@article {pmid41211940,
year = {2025},
author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ},
title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70101},
pmid = {41211940},
issn = {1529-8817},
support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; },
abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.},
}

@article {pmid41206740,
year = {2025},
author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP},
title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf056},
pmid = {41206740},
issn = {1574-6976},
abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.},
}

@article {pmid41204634,
year = {2025},
author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q},
title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.},
journal = {Journal of food science},
volume = {90},
number = {11},
pages = {e70654},
doi = {10.1111/1750-3841.70654},
pmid = {41204634},
issn = {1750-3841},
support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; },
abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.},
}

Animals
*Gastrointestinal Microbiome
*Probiotics/pharmacology
Rats, Inbred SHR
*Antihypertensive Agents/pharmacology
Rats
*Hypertension/diet therapy
Male
Blood Pressure/drug effects
*Cultured Milk Products/microbiology
Fermentation
Lactobacillus plantarum/metabolism
Renin-Angiotensin System/drug effects
Metabolomics
Multiomics

@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}

Humans
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Intensive Care Units, Neonatal
Metagenomics
Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Gestational Age
Enteral Nutrition

@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001541},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}

Animals
Phylogeny
Genome, Viral
*Skates, Fish/virology
*Papillomaviridae/genetics/isolation & purification/classification
*Papillomavirus Infections/virology/veterinary
Sequence Analysis, DNA
DNA, Viral/genetics

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid40815091,
year = {2025},
author = {Garcia-Pichel, F and Farias, J and Fernandes, V and Roush, D and Swenson, TL and Kosina, SM and Northen, TR and Cao, H and Jaunin, S and Kandel, R and Gaxiola, R},
title = {Swift microbiome-mediated phenotype transfer from transgenic plants.},
journal = {Journal of environmental quality},
volume = {54},
number = {6},
pages = {1368-1382},
doi = {10.1002/jeq2.70070},
pmid = {40815091},
issn = {1537-2537},
mesh = {*Plants, Genetically Modified/microbiology ; *Arabidopsis/microbiology/genetics/physiology ; *Microbiota ; Phenotype ; Plant Roots/microbiology ; Soil Microbiology ; Butylene Glycols/metabolism ; },
abstract = {The expression of an organism's genes determines its own characteristics in any given environment. In this study, we demonstrate that the phenotypic traits of genetically modified transgenic Arabidopsis thaliana plants, designed for nutrient efficiency and enhanced yield, can be naturally and readily transferred to neighboring wild-type plants. Our findings reveal that the transgenic plants significantly influence the populational, compositional, and functional traits of their root-associated microbiome (RAM), resulting in a larger population, with distinct composition and high functional potential compared to wild-type plants, regardless of soil type. This phenomenon appears to stem from altered metabolite exudation patterns, which enhance root recruitment. Notably, the RAM plays a dual role: it not only contributes to the robust phenotype of the transgenic plants but also facilitates the transfer of these traits to adjacent wild-type plants. Upon transplanting wild-type plants into the presence of transgenics, we observed the induction of transgenic-like phenotypes. Metagenomic and compositional analyses indicate that this transfer is linked to an increase in 2,3-butanediol (2,3-BD) fermenting bacteria. Furthermore, exposure to 2,3-BD alone was sufficient to elicit transgenic phenotypes in wild-type plants. These results suggest that factors external to plant tissues, such as root-associated bacteria and their volatile metabolic products, play a crucial role in the transferability of plant phenotypes to neighboring plants. Our findings underscore the importance of evaluating microbiome interactions in the context of transgenic organisms and open new avenues for alternative agricultural practices that may reduce reliance on genetic modification.},
}

*Plants, Genetically Modified/microbiology
*Arabidopsis/microbiology/genetics/physiology
*Microbiota
Phenotype
Plant Roots/microbiology
Soil Microbiology
Butylene Glycols/metabolism

@article {pmid41198823,
year = {2025},
author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, Ó},
title = {The association of the rumen virome with methane emissions in dairy cattle.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1534},
pmid = {41198823},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; },
abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.},
}

Animals
Cattle
*Methane/metabolism/biosynthesis
*Rumen/virology/microbiology/metabolism
*Virome
Female
Viruses/genetics/classification
Metagenome
Bacteria/metabolism
Metagenomics

@article {pmid41195309,
year = {2025},
author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F},
title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.},
journal = {Pediatric diabetes},
volume = {2025},
number = {},
pages = {3013063},
pmid = {41195309},
issn = {1399-5448},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; },
abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.

METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included α/β-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.

RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2] = 0.0562, p=0.003 and R [2] = 0.0343, p=0.003). HLA-C [∗] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2] = 0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2] = 0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [∗] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19 ± 0.14 vs. 0.26 ± 0.19 µg/mL, p=0.029).

CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [∗] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.},
}

Humans
*Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology
*Gastrointestinal Microbiome/genetics
Child
Male
Female
Cross-Sectional Studies
Adolescent
Child, Preschool
Age of Onset
Cohort Studies
Infant

@article {pmid41194562,
year = {2025},
author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A},
title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70199},
doi = {10.1111/1462-2920.70199},
pmid = {41194562},
issn = {1462-2920},
support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnología/ ; },
mesh = {*Archaea/genetics/metabolism/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.},
}

*Archaea/genetics/metabolism/classification/isolation & purification
*Bacteria/metabolism/genetics/classification/isolation & purification
*Genome, Bacterial
Metagenome
*Microbiota
Sulfur/metabolism
*Geologic Sediments/microbiology
Salinity
Genome, Archaeal
Carbon/metabolism
Nitrogen/metabolism
Phylogeny

@article {pmid41183096,
year = {2025},
author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ},
title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013667},
pmid = {41183096},
issn = {1553-7374},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/virology/immunology ; Immunocompromised Host ; Aged ; Bacteria/isolation & purification/genetics ; Microbiota ; Coinfection/microbiology ; Lung/microbiology/virology ; },
abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.},
}

Humans
*Kidney Transplantation/adverse effects
Male
Female
Middle Aged
Adult
Transplant Recipients
Bronchoalveolar Lavage Fluid/microbiology/virology
*Pneumonia/microbiology/virology/immunology
Immunocompromised Host
Aged
Bacteria/isolation & purification/genetics
Microbiota
Coinfection/microbiology
Lung/microbiology/virology

@article {pmid41194219,
year = {2025},
author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH},
title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {136},
pmid = {41194219},
issn = {2524-6372},
support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; },
abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.

RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and α-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.

CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.},
}

@article {pmid41192488,
year = {2025},
author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y},
title = {Microbial necromass analogues reshape composting humification pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133583},
doi = {10.1016/j.biortech.2025.133583},
pmid = {41192488},
issn = {1873-2976},
abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.},
}

@article {pmid41189709,
year = {2025},
author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J},
title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619059},
pmid = {41189709},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation & purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.

METHODS: We recruited 91 participants, including 31 treatment-naïve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.

RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in α-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.

DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.},
}

Humans
*HIV Infections/immunology/drug therapy/microbiology/blood/virology
Metagenomics
Male
Female
Adult
*Microbiota
Middle Aged
Disease Progression
Viral Load
*Bacteria/classification/genetics/isolation & purification
*Immune Reconstitution
*Blood/microbiology
CD4-CD8 Ratio

@article {pmid41189414,
year = {2025},
author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y},
title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70201},
doi = {10.1111/1462-2920.70201},
pmid = {41189414},
issn = {1462-2920},
support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation & purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation & purification ; },
abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.},
}

*Genome, Viral
Metagenomics
*Bacteriophages/genetics/isolation & purification/classification
Phylogeny
*Pseudoalteromonas/virology
Genomics
*Viruses/genetics/classification/isolation & purification

@article {pmid41188680,
year = {2025},
author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA},
title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {547},
pmid = {41188680},
issn = {1573-2983},
support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; },
mesh = {*Geologic Sediments/microbiology ; *Biofilms ; Mining ; *Microbiota ; Metagenomics ; *Water Microbiology ; Western Australia ; Water Pollutants, Chemical/analysis ; Zinc/analysis ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.},
}

*Geologic Sediments/microbiology
*Biofilms
Mining
*Microbiota
Metagenomics
*Water Microbiology
Western Australia
Water Pollutants, Chemical/analysis
Zinc/analysis
Metagenome
Bacteria/genetics/classification

@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0173025},
pmid = {41081627},
issn = {2165-0497},
support = {ZY2022018//WMSTB | Science and Technology Plan Project of Wenzhou Municipality ()/ ; },
mesh = {Humans ; *Pterygium/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Conjunctiva/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Middle Aged ; Aged ; Virulence Factors/genetics ; Adult ; Dysbiosis/microbiology ; },
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}

Humans
*Pterygium/microbiology
*Metagenomics/methods
*Microbiota/genetics
Conjunctiva/microbiology
*Bacteria/genetics/classification/isolation & purification
Male
Female
Middle Aged
Aged
Virulence Factors/genetics
Adult
Dysbiosis/microbiology

@article {pmid41069107,
year = {2025},
author = {Ozel, B and Agirman, B and Simsek, O and Erten, H},
title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.},
journal = {Yeast (Chichester, England)},
volume = {42},
number = {11},
pages = {222-234},
doi = {10.1002/yea.70003},
pmid = {41069107},
issn = {1097-0061},
support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; },
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Yeasts/classification/genetics/metabolism/isolation & purification ; Hydrogen-Ion Concentration ; *Biodiversity ; Temperature ; Food Microbiology ; *Fermented Foods/microbiology ; *Bread/microbiology/analysis ; },
abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.},
}

