. Infectious pathogens are among the primary causes of this disease. In this study, the prevalence of 7 pathogens—bovine rotavirus (BRV), bovine coronavirus (BCV), bovine viral diarrhea virus (BVDV) types 1 and 2, Cryptosporidium parvum, Giardia spp., and Eimeria spp.—associated with calf diarrhea was investigated using polymerase chain reaction (PCR). A metagenomic approach was also applied to identify additional RNA viral pathogens from unknown causes of diarrheic fecal samples in the Republic of Korea (ROK).

RESULTS: A total of 810 fecal samples from Hanwoo calves (Bos taurus coreanae) were collected, consisting of 526 normal samples (267 with a fecal score of 0 and 259 with a fecal score of 1) and 284 diarrheic samples (178 with a fecal score of 2 and 106 with a fecal score of 3). All 7 pathogens were detected by PCR in feces and their detection rates and mean fecal scores for each were as follows: BRV (14.0%, 1.41), BCV (3.2%, 1.42), BVDV1 (2.1%, 1.35), BVDV2 (4.9%, 1.33), C. parvum (9.8%, 1.66), Eimeria spp. (1.9%, 1.73), and Giardia spp. (0.9%, 0.71). Among these pathogens, BRV (p = 0.004), C. parvum (p < 0.001), and Eimeria spp. (p = 0.027) showed an increase in prevalence with higher fecal scores. Twenty-one fecal samples negative for all pathogens were randomly selected and subjected to high-throughput sequencing to identify RNA viral pathogens associated with calf diarrhea. This approach led to the identification of nearly complete genomic sequences for bovine astrovirus, bovine enterovirus, bovine kobuvirus, bovine nebovirus, bovine norovirus, bovine boosepivirus B, bovine parechovirus, bovine torovirus, C. parvum virus 1, and hunnivirus.

CONCLUSIONS: This study represents the first investigation of hunnivirus presence and provides a comprehensive description of the nearly complete genomes of 10 viruses associated with calf diarrhea in the ROK. The findings contribute to a better understanding of the epidemiology and molecular characteristics of calf diarrhea-associated pathogens in the ROK, highlighting the potential application of high-throughput sequencing for diagnosing other diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-025-04926-2.},
}

@article {pmid40659786,
year = {2025},
author = {Lin, NY and Fukuoka, S and Koyama, S and Motooka, D and Tourlousse, DM and Shigeno, Y and Matsumoto, Y and Yamano, H and Murotomi, K and Tamaki, H and Irie, T and Sugiyama, E and Kumagai, S and Itahashi, K and Tanegashima, T and Fujimaki, K and Ito, S and Shindo, M and Tsuji, T and Wake, H and Watanabe, K and Maeda, Y and Enokida, T and Tahara, M and Yamashita, R and Fujisawa, T and Nomura, M and Kawazoe, A and Goto, K and Doi, T and Shitara, K and Mano, H and Sekiguchi, Y and Nakamura, S and Benno, Y and Nishikawa, H},
title = {Microbiota-driven antitumour immunity mediated by dendritic cell migration.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40659786},
issn = {1476-4687},
abstract = {Gut microbiota influence the antitumour efficacy of immune checkpoint blockade[1-6], but the mechanisms of action have not been fully elucidated. Here, we show that a new strain of the bacterial genus Hominenteromicrobium (designated YB328) isolated from the faeces of patients who responded to programmed cell death 1 (PD-1) blockade augmented antitumour responses in mice. YB328 activated tumour-specific CD8[+] T cells through the stimulation of CD103[+]CD11b[-] conventional dendritic cells (cDCs), which, following exposure in the gut, migrated to the tumour microenvironment. Mice showed improved antitumour efficacy of PD-1 blockade when treated with faecal transplants from non-responder patients supplemented with YB238. This result suggests that YB328 could function in a dominant manner. YB328-activated CD103[+]CD11b[-] cDCs showed prolonged engagement with tumour-specific CD8[+] T cells and promoted PD-1 expression in these cells. Moreover, YB238-augmented antitumour efficacy of PD-1 blockade treatment was observed in multiple mouse models of cancer. Patients with elevated YB328 abundance had increased infiltration of CD103[+]CD11b[-] cDCs in tumours and had a favourable response to PD-1 blockade therapy in various cancer types. We propose that gut microbiota enhance antitumour immunity by accelerating the maturation and migration of CD103[+]CD11b[-] cDCs to increase the number of CD8[+] T cells that respond to diverse tumour antigens.},
}

@article {pmid40659687,
year = {2025},
author = {Zhang, N and Zhao, Y and Zhang, Z and Zhan, M and Zhao, X and Zhang, Y and Sun, J and Zhang, Y and Teng, L and Liu, Z},
title = {Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1219},
pmid = {40659687},
issn = {2052-4463},
support = {32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Transcriptome ; Metagenomics ; *Ranidae/genetics/microbiology ; *Metagenome ; Climate Change ; Microbiota ; China ; Adaptation, Physiological ; },
abstract = {Global climate change has become a primary driving factor behind the biodiversity crisis in amphibians, making it crucial to understand how climate change affects species and their potential responses. The plateau brown frog (Rana kukunoris) is often regarded as an ideal ecological indicator species, yet research on its environmental adaptation mechanisms based on transcriptomic and microbiomic studies remains limited. Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). We gathered transcriptomic data from three tissues (blood, liver, and muscle), resulting in 294,962 unigenes and 570,192 transcripts. Metagenomic sequencing identified major bacterial groups, including Firmicutes, Proteobacteria, Bacteroidetes, Spirochetes, and Actinobacteria. In summary, the results of this study can be used to further explore the associations among microbiota, host, and environment, which are crucial for comprehending the mechanisms of environmental adaptation in this species and contributing to the conservation of amphibian biodiversity.},
}

Animals
*Transcriptome
Metagenomics
*Ranidae/genetics/microbiology
*Metagenome
Climate Change
Microbiota
China
Adaptation, Physiological

@article {pmid40659683,
year = {2025},
author = {Li, P and Wu, Z and Liu, T and Deng, C and Liu, Q and Ni, J},
title = {The defensome of prokaryotes in aquifers.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6482},
pmid = {40659683},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Groundwater/microbiology ; *Bacteria/genetics/immunology/virology ; China ; *Prokaryotic Cells ; Metagenomics ; Bacteriophages ; CRISPR-Cas Systems/genetics ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {Groundwater harbors a pristine biosphere where microbes co-evolve with less human interference, yet the ancient and ongoing arms race between prokaryotes and viruses remains largely unknown in such ecosystems. Based on our recent nationwide groundwater monitoring campaign across China, we construct a metagenomic groundwater prokaryotic defensome catalogue (GPDC), encompassing 190,810 defense genes, 90,824 defense systems, 139 defense families, and 669 defense islands from 141 prokaryotic phyla. Over 94% of the defense genes in GPDC are novel and contribute vast microbial immune resources in groundwater. We find that candidate phyla radiation (CPR) bacteria possess higher defense system density and diversity against intense phage infection, while microbes as a whole exhibit an inverse relationship between defense systems and adaptive traits like resistance genes in groundwater. We further identify five first-line defense families covering 69.2% of the total defense systems, and high-turnover accessory immune genes are mostly conveyed to defense islands by mobile genetic elements. Our study also reveals viral resistance to microbial defense through co-localized anti-defense genes and interactions between CRISPR-Cas9 and anti-CRISPR protein. These findings expand our understanding of microbial immunity in pristine ecosystems and offer valuable immune resources for potential biotechnological applications.},
}

*Groundwater/microbiology
*Bacteria/genetics/immunology/virology
China
*Prokaryotic Cells
Metagenomics
Bacteriophages
CRISPR-Cas Systems/genetics
Ecosystem
Metagenome
Phylogeny

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40659339,
year = {2025},
author = {Singh, A and Juyal, G and Gacesa, R and Joshi, MC and Midha, V and Thelma, BK and Weersma, RK and Sood, A},
title = {Cross-ethnic evaluation of gut microbial signatures reveal increased colonization with oral pathobionts in the north Indian inflammatory bowel disease cohort.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2024.00216},
pmid = {40659339},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Inflammatory bowel disease (IBD) has become a global health concern. With the growing evidence of the gut microbiota's role in IBD, studying microbial compositions across ethnic cohorts is essential to identify unique, populationspecific microbial signatures.

METHODS: We analyzed stool samples and clinical data from 254 IBD patients (226 ulcerative colitis, 28 Crohn's disease) and 66 controls in northern India using metagenomic shotgun sequencing to assess microbiota diversity, composition, and function. Results were replicated in 436 IBD patients and 903 controls from the Netherlands using identical workflows. Using machine learning, we evaluated the generalizability of Indian IBD signals to the Dutch cohort, and vice versa.

RESULTS: Indian IBD patients exhibited reduced bacterial diversity and an abundance of opportunistic pathogens, including Clostridium, Streptococcus, and oral bacteria like Streptococcus oralis and Bifidobacterium dentium. There was a significant loss of energy metabolic pathways and distinct co-occurrence patterns among microbial species. Notably, 39% of these signals replicated in the Dutch cohort. Unique to the Indian cohort were oral pathobionts such as Scardovia, Oribacterium, Actinomyces dentalis, and Klebsiella pneumoniae. Both Indian and Dutch IBD patients shared reduced butyrate producers. Machine-learning diagnostic models trained on the Indian cohort achieved high predictive accuracy (sensitivity 0.84, specificity 0.95) and moderately generalized to the Dutch cohort (sensitivity 0.77, specificity 0.69).

CONCLUSIONS: IBD patients across populations exhibit shared and unique microbial signatures, suggesting a role for the oral-gut microbiome axis in IBD. Crossethnic diagnostic models show promise for broader applications in identifying IBD.},
}

@article {pmid40658318,
year = {2025},
author = {Yu, S and Li, J and Ye, Z and Zhang, M and Guo, X and Wang, X and Liu, L and Wang, Y and Zhou, X and Fu, W and Zhang, MQ and Chen, YG},
title = {Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {32},
pmid = {40658318},
issn = {2045-9769},
support = {2023YFA1800603//National Key Research and Development Program of China/ ; 31988101//Natural Science Foundation of China/ ; 92354306//Natural Science Foundation of China/ ; Z231100007223006//Beijing Science and Technology Plan/ ; B2302022//Shenzhen Medical Research Fund/ ; 20224ACB209001//Natural Science Foundation of Jiangxi Province/ ; O0390302//Guangdong Provincial Postdoctoral Science Foundation/ ; },
abstract = {Genetic and microbial factors influence inflammatory bowel disease (IBD), prompting our study on non-invasive biomarkers for enhanced diagnostic precision. Using the XGBoost algorithm and variable analysis and the published metadata, we developed the 10-species signature XGBoost classification model (XGB-IBD10). By using distinct species signatures and prior machine and deep learning models and employing standardization methods to ensure comparability between metagenomic and 16S sequencing data, we constructed classification models to assess the XGB-IBD10 precision and effectiveness. XGB-IBD10 achieved a notable accuracy of 0.8722 in testing samples. In addition, we generated metagenomic sequencing data from collected 181 stool samples to validate our findings, and the model reached an accuracy of 0.8066. The model's performance significantly improved when trained on high-quality data from the Chinese population. Furthermore, the microbiome-based model showed promise in predicting active IBD. Overall, this study identifies promising non-invasive biomarkers associated with IBD, which could greatly enhance diagnostic accuracy.},
}

@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}

@article {pmid40657968,
year = {2025},
author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC},
title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {40},
doi = {10.1167/iovs.66.9.40},
pmid = {40657968},
issn = {1552-5783},
mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation & purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; },
abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.

METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.

RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.

CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.},
}

Humans
*Microbiota/genetics
Middle Aged
Adult
*Tears/microbiology/metabolism
*Conjunctiva/microbiology
Female
Male
Tandem Mass Spectrometry
*Eyelids/microbiology
*Bacteria/genetics/isolation & purification
Chromatography, Liquid
Eye Proteins/metabolism

@article {pmid40657866,
year = {2025},
author = {Babiker, A and Van Riel, J and Lohsen, S and Page, A and Strudwick, A and Wilber, E and Woodworth, M and Satola, S},
title = {Evaluation of swabbing methods for culture and non-culture-based recovery of multidrug-resistant organisms from environmental surfaces.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/ice.2025.10214},
pmid = {40657866},
issn = {1559-6834},
abstract = {OBJECTIVES: Sponge-Sticks (SS) and ESwabs are frequently utilized for detection of multidrug-resistant organisms (MDROs) in the environment. Head-to-head comparisons of SS and ESwabs across recovery endpoints are limited.

DESIGN: We compared MDRO culture and non-culture-based recovery from (1) ESwabs, (2) cellulose-containing SS (CS), and (3) polyurethane-containing SS (PCS).

METHODS: Known quantities of each MDRO were pipetted on a stainless-steel surface and swabbed by each method. Samples were processed, cultured, and underwent colony counting. DNA was extracted from sample eluates, quantified, and underwent metagenomic next-generation sequencing (mNGS). MDROs underwent whole genome sequencing (WGS). MDRO recovery from paired patient perirectal and PCS-collected environmental samples from clinical studies was determined.

SETTING: Laboratory experiment, tertiary medical center, and long-term acute care facility.

RESULTS: Culture-based recovery varied across MDRO taxa, it was highest for vancomycin-resistant Enterococcus and lowest for carbapenem-resistant Pseudomonas aeruginosa (CRPA). Culture-based recovery was significantly higher for SS compared to ESwabs except for CRPA, where all methods performed poorly. Nucleic acid recovery varied across methods and MDRO taxa. Integrated WGS and mNGS analysis resulted in successful detection of antimicrobial resistance genes, construction of high-quality metagenome-assembled genomes, and detection of MDRO genomes in environmental metagenomes across methods. In paired patient and environmental samples, multidrug-resistant Pseudomonas aeruginosa (MDRP) environmental recovery was notably poor (0/123), despite detection of MDRP in patient samples (20/123).

CONCLUSIONS: Our findings support the use of SS for the recovery of MDROs. Pitfalls of each method should be noted. Method selection should be driven by MDRO target and desired endpoint.},
}

@article {pmid40657495,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644681},
doi = {10.3389/fmicb.2025.1644681},
pmid = {40657495},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].},
}

@article {pmid40657403,
year = {2025},
author = {Akram, F and Safdar, M and Shabbir, I and Fatima, T and Ikram-Ul-Haq, },
title = {Insight into the eminent biotechnological applications of xylanolytic enzymes for sustainable bioprocessing.},
journal = {3 Biotech},
volume = {15},
number = {8},
pages = {249},
pmid = {40657403},
issn = {2190-572X},
abstract = {Xylan is one of the most abundant polysaccharides in nature and presents a structural complexity characterized by a heterogeneous polymer composition. Comprising various sugar subunits and associated acids linked through a diverse array of bonds, xylan poses challenges for complete degradation. This review article provides a comprehensive overview of xylan's structure, the role of xylanolytic enzymes in its degradation, and the industrial applications of xylanases in sectors, such as paper and pulp, food, textiles, and pharmaceuticals. Furthermore, it also discusses the use of advanced biotechnology tools, such as nano-biotechnology and genetic engineering, particularly through CRISPR/CAS technology, for enhancing the thermostability of xylanases. This article also provides insights into emerging trends in xylanase research, including bioprospecting novel thermostable xylanases from metagenomes, protein engineering, synthetic biology, and the integration of biorefinery. Finally, it highlights the importance of regulatory frameworks and standardization initiatives for ensuring the quality and the sustainability of xylanase-based technologies. Overall, this review offers valuable insights into the multifaceted role of xylanases in biotechnology and industrial bioprocessing while outlining future directions for research and innovation in this field.},
}

@article {pmid40657278,
year = {2025},
author = {Chen, Q and Gao, B and Guo, W and Liu, H and Guo, J},
title = {Clinical Features of Patients with Tropheryma Whipplei Detected in Lower Respiratory Tract Samples in China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3439-3448},
pmid = {40657278},
issn = {1178-6973},
abstract = {INTRODUCTION: Tropheryma whipplei (TW) can cause various infections that are relatively rare worldwide. With the development of molecular biology, the ability to detect TW has increased in recent years. However, its significance in lower respiratory tract samples remains unclear.

PATIENTS AND METHODS: We collected the clinical data of 5 patients admitted to a tertiary care hospital in Beijing with TW detected by bronchoalveolar lavage fluid (BALF) mNGS and reviewed all case reports of TW-related pneumonia in China (up to November 2024) to analyse the features of this disease among Chinese patients.

RESULTS: A total of 41 articles reporting 55 cases were identified. Fifty-two (94.5%) patients had respiratory symptoms. Fifteen (27.3%) patients developed severe pneumonia. Confirmation of TW infection was achieved through methods including the assessment of TW reads and relative abundance (63.6%), empirical treatment (18.2%), lung biopsy histopathology (14.5%), and qPCR confirmation (3.6%). Fifty (90.9%) patients received antibiotic therapy. Fifty-one (92.7%) patients had a good prognosis.

CONCLUSION: TW can enter the lower respiratory tract through multiple routes. When TW sequences are detected in lower respiratory tract samples, it is important to consider not only the read and relative abundance but also histopathological findings such as interstitial pneumonia and the presence of PAS- or PASM-positive bacilli within foamy macrophages as they can aid in diagnosing TW infection. MDT discussions and empirical antibiotic therapy targeting TW are viable options when a patient's condition deteriorates. Microbiological testing of saliva, gastric fluid, blood, and faeces may help clarify the source of TW.},
}

@article {pmid40657275,
year = {2025},
author = {Fu, Y and Zhou, J and He, P and Li, X},
title = {A Rare Case Report of Tropheryma Whipplei-Induced Acute Respiratory Distress Syndrome in an Immunocompetent Patient.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3409-3414},
pmid = {40657275},
issn = {1178-6973},
abstract = {Tropheryma whipplei is a rare gram-positive bacterium traditionally associated with Whipple's disease, primarily presenting with gastrointestinal symptoms. Pulmonary involvement, particularly acute respiratory distress syndrome (ARDS), is extremely rare and poses diagnostic challenges, especially in immunocompetent individuals. We report a rare case of ARDS caused by Tropheryma whipplei in a 28-year-old immunocompetent male with no significant medical history. Traditional diagnostic methods failed to identify the causative pathogen. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid enabled rapid and accurate detection of T. whipplei, allowing timely initiation of targeted antimicrobial therapy with ceftriaxone and trimethoprim-sulfamethoxazole. The patient demonstrated marked clinical improvement and was discharged with no relapse at follow-up. This case highlights the critical diagnostic value of mNGS in atypical ARDS cases and emphasizes the importance of considering T. whipplei in the differential diagnosis, even among immunocompetent individuals.},
}