*Volatile Organic Compounds/analysis/metabolism
Fermentation
*Yeasts/classification/genetics/metabolism/isolation & purification
Hydrogen-Ion Concentration
*Biodiversity
Temperature
Food Microbiology
*Fermented Foods/microbiology
*Bread/microbiology/analysis

@article {pmid41025824,
year = {2025},
author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J},
title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0117825},
pmid = {41025824},
issn = {2165-0497},
mesh = {Humans ; *Skin/virology/microbiology ; *Virome/genetics ; Microbiota/genetics ; *Viruses/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; *DNA, Viral/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.

IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.},
}

Humans
*Skin/virology/microbiology
*Virome/genetics
Microbiota/genetics
*Viruses/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification/virology
Metagenome
Bacteriophages/genetics/classification/isolation & purification
*DNA, Viral/genetics
Metagenomics

@article {pmid41025799,
year = {2025},
author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ},
title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0056325},
pmid = {41025799},
issn = {2165-0497},
support = {BB/T00875X/1, BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; UKSBS PR18037//Natural Environment Research Council/ ; },
mesh = {*Rumen/microbiology ; Animals ; *Bacteria/classification/isolation & purification/growth & development/genetics/metabolism ; *Culture Media/chemistry ; Anaerobiosis ; Methane/metabolism ; Gastrointestinal Microbiome ; Cattle ; Phylogeny ; },
abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.},
}

*Rumen/microbiology
Animals
*Bacteria/classification/isolation & purification/growth & development/genetics/metabolism
*Culture Media/chemistry
Anaerobiosis
Methane/metabolism
Gastrointestinal Microbiome
Cattle
Phylogeny

@article {pmid40996249,
year = {2025},
author = {Luo, Y and Xu, X and Qiao, R and Zhao, R-P and Zhou, Z-W and Li, D-A and Wen, Y and Song, J-M and Chen, L-L},
title = {Comparative analysis of rhizosphere microbiomes of cultivated and wild rice under contrasting field water regimes.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0026325},
pmid = {40996249},
issn = {2165-0497},
mesh = {*Oryza/microbiology/growth & development ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Archaea/classification/genetics/isolation & purification/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Water/metabolism ; Plant Roots/microbiology ; },
abstract = {UNLABELLED: Asian cultivated rice (Oryza sativa L.) is domesticated from the common wild rice (Oryza rufipogon Griff.). However, the increasing water stress caused by climate change in recent years has become a major threat to rice growth and yield. To explore the adaptive changes of rhizosphere microbiomes in annual cultivated and perennial wild rice under different water limitation conditions, we conducted metagenomic sequencing analysis on rice rhizosphere soil samples from natural environments with varying water conditions. In particular, the genus Pseudomonas plays a dominant role in the rhizosphere microbiome of wild rice under non-irrigated condition. For archaea, we found that, compared to non-irrigated condition, submergence condition enriched methanogenic Methanosarcina. In comparison to cultivated rice, wild rice showed significant enrichment of Nitrosarchaeum, as ammonia-oxidizing archaea play a key role in the nitrogen cycle, whereas cultivated rice tends to enrich methanogenic archaea (Methanosarcina), which may increase methane emissions and have adverse environmental impacts. The rhizosphere metabolites of wild rice also enriched DL-Norleucine, L-Phenylalanine, and Palmitic acid, which may enhance root water absorption and provide essential nutrients to help rice resist water-limiting stress. In terms of rhizosphere microbiome function, asnB and nirK were particularly enriched in wild rice under non-irrigated condition, suggesting that wild rice may exhibit higher ecological adaptability to water stress by enhancing nitrogen assimilation and denitrification processes. Excavating these microbiome communities and functional changes in rice rhizospheres is crucial for optimizing water-limiting resistance, protecting the environment, and improving rice yield.

IMPORTANCE: This study highlights the differences in rhizosphere microbiomes and metabolites between wild and cultivated rice, providing new insights into how water limitation impacts their interaction with the rhizosphere microbiome. These findings are crucial for advancing rice cultivation under submergence and non-irrigated conditions, offering strategies to optimize farming practices, manage water scarcity, and reduce methane emissions. In contrast to cultivated rice, wild rice may regulate its rhizosphere microbial community to enhance resistance to water stress. This discovery offers valuable theoretical support for improving rice growth and adaptation across diverse ecological environments.},
}

*Oryza/microbiology/growth & development
*Rhizosphere
Soil Microbiology
*Microbiota/genetics
Archaea/classification/genetics/isolation & purification/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
*Water/metabolism
Plant Roots/microbiology