@article {pmid40656756,
year = {2025},
author = {Huang, Y},
title = {Investigation of protists in Momoge wetland (China) through metagenomic next-generation sequencing.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e153721},
pmid = {40656756},
issn = {1314-2828},
abstract = {The Momoge wetland plays an important role in maintaining the ecosphere and protist is an indispensable component of it. In order to reveal community structure and diversity of protists in Momoge wetland, metagenomic next-generation sequencing (mNGS) was performed. The main results are as follows: 1) A total of 224 species were identified, belonging to 17 phyla, 32 classes, 75 orders, 94 families and 146 genera. Among them, Bacillariophyta, Evosea, Oomycota, Rhodophyta, Ciliophora, Haptophyta, and Salpingoecarosetta, Guillardiatheta, Polarellaglacialis, Cladocopiumgoreaui were the dominant phyla and species, respectively; 2) Most of them were species adapted to the saline-alkali environment, and the protists of Momoge wetland had higher diversity, fewer dominant species, and higher evenness than those of the harsher environment; 3) KEGG analysis showed that some protistan pathways were related to the saline-alkali environmental adaptation. This research is beneficial to ecological protection and provides valuable information for future studies.},
}

@article {pmid40656634,
year = {2025},
author = {Hieta, J and Benchraka, C and Pärnänen, K and Houttu, N and Mokkala, K and Lotankar, M and Kataja, EL and Lahti, L and Laitinen, K},
title = {Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity.},
journal = {Brain, behavior, & immunity - health},
volume = {47},
number = {},
pages = {101042},
pmid = {40656634},
issn = {2666-3546},
abstract = {The associations of gut microbiota with depressive and anxiety symptoms have been investigated mainly in non-pregnant humans, and currently there is a significant gap in research on pregnant women, especially those who are living with overweight and thus at a higher risk for experiencing perinatal mental health problems. In this study, we used shotgun metagenomic sequencing to analyze the gut microbiota of pregnant women with overweight and obesity, both in early and late pregnancy. We compared gut microbial diversity, composition, and function across groups with different trajectories of depressive (n=419) and anxiety (n=408) symptoms. Depressive symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS), and anxiety symptoms were evaluated with the Symptom Checklist 90 (SCL-90, anxiety subscale) at five time points spanning from early pregnancy to one year postpartum. Latent growth mixture modeling (LGMM) was used to model symptom trajectories from early pregnancy until one year postpartum and further symptom sum scores at five time points cross-sectionally. We observed differences in several bacterial species abundances between the trajectory groups and in cross-sectional analyses, including higher abundance of Hungatella hathewayi in the Moderate and increasing depressive symptoms group (FDR<0.25), and Bacteroides clarus in the High and decreasing depressive symptoms group (FDR<0.25) and in women experiencing clinically significant postpartum anxiety symptoms (FDR<0.05). No differences were found regarding the gut microbiota diversity (α or β) or function. The results suggest that maternal gut microbiota, particularly the increased abundance of possible pro-inflammatory species, could be one of the factors affecting perinatal distress.},
}

@article {pmid40655931,
year = {2025},
author = {Redondo, MA and Jones, CM and Legendre, P and Guénard, G and Hallin, S},
title = {Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf087},
pmid = {40655931},
issn = {2730-6151},
abstract = {Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.},
}

@article {pmid40655380,
year = {2025},
author = {Siraj, K and Kaliyaperumal, KA and Gururajan, G and Saravanan, TG},
title = {Metagenomics Analysis of Microbiota in Raw Chicken Stored at Different Temperature over Storage Time in Chennai.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {955-960},
pmid = {40655380},
issn = {0046-8991},
abstract = {Poultry meat consumption nowadays demands the need for efficient storage practices for safe and healthy meat. Studying the putative microorganisms for meat spoilage therefore necessitates the effectiveness of storage Microbial types. In this study, poultry meat from Chennai was analyzed for spoilage considering the Microbial types of temperature (- 18 °C and 0-5 °C) and storage time (2, 4, 6 months). Conventional pour plate method was assisted with next generation sequencing to analyze the microbiota and potent spoilage bacteria. Irrespective of the storage temperature, all the samples showed bacteria of phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidota predominantly. Hafnia-Obesumbacterium and Wohlfahrtiimonas (nearly 10%), Enterococcus (~ 5%), Moellerella and Bacillus (~ 1%) genera were observed in sample stored at the slightly higher temperature. This preliminary study points out that storage temperature is important to maintain shelf life of chicken sample and sample stored at even slightly raised temperature will be spoiled within 10 days. In addition, the need for equipping metagenomics analysis along with conventional method would be required to observe the spoilage at intricate levels.},
}

@article {pmid40655373,
year = {2025},
author = {Sabarish, S and Dhanasekaran, D},
title = {Bacterial Community Profile of Bovine Mastitis Infected Dairy Cow Milk by 16S rRNA Amplicon Sequencing.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1142-1151},
pmid = {40655373},
issn = {0046-8991},
abstract = {UNLABELLED: The prevalence of Bovine mastitis, an important disease of cow, causing huge economic loss in dairy industries, was tested in cows and other types of breeds reared at Salem and Trichirappalli district. It was interesting to note that the country breed cow was free from disease. The presence of mastitis microbes was identified by culture dependent method. Staphylococcus aureus, Staphylococcus agalactiae, Klebsiella sp. and Pseudomonas sp. were the most common bacteria found in mastitis-infected milk. Opportunistic anaerobic bacteria such as Fusobacterium necrophorum and Porphyromonas levii were found in abundance in mastitis milk samples, but not in non-mastitis milk samples. Milk samples from a mastitis-infected Jersey cow and healthy cow as a control cow were utilized to construct V3-V4 sections of 16S rRNA gene profiles, which were compared to bacterial diversity and abundance. A total of 16,000 sequence numbers were acquired from the 16S rRNA dataset, with a cumulative length of base pairs (bp) of 250. About 321 OTUs were created from these readings. Among these, 190 OTUs are similar in milk from both uninfected healthy and infected Jersey cow. A total of 70 OTUs and 61 OTUs were unique to milk obtained from healthy milk and mastitis infected milk respectively. The hierarchically clustered heat map depicted the overall perspective of the found relationships of bacterial populations among milk samples. The relative abundance of the Ochrobactrum, Pseudomonas and Stenotrophomonas (Kamilari) were associated in the milk. The Shannon index of a healthy cow milk sample was greater (4.136), suggesting the quantity and evenness of the microbial species present. The Simpson index also revealed that during a cow infection, the species richness and evenness declined. Metagenomic analysis can help us better understanding the pathophysiology of bovine mastitis, and it has the potential to be employed as a diagnostic tool as well.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01310-w.},
}

@article {pmid40655366,
year = {2025},
author = {Yadav, S and Kapley, A},
title = {Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1181-1200},
pmid = {40655366},
issn = {0046-8991},
abstract = {UNLABELLED: Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes & bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) & 27 (Mysore) ARG category and 431 & 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin & tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01349-9.},
}

@article {pmid40655305,
year = {2025},
author = {Yuan, X and Wang, Q and Ding, H and Li, H and Fang, X and Zhang, W and Huang, Z},
title = {The Role of Applying Metagenomic Next-Generation Sequencing (mNGS) in Periprosthetic Joint Infection with Sinus Tract: A Retrospective Study.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {3787-3795},
pmid = {40655305},
issn = {1178-7074},
abstract = {BACKGROUND: Diagnosing periprosthetic joint infection (PJI), especially with sinus tracts, is challenging using traditional cultures. Metagenomic next-generation sequencing (mNGS) offers a culture-independent diagnostic approach. We evaluated mNGS's role in diagnosing and guiding treatment for PJI with sinus tracts.

METHODS: This retrospective analysis included 52 PJI patients (2019-2024). An mNGS group (n=43; 18 sinus PJI, 25 non-sinus PJI) was compared to a non-mNGS control group (n=9; all sinus PJI, culture-diagnosed). We compared pathogen detection rates. For sinus PJI patients (two-stage revision), 2-year cure rates and antibiotic duration were compared between mNGS-guided and non-mNGS-guided therapy.

RESULTS: In sinus PJI cases (n=18), mNGS achieved significantly higher pathogen detection (88.9%, 16/18) versus culture (50.0%, 9/18) (Relative Risk [RR] 1.78; P=0.027). mNGS also detected more polymicrobial infections (38.9%, 7/18) compared to culture (5.6%, 1/18) (RR 7.00; P=0.041). For sinus PJI treatment, mNGS-guided therapy yielded a significantly higher 2-year cure rate (94.4%, 17/18) than non-mNGS therapy (55.6%, 5/9) (Absolute Risk Increase 38.9%; RR 1.70; P=0.03). Mean antibiotic duration was significantly shorter with mNGS guidance (35.62 ± 5.42 vs 47.11 ± 6.53 days; difference 11.49 days; P<0.01), with a trend towards fewer antibiotic-related complications (11.1% vs 55.6%; P=0.23).

CONCLUSION: mNGS significantly improves pathogen detection, especially polymicrobial infections, in sinus tract PJI. mNGS-guided therapy for sinus PJI is associated with substantially improved cure rates and shorter antibiotic duration, highlighting its utility in guiding targeted anti-infection strategies for these complex cases.},
}

@article {pmid40655196,
year = {2025},
author = {Fuentes-Santander, F and Curiqueo, C and Araos, R and Ugalde, JA},
title = {BugBuster: a novel automatic and reproducible workflow for metagenomic data analysis.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf152},
pmid = {40655196},
issn = {2635-0041},
abstract = {SUMMARY: Metagenomic sequencing generates massive datasets that capture the complete genetic content of a sample, enabling detailed characterization of microbial communities. Yet the software and processes necessary to transform raw data into biologically meaningful results have become increasingly complex, limiting accessibility for researchers without specialist expertise. In this work, we present a novel modular a reproducible workflow developed to facilitate the analysis of metagenomic data. BugBuster is a fully containerized, modular, and reproducible workflow implemented in Nextflow. The pipeline streamlines analysis at level of reads, contigs, and metagenome-assembled genomes, offering dedicated modules for taxonomic profiling and resistome characterization. Thanks to the use of containers, BugBuster can be deployed with minimal configuration on workstations, high-performance clusters, or cloud platforms. Together, these features allow the robust, scalable, and reproducible analysis of metagenomic datasets.

BugBuster was written in Nextflow-DSL2. The program applications, user manual, example data and code are freely available at https://github.com/gene2dis/BugBuster.},
}

@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}

@article {pmid40654764,
year = {2025},
author = {Myers, JM and Schulz, F and Rahimlou, S and Yadav, V and Amses, KR and Simmons, DR and Sun, S and Orozco-Quime, M and Heitman, J and Stajich, JE and James, TY},
title = {Discovery of giant viruses as past and present infections of zoosporic fungi.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.04.574182},
pmid = {40654764},
issn = {2692-8205},
abstract = {Giant viruses of the phylum Nucleocytoviricota have emerged as particularly notable due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes, and they have been detected in hosts that span the eukaryotic tree of life. But surprisingly, such viruses have not been definitively found in Kingdom Fungi, though genomic and metagenomic work suggests a putative association. Here we report both "viral fossils" and active infection by giant viruses in fungi, particularly in the zoosporic phyla Blastocladiomycota and Chytridiomycota. The recovered viral genomes span up to 350 kb, encode over 300 genes, and form a monophyletic family-level clade within the Nucleocytoviricota related to orders Imitervirales and Algavirales , which we name Mycodnaviridae . We observed variation in infection status among the isolates including apparent active infection and transcriptionally-suppressed states, suggesting that viral activation may be constrained to certain life stages of the host. Our experimental findings add to the limited natural virus-host systems available in culture for the study of giant viruses. These viruses may have shaped the early evolution of these fungal lineages by the shuttling of genes between major kingdoms and domains of life. Our findings expand the known host range of Nucleocytoviricota into a new kingdom that contains many model species. Mycodnaviridae have a global distribution, which invites inquiry into the implications of these infections for host traits, host genome evolution, and the metabolic impacts to ecosystems.},
}

@article {pmid40654740,
year = {2025},
author = {Azhieh, A and Hernandez, P and Anderson, AC and Sychantha, D and Verster, AJ and Whitney, JC and Ross, BD},
title = {Rapidly evolving orphan immunity genes protect human gut bacteria from intoxication by the type VI secretion system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.03.651265},
pmid = {40654740},
issn = {2692-8205},
abstract = {Bacteria encode diverse mechanisms for mediating interbacterial antagonism through the exchange of toxic effector proteins. Although the structure, function, and regulation of these pathways has been well established for many organisms, an understanding of their ecological and evolutionary dynamics lags behind. Type VI secretion systems (T6SS) deliver effectors between competing Gram-negative bacteria, including among mammalian gut Bacteroidales, resulting in the evolution of elaborate defense mechanisms that protect against T6SS attack. One such mechanism is the r ecombinase-associated a cquired interbacterial d efence (rAID) system, which harbors arrays of orphan immunity genes that diverge in sequence from T6SS-associated cognate immunity genes. It is not known if such sequence divergence impacts rAID orphan immunity function, or how rAID distribution across microbiomes relates to the T6SS. Here, we show that divergent rAID orphan immunity factors that possess SUKH domains allow bacteria to survive intoxication by cognate effectors. Such protection is due to high affinity protein-protein interactions between orphan immunity and effector that are comparable to that of cognate effector-immunity. Unlike other examples of T6SS effector-immunity interactions, we find that the binding interface is comprised of electrostatic interactions with a high degree of redundancy underlying its protective capacity. Finally, we quantify orphan immunity and effector gene abundance and dynamics across human gut metagenomes, revealing patterns of co-occurrence indicative of positive selection. Population genetic analyses of longitudinal data suggests that orphan immunity genes accumulate non-synonymous mutations that lie at the predicted effector-immunity interface. Together, our findings establish rAID orphan immunity genes as important bacterial fitness determinants in the human gut.},
}

@article {pmid40654714,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling Bile Acids in the Stools of Humans and Animal Models of Cystic Fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.651222},
pmid = {40654714},
issn = {2692-8205},
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with dysbiosis of the gut microbiome, alterations in intestinal mucus production, aberrant bile acid (BA) metabolism, fat malabsorption, and chronic inflammation. As little is known about BAs in CF, we performed both comprehensive and targeted BA profiling in stool of children with or without CF. Our results reveal that select BA species and metabolites are significantly different between children with CF (cwCF) and healthy controls. There is also a trend towards higher primary cBA and total BA levels for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in our small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroides (lower) and E. coli (increased) species is consistent with prior reports. A robust trend was noted toward reduced abundance of bsh gene families (Wilcox test, p = 0.052), a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Modest changes in both BAs and microbial BA metabolism-related gene abundances may be attributable to small sample sizes, but also suggest likely combination defects in both host and microbial BA metabolic pathways in cwCF. Importantly, although fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, only the ferret model reproduced significant differences between CF and nonCF animals, highlighting ferrets as a potentially more appropriate model for studying BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF, and highlight limitations of CF animal models for BA functional studies.

IMPORTANCE: Changes in the abundance and/or composition of intestinal bile acids (BAs) may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for children with CF (cwCF). Matched metagenomic analysis suggest possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}

@article {pmid40654689,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651704},
pmid = {40654689},
issn = {2692-8205},
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}

@article {pmid40654580,
year = {2025},
author = {Chen, J and Du, Y and Sun, L and Dai, Y and Zhang, L and Ding, X and Liu, T and Yang, K and Han, X and Li, M and Zhou, X},
title = {The boundaries between PML and PML-IRIS: difficult to define, pathology may predict.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1607428},
pmid = {40654580},
issn = {2235-2988},
mesh = {Humans ; *Leukoencephalopathy, Progressive Multifocal/pathology/diagnosis/virology ; Male ; Adult ; Female ; *Immune Reconstitution Inflammatory Syndrome/pathology/diagnosis ; Middle Aged ; JC Virus/genetics/isolation & purification ; Viral Load ; CD4 Lymphocyte Count ; Immunohistochemistry ; Brain/pathology ; },
abstract = {BACKGROUND: Progressive multifocal leukoencephalopathy (PML), caused by John Cunningham (JC) virus reactivation, represents a critical neurological complication in AIDS-related immunosuppression. This single-center study conducted a clinicopathological analysis of 19 confirmed PML cases in an AIDS cohort (16 biopsy; 3 surgical specimens), employing comprehensive neuropathological evaluation. Immunohistochemical testing included SV40, NF, NeuN, P53, Ki-67, GFAP, Oligo-2, and CD68. Myelin architecture was evaluated through Luxol fast blue staining, complemented by molecular diagnostics incorporating quantitative JC viral load PCR and metagenomic next-generation sequencing (mNGS).

RESULTS: Notably, 63.2% (12/19) of them had blood CD4+ T-cell counts < 200 cells/μl, and 36.8% (7/19) had ≥ 200 cells/μl. 52.9% (9/17) of the patients had elevated CSF protein, 5.3% (1/19) had decreased CSF glucose. Statistical analysis revealed significant correlations between mass effect and both blood CD4+ T-cell counts (P = 0.022) and CSF protein levels (P < 0.001). It also demonstrated significant positive correlations between the duration of HIV diagnosis and the degree of inflammatory infiltration (P = 0.038) and perivascular inflammatory infiltration (P = 0.005), as well as plasma cell infiltration (P = 0.011). The degree of inflammatory infiltration was significantly positively correlated with antiretroviral therapy (ART) (P = 0.036). The degree of inflammatory infiltration, the presence of plasma cells, and perivascular lymphocytic cuffing were significantly associated with contrast enhancement on imaging studies (P = 0.044, P = 0.011, and P = 0.018, respectively). These cases display characteristics that deviate from the classic PML previously reported, exhibiting a tendency towards MRI enhancement and histologically indicating a more severe inflammatory response, especially for patients following ART treatment.

CONCLUSION: Our findings suggest that PML and PML-immune reconstitution inflammatory syndrome (IRIS) represent a continuous pathological spectrum, potentially bridged by an intermediate stage with distinct clinicopathological features. This transitional phase may constitute a critical link in the continuum between classic PML and fully developed PML-IRIS. Importantly, it implicates synergistic mechanisms of viral oncogenesis and immune reconstitution, which could redefine therapeutic strategies for this emerging PML variant.},
}

Humans
*Leukoencephalopathy, Progressive Multifocal/pathology/diagnosis/virology
Male
Adult
Female
*Immune Reconstitution Inflammatory Syndrome/pathology/diagnosis
Middle Aged
JC Virus/genetics/isolation & purification
Viral Load
CD4 Lymphocyte Count
Immunohistochemistry
Brain/pathology

@article {pmid40654574,
year = {2025},
author = {Yang, S and Sun, Y and Wang, M and Xu, H and Wang, S},
title = {Risk factors for identifying pulmonary aspergillosis in pediatric patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616773},
pmid = {40654574},
issn = {2235-2988},
mesh = {Humans ; Risk Factors ; Retrospective Studies ; Male ; Female ; Child ; Child, Preschool ; Infant ; ROC Curve ; *Pulmonary Aspergillosis/diagnosis/epidemiology/microbiology ; Adolescent ; Logistic Models ; China/epidemiology ; },
abstract = {OBJECTIVES: This study aimed to identify the independent risk factors and develop a predictive model for pulmonary aspergillosis (PA) in pediatric populations.

METHODS: This retrospective study compromised 97 pediatric patients with pulmonary infections (38 PA cases and 59 non-PA cases) at Children's Hospital Affiliated to Shandong University between January 2020 and October 2024. Multivariate binary logistic regression was used to identify PA-associated risk factors. Receiver operating characteristic (ROC) curves, calibration plots, and Brier scoring were used to evaluate the diagnostic model.

RESULTS: 8 clinical variables significantly differed between the PA and non-PA groups. Multivariate binary logistic regression analysis identified six significant independent risk factors: a history of surgery (OR: 9.52; 95% CI: 1.96-46.23; P = 0.005), hematologic diseases (OR: 11.68; 95% CI: 0.89-153.62; P = 0.062), absence of fever (OR: 8.244; 95% CI: 1.84-36.932; P = 0.006), viral coinfection (OR: 15.99; 95% CI: 3.55-72.00; P < 0.001), elevated (1, 3) -β -D-glucan levels (BDG, > 61.28 pg/mL; OR: 7.38; 95% CI: 1.26-43.31; P = 0.027), and shorter symptom-to-admission interval (< 4.5 days; OR: 38.68; 95% CI: 5.38-277.94; P < 0.001) were risk factors for PA. The predictive model demonstrated excellent discrimination (AUC 0.93, 95% CI 0.88-0.98) and calibration (Hosmer-Lemeshow p=0.606, R²=0.96, Brier score 0.097). metagenomic next - generation sequencing (mNGS) revealed significantly higher rates of polymicrobial infections in PA cases (86.84% vs 18.64%, p<0.001).

CONCLUSIONS: This study established and validated a high-performance predictive model incorporating six clinically accessible parameters for the diagnosis of pediatric PA.},
}

Humans
Risk Factors
Retrospective Studies
Male
Female
Child
Child, Preschool
Infant
ROC Curve
*Pulmonary Aspergillosis/diagnosis/epidemiology/microbiology
Adolescent
Logistic Models
China/epidemiology

@article {pmid40654462,
year = {2025},
author = {Yu, JJ and Hernandez-Kapila, Y and Wang, CW},
title = {Probiotics to reduce microbiota-related dental stains: A potential approach.},
journal = {Journal of dental sciences},
volume = {20},
number = {3},
pages = {1890-1893},
pmid = {40654462},
issn = {2213-8862},
abstract = {Adult extrinsic black stains on teeth, caused by bacterial colonization, impact aesthetics and confidence. Conventional treatments can be abrasive and have a high recurrence rate. This pilot case study explores probiotics as an adjunctive approach. Direct application of probiotic powder over the black stains of the teeth was carried out prior to routine home care. Results showed black stain removal was possible with tooth brush and dental floss. Saliva and biofilm samples were analyzed via 16S rRNA sequencing. Microbiome revealed a noticeable reduction in Corynebacterium, a key black stain-associated bacterium, with slight shifts in major phyla like Actinobacteriota and Firmicutes. This case study aimed to evaluate the potential of probiotics in reducing black stains on teeth and assess the associated microbiome changes.},
}

@article {pmid40653865,
year = {2025},
author = {Wang, W and Dong, Y and Wang, HB and Xue, DH and Zhang, HF and Li, ZJ and Wang, H and Bo, HJ and Zhang, WJ and Zhang, BH and Xiong, YC and Zhang, Q and Jin, DS},
title = {Long-Term Legume Cultivation Affects the Soil Bacterial Community via Altering the Soil Pore Structure in Coal Mine Reclamation Agroecosystems.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70063},
pmid = {40653865},
issn = {1365-3040},
support = {//This research was supported by the Research Start-up Project of Shanxi Agricultural University for Recruited Talents (2023BQ120), Promotive Scientific Research Fund for New PhD Graduates working in Shanxi Province (SXBYKY2023038), Youth Science and Technology Research Program of Shanxi Province Basic Research Program (202303021222077; 202303021212104), Merit-based Open Competition Project of Shanxi Major Science and Technology Special Program (202201140601028-4). Open Project Funding Project of the Engineering Technology Innovation Center for Ecological Protection and Restoration of the Middle Reaches of the Yellow River, Ministry of Natural Resources (2025080)./ ; },
abstract = {Legume cultivation has great potential for improving soil microbial communities and soil quality in reclaimed ecosystems. However, little is known about the effects of long-term legume cultivation on the soil microbial community structure in agroecosystems in coal mine reclamation areas. To address this issue, we used metagenomics to examine the variations in the soil bacterial community composition and functionality under three leguminous crops in a 10-year reclamation experiment. After 10 years, we found dissimilarity in the microbial communities between the control and leguminous crops. Furthermore, three legume cultivation greatly promoted the diversity and abundance of the dominant bacteria The keystone phyla of the soil bacterial communities in the reclamation area included Proteobacteria, Acidobacteriota, Gemmatimonadota and Myxococcota. In particular, soil pore structure was the main factor influencing the variation in the bacterial community. Therefore, long-term legume cultivation can significantly improve the soil microbial community structure, which likely serves as the basis for soil microbial abundance and functionality and soil health. This study confirmed the ability of the spongy structure formed by legumes to optimize resource use in a nutrient-impoverished mine reclamation agroecosystem. These findings may have important implications for assessing microbial multifunctionality in agroecosystems in coal mine reclamation areas.},
}

@article {pmid40653476,
year = {2025},
author = {Bi, BY and Lin, L and Huang, L and Zhou, J and Yan, WJ and Huang, L and Wang, J and Li, XB},
title = {Effects of arabinoxylan on BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex and intestinal microbiome in post-stroke depressed rats.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {40},
pmid = {40653476},
issn = {1471-2202},
support = {No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; },
mesh = {Animals ; *Prefrontal Cortex/metabolism/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Signal Transduction/drug effects ; Rats ; Receptor, trkB/metabolism ; *Depression/metabolism/drug therapy/etiology ; *Xylans/pharmacology ; Rats, Sprague-Dawley ; *Stroke/complications/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; },
abstract = {AIM: To explore the effects of arabinoxylan on the BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex of post-stroke depressed rats, and to explore its neuronal protective effects through the microbial-gut-brain axis in the regulation of this pathway.

METHODS: The rat model of post-stroke depression (PSD) was established by middle cerebral artery occlusion (MCAO) combined with chronic unpredictable mild stimulation (CUMS). They were randomly divided into 5 groups (blank control, post-stroke depression, arabinoxylan, fluoxetine hydrochloride, fluoxetine hydrochloride combined arabinoxylan). The rats were treated differently for 28 days according to their grouping. Body mass, sugar and water consumption experiments and open-field experiments were used to evaluate the behavior of rats. The pathological changes were observed by H&E staining. The expression levels of amine neurotransmitters were detected by ELISA. The expression levels of BDNF mRNA and BDNF, TrkB and p-CREB were detected by RT-PCR and Western blot. The analysis of intestinal metagenomics was conducted by 16 S rDNA sequencing.

RESULTS: Compared with the post-stroke depression group, the body weight, activity and sugar water consumption rate of the arabinoxylan group were increased. The expression levels of 5-HT in the prefrontal cortex, colon and serum levels of 5-HT, DA and NE were increased. The expression levels of BDNF mRNA and BDNF, TrkB and P-CREB in the prefrontal cortex were also upregulated. The number of neurons in the prefrontal cortex increased; Colon mucosal injury and inflammatory cell infiltration decreased, the intestinal microbial diversity increased; The relative abundance of probiotics such as bifidobacterium, Christensenia, Dubosiella New York and ruminococcus increased. The relative abundance of Prevotella NK3B31 group was reduced. The level of 5-HT in the prefrontal cortex was negatively correlated with the abundance of Prevotellaceae NK3B31 group.

CONCLUSION: Arabinoxylan improved depressive-like behavior in rats and its neuroprotective role was achieved by promoting the growth of intestinal probiotics, improving the intestinal barrier, affecting the BDNF/TrkB/p-CREB signaling pathway, and increasing the expression levels of monoamine neurotransmitters 5-HT, DA and NE.},
}

Animals
*Prefrontal Cortex/metabolism/drug effects
*Brain-Derived Neurotrophic Factor/metabolism
*Gastrointestinal Microbiome/drug effects
Male
Signal Transduction/drug effects
Rats
Receptor, trkB/metabolism
*Depression/metabolism/drug therapy/etiology
*Xylans/pharmacology
Rats, Sprague-Dawley
*Stroke/complications/metabolism
Cyclic AMP Response Element-Binding Protein/metabolism

@article {pmid40653257,
year = {2025},
author = {Shantha, JG and Moussa, K and Laovirojjanakul, W and Yeh, S and Tsui, E and Chen, JL and Vitale, AT and Shakoor, A and Larochelle, M and Niemeyer, K and Mentreddy, A and Livnat, I and Safo, M and Ao, W and Choo, C and Yan, D and Zhong, L and Chen, C and Da Silva, K and Reddy, AK and Lee, J and Sura, A and Crowell, EL and Qian, Y and Sharon, Y and Hinterwirth, A and Porco, T and Arnold, BF and Gonzales, J and Acharya, NR and Lietman, TM and Doan, T and , },
title = {The Effect of Metagenomic Sequencing on Patient Clinical Outcomes for Intraocular Infections: A Multicenter Randomized Controlled Trial.},
journal = {American journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajo.2025.07.003},
pmid = {40653257},
issn = {1879-1891},
abstract = {OBJECTIVE: To determine whether the addition of an unbiased test, metagenomic sequencing of intraocular fluid, compared to standard-of-care diagnostics alone, leads to better patient outcomes in presumed infectious intraocular inflammatory eye diseases.

DESIGN: A randomized controlled trial was conducted from May 2022 through February 2024.

PARTICIPANTS: Eligible participants had intraocular inflammation concerning for an infectious etiology, were 18 years or older, and had vision better than no light perception (NLP). This study enrolled participants at 6 tertiary referral eye centers in the United States (5 sites) and Thailand (1 site).

INTERVENTIONS: Participants were randomized to have their physicians have access to deep sequencing results or not.

MAIN OUTCOMES AND MEASURES: The main outcomes were 1) clinical improvement on examination at 4 weeks after randomization and 2) appropriate therapy administered by the treating physician as determined by an independent expert panel.

RESULTS: Among the 100 participants enrolled (median [IQR] age, 62.0 [47.5-71.0] years; 57 (57.0%) were women), 92 participants completed the study. Forty-one (41.0%) participants had resolution of inflammation at their 2-week follow-up and 23 (23.0%) participants had a pathogen identified with routine diagnostics and exited the study. Twenty-one (21.0%) participants met the criteria for randomization. At the primary endpoint, 8 (88.9%) patients in the metagenomic sequencing group had clinical improvement compared to 7 (63.6%) patients in the no metagenomic sequencing group (risk difference, 30% [95% CI: 0.6% to 59.1%]; relative risk (RR)=1.35 [95% CI: 1.01 to 1.81]; P=0.045). Eight (88.9%) patients were considered to receive the appropriate therapy in the metagenomic sequencing group compared to 11 (100%) patients in the no metagenomic sequencing group (risk difference, -12.0% [95% CI: -38.0% to 14.0%]; RR= 0.89 [95% CI: 0.68 to 1.15]; P=0.37). There were 3 non-study related adverse events.

CONCLUSIONS: Having access to metagenomic sequencing results modestly improved clinical outcomes in a subset of patients with suspected intraocular infections. Larger studies are needed to determine the long-term impact on management and clinical outcomes.

TRIAL REGISTRATION: https://clinicaltrials.gov/ct2/show/NCT05286203.},
}

@article {pmid40652761,
year = {2025},
author = {Gupta, A and Saleena, LM and Sivachandran, A},
title = {Genomic insights into antibiotic resistance in dental caries among the south indian population: A bioinformatics approach with abrit AMR.},
journal = {Computers in biology and medicine},
volume = {196},
number = {Pt A},
pages = {110753},
doi = {10.1016/j.compbiomed.2025.110753},
pmid = {40652761},
issn = {1879-0534},
abstract = {OBJECTIVE: This research aims to explore the prevalence, diversity, and impact of Antibiotic Resistance Genes (ARGs) in dental caries within the South Indian population, as well as their association with microbial communities, with the goal of improving treatment outcomes and management strategies.

METHODS: Metagenomic shotgun sequencing was performed on 24 dental caries samples using the Illumina NovaSeq platform. The quality assessment was done using the FASTQC tool. The assembly of sequences was conducted using MEGAHIT and Velvet, which generate contigs, with MEGAHIT producing longer contigs than Velvet. ARGs were identified using AbritAMR (NCBI AMRFinderPlus) with a 90 % similarity threshold. Taxonomic profiling was conducted using SqueezeMeta (Silva database).

RESULTS: The analysis revealed a total of 55 distinct antibiotic resistance genes (ARGs), including 9 efflux pump genes, 8 beta-lactam resistance genes, 4 aminoglycoside resistance genes, and 4 tetracycline resistance genes. Fourteen metal resistance genes were identified, of which copper and mercury resistance genes were the most prevalent. Taxonomic profiling revealed Pseudomonas, Stenotrophomonas, and Acinetobacter as common genera associated with ARGs in dental caries samples from the South Indian population.

CONCLUSION: This is the first study to uncover a significant number of ARGs using shotgun metagenomic sequencing of dental caries samples in the South Indian population. This work contributes to our knowledge of the genetic foundation of antibiotic resistance in dental caries in the South Indian population. To address antibiotic resistance in oral health conditions, unique ARGs and their associations with bacterial taxa offer important new insights for future study and the creation of focused treatment approaches.

CLINICAL SIGNIFICANCE: The detection of unique ARGs and their association with specific bacterial taxonomy offers valuable insights for developing more effective interventions against antibiotic resistance in oral health.},
}

@article {pmid40652718,
year = {2025},
author = {Tang, R and Luo, X and He, W and Cai, X and Huang, L and Zhou, L and Yuan, Y},
title = {Microbial electrotrophs-driven molecular transformations of dissolved organic matter in paddy soil.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126562},
doi = {10.1016/j.jenvman.2025.126562},
pmid = {40652718},
issn = {1095-8630},
abstract = {Microbial electrotrophs are key players in biogeochemical cycles, but the impact of electrotrophic communities on the diverse chemical composition and properties of dissolved organic matter (DOM) molecules in paddy soils has not been comprehensively explored. Herein, we investigated the response of DOM molecules in paddy soil-based microcosms to electrotrophic communities using microbial electrosynthesis systems (MESs), high-resolution mass spectrometry, and genome-centric metagenomics techniques. Compared to the open-circuit control, the closed-circuit system exhibited a 2.6-fold increase in dissolved organic carbon concentration after 120 days of incubation in the MESs, with aromatic and tannin molecular abundances rising by 3.5-fold and 4.4-fold, respectively. These results indicate that electrotrophic activity enhances both the structural complexity and aromatization (humification degree) of soil DOM. Functional annotation revealed significant enrichment of the reductive tricarboxylic acid (rTCA) cycle and Calvin-Benson-Bassham (CBB) cycle, demonstrating active CO2 assimilation by electrotrophs into complex organic compounds. Electrotrophic genera such as Pseudomonas, Hyphomicrobium, Phenylobacterium, Achromobacter, Geobacter, Anaeromyxobacter, and Magnetospirillum were substantially enriched under the closed-circuit conditions, with relative abundances increasing from 0.02-0.72 % to 1.65-13.68 %. These microbes likely facilitated DOM stabilization by coupling extracellular electron uptake with CO2 fixation, thereby transforming labile organic carbon into more stable molecular structures. These findings elucidate the impact of electrotrophic bacteria in regulating the DOM transformation, providing a deeper understanding of the transformation mechanisms of DOM in paddy soils.},
}

@article {pmid40652689,
year = {2025},
author = {Schaeffer, J and Indio, V and Troja, F and Desdouits, M and de Cesare, A and Le Guyader, FS},
title = {Use of capture based metagenomic to assess human enteric virus diversity in sewage and shellfish samples.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118417},
doi = {10.1016/j.marpolbul.2025.118417},
pmid = {40652689},
issn = {1879-3363},
abstract = {Human sewage is the main source of contamination of environmental waters with human enteric viruses, that can contaminate food such as shellfish. Metagenomic represents a new way of analyzing viral diversity through an a priori massive parallel sequencing approach. However, the precise identification of enteric viruses in sewage or shellfish matrices, is still challenging due to the low viral load, large diversity of viral genera and the large amounts of matrix masking viral sequences. This work compared three commercial kits using capture-based enrichment during the library preparation, for the diversity of detected enteric viruses and for the identification of viral strains in sewage and shellfish samples, focusing on four families impacting human health. Triplicate libraries were prepared for each sample and each kit. All three kits allowed the characterization of a variety of viral genera. In sewage samples, a large number of long contigs was obtained allowing a precise identification of more than 35 strains. In shellfish samples, long contigs were rarer but allowed the identification of one human astrovirus and one norovirus strains. Of the tested kits, one displayed lower variation between replicates, allowed to sequence a higher diversity of viruses from the four families of interest and yielded a higher number of nearly-whole genomes.},
}

@article {pmid40652650,
year = {2025},
author = {Meng, X and Chen, S and Liu, Z and Cheng, L and Hu, Y and Huang, X},
title = {Mechanism of electro-acclimation shaped microbiota facilitating phosphorus release from iron-containing sludge: microbial reduction and induced dissolution.},
journal = {Water research},
volume = {286},
number = {},
pages = {124197},
doi = {10.1016/j.watres.2025.124197},
pmid = {40652650},
issn = {1879-2448},
abstract = {Iron-based Chemically Enhanced Primary Treatment (Fe-CEPT) can efficiently concentrate phosphorus (P) from municipal wastewater into sludge; however, unfavorable P release efficiency impedes P recovery from Iron-based Chemically Enhanced Primary Sludge (Fe-CEPS). This study developed an electro-digester by applying controlled potentials to bio-electrodes. The electro-acclimated microorganisms on bio-electrodes achieved efficient P release due to microbial Fe(III) reduction and microbial metabolism-induced P-Fe complexes dissolution. In P release potential tests, 53.2 % of total P was released within 60 h after +1.0 V acclimation, 2.2-fold of the control. P fractionation analysis revealed that the proportion of Fe(II)-P, Fe(III)-P, and Reductant-P in Fe-CEPS (substrate) decreased by 9.7 %, 44.8 %, and 37.5 % after P release, respectively, combined with X-ray diffraction analysis, indicating P-release process followed Fe(III)-P and reductant-P first being reduced to Fe(II)-P and then dissolved into P(liquid), while inherent Fe(II)-P directly dissolved into P(liquid). The enhanced electron transfer capacity of electro-acclimated microorganisms, demonstrated by cyclic voltammetry analysis, promoted Fe(III)-P reduction. The lower pH (a minimum of 5.7) in mixed liquor, achieved by the enhanced metabolism of electro-acclimated microorganisms and elevated enzyme activities relating to hydrolysis-acidification, facilitated the dissolution of Fe(II)-P into the liquid phase. These two steps were dominated by enriched iron-reducing bacteria as Deferribacteraceae and fermentative bacteria as Clostridiaceae in electro-acclimation shaped microbiota. Metagenomic analysis showed consistent results as genes encoding cellular respiratory, metabolism and electron transportation upregulated significantly. These findings provided an eco-friendly, cost-effective solution for treating iron-containing chemical sludge and recovering valuable P resources.},
}

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}

@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
*Interspersed Repetitive Sequences
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Plasmids/genetics
Gene Transfer, Horizontal
*Gastrointestinal Tract/microbiology
Metagenome

@article {pmid40652235,
year = {2025},
author = {Wang, Z and Piao, Y and An, Z and Piao, H},
title = {Pneumonia due to scrub typhus infection: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {340},
pmid = {40652235},
issn = {1471-2466},
support = {Nos.2024A060//Health Science and Technology Ability Improvement Program of Jilin Province/ ; },
mesh = {Humans ; *Scrub Typhus/complications/diagnosis/drug therapy ; Female ; Middle Aged ; *Orientia tsutsugamushi/isolation & purification/genetics ; Doxycycline/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Bronchoscopy ; },
abstract = {BACKGROUND: Scrub typhus is an acute febrile illness caused by the rickettsial bacterium Orientia tsutsugamushi, transmitted to humans through infected mite bites. Patients typically present with sudden onset high fever, headache, myalgia, and eschar formation at the site of the bites. Respiratory symptoms, such as cough and shortness of breath, can also occur, especially in severe cases that lead to pneumonia or acute respiratory distress syndrome (ARDS). This report presents a case of scrub typhus pneumonia, diagnosed by metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid(BALF).

CASE PRESENTATION: A 58-year-old woman was admitted with cough, sputum production, and fever. Imaging revealed pneumonia. During hospitalization, bronchoscopy was performed to identify the causative pathogen. mNGS of the bronchoalveolar lavage fluid confirmed Orientia tsutsugamushi infection. Patient's pneumonia was improved after oral administration of doxycycline(100 mg two times daily) for 1 month.

CONCLUSION: This report highlights the diagnostic challenges of scrub typhus-induced pneumonia and demonstrates usefulness and the advantages of mNGS in identifying rare pathogens.},
}

Humans
*Scrub Typhus/complications/diagnosis/drug therapy
Female
Middle Aged
*Orientia tsutsugamushi/isolation & purification/genetics
Doxycycline/therapeutic use
Anti-Bacterial Agents/therapeutic use
Bronchoalveolar Lavage Fluid/microbiology
*Pneumonia, Bacterial/drug therapy/diagnosis/microbiology
High-Throughput Nucleotide Sequencing
Bronchoscopy

@article {pmid40652142,
year = {2025},
author = {Fang, H and Yu, Y and Su, Y and Li, H and Gao, H and Li, D and Xia, D and Liu, C and Mao, D},
title = {Characterization of Human Viral Diversity and Adenovirus Isolates in a Sewage Treatment Plant in Tianjin: Implications for Public Health and Advanced Monitoring.},
journal = {Food and environmental virology},
volume = {17},
number = {3},
pages = {39},
pmid = {40652142},
issn = {1867-0342},
support = {42077382//National Natural Science Foundation of China/ ; 42377426//National Natural Science Foundation of China/ ; },
mesh = {*Sewage/virology ; Humans ; China ; Phylogeny ; *Adenoviruses, Human/isolation & purification/classification/genetics ; Public Health ; *Adenoviridae/classification/isolation & purification/genetics ; Wastewater/virology ; Genetic Variation ; Environmental Monitoring ; },
abstract = {This study focuses on the characterization of human viral diversity within a major Wastewater Treatment Plant (WWTP) in the central area of Tianjin, China, with a particular emphasis on adenoviruses due to their robust survivability and potential health implications. By employing metagenomic sequencing, targeted sequencing, quantitative polymerase chain reaction (qPCR) analysis, and cell culture methodologies, we identified a broad spectrum of human viruses, encompassing 25 viral families and 45 viral genera, including enteric, respiratory, and contact viruses. Our findings demonstrate that adenoviruses were stably present in sewage from January to May and retained their infectious activity. The temporal analysis of viral loads across different months revealed no significant changes, suggesting a consistent risk of exposure. Additionally, our phylogenetic analysis of adenoviruses isolated from A549 cell cultures provides insights into their genotypic diversity and potential transmission dynamics. This comprehensive assessment underscores the critical need for improved viral surveillance in urban wastewater systems to mitigate public health risks and highlights the importance of advanced treatment technologies to address the challenges posed by adenoviruses and other pathogenic viruses in municipal wastewater.},
}

*Sewage/virology
Humans
China
Phylogeny
*Adenoviruses, Human/isolation & purification/classification/genetics
Public Health
*Adenoviridae/classification/isolation & purification/genetics
Wastewater/virology
Genetic Variation
Environmental Monitoring

@article {pmid40651825,
year = {2025},
author = {Kenney, GE},
title = {Genome mining with hypothetical proteins.},
journal = {Methods in enzymology},
volume = {717},
number = {},
pages = {199-240},
doi = {10.1016/bs.mie.2025.04.004},
pmid = {40651825},
issn = {1557-7988},
mesh = {Biological Products/metabolism ; *Data Mining/methods ; *Genomics/methods ; Bacteria/genetics/metabolism ; Biosynthetic Pathways/genetics ; Computational Biology/methods ; Genome, Bacterial ; },
abstract = {Natural products are diverse compounds made by many organisms, though bacteria, fungi, and plants are particularly prolific producers. While they have a range of biological roles, bioactive natural products have long been of interest as drug candidates. With the advent of accessible genome mining tools like antiSMASH, it is possible to search through genomes and metagenomes, identifying genes associated with natural product production and even predicting potential structures for experimentally uncharacterized compounds. However, most genome mining tools rely on similarity to previously characterized natural product pathways, and so they can fail to detect unusual or novel pathways and pathways that rely on "hypothetical proteins" for key biosynthetic steps. This is unfortunate, because natural products from new classes or with potentially divergent scaffolds are of particular interest in efforts to identify compounds with antibiotic and anticancer activity. This chapter will document some of the approaches that can be used to explore and develop biosynthetic hypotheses for these challenging-to-detect natural product pathways.},
}

Biological Products/metabolism
*Data Mining/methods
*Genomics/methods
Bacteria/genetics/metabolism
Biosynthetic Pathways/genetics
Computational Biology/methods
Genome, Bacterial

@article {pmid40651702,
year = {2025},
author = {Yu, PF and Wang, D and Fu, YB and Ma, XG and Zheng, H and Han, LY and Wang, A and Jiang, DL and Sun, HW and Jin, X},
title = {The recovery mechanism of granular sludge fragmentation and re-granulation caused by long-term high-concentration organic matter erosion in the SAD process: performance, sludge evolution, and metagenomic sequencing.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132966},
doi = {10.1016/j.biortech.2025.132966},
pmid = {40651702},
issn = {1873-2976},
abstract = {The Simultaneous Anammox and Denitrification (SAD) process effectively removes organic carbon sources, the impact of high-concentration carbon sources on the SAD process remains unclear. This study investigated the performance, sludge characteristics, microbial community correlations, and metagenomic sequencing of the SAD system under conditions of excessive organic matter exposure. The results showed that the organic matter metabolism ability of SAD granular sludge increased from 90.16 ± 1.16 % to 95.2 ± 2.3 %. The Mantel test revealed that Anaerobic Ammonium Oxidation Bacteria (AnAOB) (Candidatus_Kuenenia) were positively correlated with VSS/SS and instability coefficient, while Denitrifying Bacteria (DNB) (Truepera, Ottowia, Deniratisoma, Arenimonas) were negatively correlated with wet density, settling velocity, granule size, protein/polysaccharides (PN/PS) ratio, and the complete coefficient. Following the recovery of the SAD system, the bacterial community correlations increased, and the stability and mechanical strength of the granular sludge were enhanced. Metagenomic sequencing showed that a decrease of Quorum sensing (QS) and the increase of c-di-GMP levels led to up-regulation of exopolysaccharide and extracellular protein expression, resulting in the disintegration of SAD granular sludge. As the sludge aggregated, recombined, and re-granulated, the system up-regulated the expression of the hzs gene in AnAOB nitrogen metabolism via c-di-GMP and QS signals. It also up-regulated the expression of genes such as Dissimilatory Nitrate Reduction to Ammonium (DNRA) and potential denitrification pathways, enhancing the metabolism of AnAOB and symbiotic bacteria.},
}

@article {pmid40651701,
year = {2025},
author = {Zhu, C and Wang, H and Liu, R and Yuan, H and Li, X},
title = {Response of anaerobic digestion of cattle manure to continuous temperature transitions: Process performance, microbial succession, key enzymes, and metabolic pathways.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132953},
doi = {10.1016/j.biortech.2025.132953},
pmid = {40651701},
issn = {1873-2976},
abstract = {This study investigated the effect of continuous temperature transitions on the anaerobic digestion (AD) performance of cattle manure (CM) and microbial response mechanisms. Experiments were conducted in a completely-stirred tank reactor (CSTR) for over 390 days with a fine 3 °C gradient from 35 °C to 65 °C. The results showed that AD achieved optimal performance at R47 (47 °C). Microbial analysis indicated that 47 °C was thecritical temperaturefor the transition from mesophilic to thermophilic communities. Metagenomic analysis revealed that, compared with R38 (38 °C) and R53 (53 °C), R47 enhanced the hydrolysis efficiency of refractory components by upregulating key enzyme expression in glycolysis and pyruvate metabolism. At R47,elevatedexpression of key enzymes inboth acetate/butyrate metabolic pathways and methylotrophic methanogenesis pathway contributed to the highest methane yield. The optimal temperature determined for CM provides important parameters for practical AD operations.},
}

@article {pmid40651403,
year = {2025},
author = {Gao, Z and Zhou, H and Han, C and Wang, Z and Hu, X and Jia, M and Wang, Z and Zhang, G and Han, G},
title = {Long-term grazing does not increase antibiotic resistance genes in the soil in an Inner Mongolia desert steppe.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126545},
doi = {10.1016/j.jenvman.2025.126545},
pmid = {40651403},
issn = {1095-8630},
abstract = {Antibiotic resistance due to overuse of antibiotics is one of the biggest challenges to global health. Furthermore, antibiotic resistance genes (ARGs) can enter the environment, for example, via the accumulation of animal excreta. However, the effect of different levels of livestock grazing under natural grazing conditions on soil ARGs is not yet clear. In this study, we examined soil ARGs from a long-term experiment manipulating levels of grazing intensity in an Inner Mongolian desert steppe using metagenomic sequencing technology. We found little influence of increasing grazing intensity on the abundances of soil ARGs. We did, however, find decreases in the absolute abundance of aminoglycoside ARGs with light grazing and increases of vancomycin ARGs under heavy grazing. We found that grazing indirectly affects soil ARGs by altering soil physicochemical properties (moisture, C/N) and bacterial diversity. Our study suggests that long-term grazing will not significantly increase ARGs in the soil of the desert steppe of Inner Mongolia. At the same time, we also believe that the risk of spreading ARGs is lower under light grazing.},
}

@article {pmid40651382,
year = {2025},
author = {Wang, H and Zeng, H and Zhang, J and Zhou, Q},
title = {Single-chamber differs from dual-chamber bioelectrochemical systems in wastewater treatment and methane recovery under combined exposure to microplastics and antibiotics.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139175},
doi = {10.1016/j.jhazmat.2025.139175},
pmid = {40651382},
issn = {1873-3336},
abstract = {The coexistence of microplastics (MPs) and antibiotics in wastewater poses important threats to microbial ecosystems and methane recovery during anaerobic digestion (AD). This study systematically compares the methanogenic performance and microbial response of single- and dual-chamber bioelectrochemical systems (BES) (0.8 V) exposed to a mixture of MPs (10 mg/L) and antibiotics (1 mg/L). Results demonstrated that single-chamber BES significantly enhanced methanogenesis, achieving a 21.19 % increase in methane production compared to conventional AD, while dual-chamber BES exhibited limited activity due to ammonia inhibition and acetate accumulation. Meanwhile, pollutant exposure dramatically altered the functional enzyme activities and microbial community structure. Metagenomic analysis revealed that methane was primarily produced via the acetoclastic pathway mediated by Methanothrix, with electrical stimulation promoting direct interspecies electron transfer. Pollutant exposure drastically altered microbial communities, reducing Euryarchaeota and enriching fermentative bacteria (e.g., Proteiniphilum). Notably, antibiotic resistance genes (ARGs) increased across all systems, with electrode carriers amplifying ARGs proliferation. However, single-chamber BES showed superior resistance to horizontal gene transfer of ARGs. Key metabolic pathways (e.g., glycolysis, TCA cycle) were markedly inhibited, highlighting the cascading effects of pollutants on microbial energetics. These findings highlight the potential of single-chamber BES for treating co-contaminated wastewater, providing critical insights for optimizing BES configurations.},
}

@article {pmid40650758,
year = {2025},
author = {Kearns, R},
title = {Gut modulation to regulate NF-κB in colorectal and gastric cancer therapy and inflammation.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {8},
pages = {264},
pmid = {40650758},
issn = {1432-0851},
mesh = {Humans ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/immunology ; *Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; *Inflammation/metabolism ; *Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; Animals ; Dysbiosis ; Fecal Microbiota Transplantation ; Signal Transduction ; },
abstract = {The nuclear factor-kappa B (NF-κB) pathway plays a pivotal role in cancer progression, immune regulation, and inflammation. Aberrant activation of this pathway, often driven by gut microbiota dysbiosis, contributes to tumorigenesis, therapy resistance, and chronic inflammation. Emerging evidence highlights the bidirectional interaction between gut microbiota and NF-κB signalling, suggesting that microbiota modulation may enhance cancer treatment efficacy and reduce treatment-induced inflammation. This review explores the mechanistic underpinnings of gut microbiota-mediated NF-κB regulation, focusing on microbial metabolites such as short-chain fatty acids (SCFAs) and microbial-associated molecular patterns, including lipopolysaccharides (LPS). It examines how conventional cancer treatments, chemotherapy, radiotherapy, and immune checkpoint inhibitors, exacerbate dysbiosis and NF-κB-driven inflammation, further complicating treatment outcomes. Additionally, this review evaluates the therapeutic potential of gut-targeted interventions, including probiotics, prebiotics, faecal microbiota transplantation (FMT), and dietary modifications, in restoring microbial homeostasis and modulating NF-κB signalling. Despite promising findings, challenges remain regarding the clinical translation of microbiota-based therapies, including the need for standardised microbiota profiling, regulatory frameworks, and long-term safety assessments. Advances in metagenomics and metabolomics are proposed as essential tools to personalise gut-targeted interventions and optimise cancer treatment strategies. Integrating gut modulation into oncology represents a paradigm shift, offering a holistic, patient-centric approach to cancer therapy. However, further research is required to validate these strategies and ensure their efficacy in clinical applications.},
}

Humans
*NF-kappa B/metabolism
*Gastrointestinal Microbiome/immunology
*Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology
*Inflammation/metabolism
*Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology
Animals
Dysbiosis
Fecal Microbiota Transplantation
Signal Transduction

@article {pmid40650567,
year = {2025},
author = {Wallenius, AJ and Venetz, J and Zygadlowska, OM and Lenstra, WK and van Helmond, NAGM and Martins, PD and Slomp, CP and Jetten, MSM},
title = {A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf075},
pmid = {40650567},
issn = {1574-6941},
abstract = {Coastal areas contribute over 75% of global marine methane emissions, a proportion predicted to increase with anthropogenic eutrophication and deoxygenation. Prolonged low oxygen and high organic matter input can disrupt the methane cycle, favoring methane production over oxidation. However, factors influencing this imbalance remain unclear. Here, we show that methanogenesis dominates microbial methane cycling in the anoxic sediments of eutrophic coastal marine Lake Grevelingen (NL) after summer stratification. A shallow sulfate-methane transition zone (SMTZ; 5-15 cm depth) was observed, with high methane concentrations below. Methane was produced in all investigated layers, while methane oxidation was restricted to the narrow SMTZ. Amplicon sequencing, metagenomics, and incubations revealed a metabolically and phylogenetically diverse methanogenic community with niche separation, and methylotrophic methanogenesis prevalent in all layers. Two clades of ANME archaea, ANME-2a/b and ANME-3, were restricted to a narrow zone together with their putative syntrophic sulfate-reducing bacteria, coinciding with the observed methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions, tilting the microbial methane cycle towards increased methanogenesis and decreasing the efficiency of the microbial methane filter.},
}