@article {pmid41188618,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1295},
pmid = {41188618},
issn = {1573-2959},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; },
mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; },
abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.},
}

*Ibuprofen/metabolism/analysis
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism/analysis
*Microbial Consortia
*Bacteria/metabolism
*Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis
RNA, Ribosomal, 16S

@article {pmid41188334,
year = {2025},
author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T},
title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38587},
pmid = {41188334},
issn = {2045-2322},
mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; },
abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.},
}

*Rumen/microbiology
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Species Specificity
Metagenomics/methods
*Bacteria/classification/genetics

@article {pmid41188324,
year = {2025},
author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI},
title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38611},
pmid = {41188324},
issn = {2045-2322},
support = {NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; R37CA249007/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; },
abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.},
}

Humans
*Colorectal Neoplasms/genetics/pathology/microbiology
*Lymphatic Metastasis/genetics
DNA Methylation
Male
Female
*Biomarkers, Tumor/genetics
Middle Aged
*Gastrointestinal Microbiome
Aged
Transcriptome
Gene Expression Regulation, Neoplastic
Gene Expression Profiling
Multiomics

@article {pmid41188219,
year = {2025},
author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P},
title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9738},
pmid = {41188219},
issn = {2041-1723},
mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.},
}

Animals
*Bacteriophages/genetics/classification/physiology
*Gastrointestinal Microbiome/genetics
Bees/microbiology/virology
*Bacteria/genetics/classification/virology
Biodiversity
Metagenomics
Metagenome

@article {pmid41187070,
year = {2025},
author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S},
title = {An Ocean of Opsins.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
doi = {10.1093/gbe/evaf189},
pmid = {41187070},
issn = {1759-6653},
support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; },
mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; },
abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.},
}

*Opsins/genetics
Animals
Phylogeny
*Evolution, Molecular
Oceans and Seas
Vertebrates/genetics

@article {pmid41186205,
year = {2025},
author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W},
title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {94},
number = {5},
pages = {e70178},
doi = {10.1111/aji.70178},
pmid = {41186205},
issn = {1600-0897},
support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.

OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.

RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.

CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.},
}

Animals
Female
Cattle
*Staphylococcus aureus/physiology
*Staphylococcal Infections/microbiology/immunology/veterinary
*Microbiota
*Uterus/microbiology/immunology
*Endometritis/microbiology/immunology/veterinary
*Cattle Diseases/microbiology/immunology

@article {pmid41185359,
year = {2025},
author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y},
title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117622},
doi = {10.1016/j.foodres.2025.117622},
pmid = {41185359},
issn = {1873-7145},
mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; },
abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.},
}

*Fermentation
Machine Learning
Metagenomics
*Temperature
Microbiota
Hot Temperature
Quality Control
*Food Microbiology

@article {pmid41185305,
year = {2025},
author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T},
title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117551},
doi = {10.1016/j.foodres.2025.117551},
pmid = {41185305},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; },
abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}

*Metagenomics/methods
*Taste
Fermentation
*Microbiota
Fungi/classification/genetics/metabolism
*Alcoholic Beverages/microbiology/analysis
China
Bacteria/classification/genetics/metabolism
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Flavoring Agents

@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation & purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.

METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.

RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.

CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}

Animals
Humans
*Campylobacter/classification/genetics/isolation & purification
Infant
*Campylobacter Infections/microbiology/epidemiology/veterinary
Ethiopia/epidemiology
*Livestock/microbiology
Rural Population
Longitudinal Studies
Female
Male
Chickens/microbiology
Feces/microbiology
Metagenomics/methods
Gastrointestinal Microbiome
Adult
Cluster Analysis
Family
Child, Preschool

@article {pmid41128412,
year = {2025},
author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H},
title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.},
journal = {ACS nano},
volume = {19},
number = {43},
pages = {37758-37782},
doi = {10.1021/acsnano.5c10625},
pmid = {41128412},
issn = {1936-086X},
mesh = {Animals ; *Manganese/chemistry/administration & dosage/pharmacology ; *Sepsis/complications/drug therapy/metabolism ; Mice ; *Carbon/chemistry/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Lung Injury/drug therapy/etiology/metabolism/pathology ; Administration, Oral ; Male ; *Quantum Dots/chemistry/administration & dosage ; Lung/drug effects/metabolism ; },
abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.},
}

Animals
*Manganese/chemistry/administration & dosage/pharmacology
*Sepsis/complications/drug therapy/metabolism
Mice
*Carbon/chemistry/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Lung Injury/drug therapy/etiology/metabolism/pathology
Administration, Oral
Male
*Quantum Dots/chemistry/administration & dosage
Lung/drug effects/metabolism

@article {pmid41020558,
year = {2025},
author = {Diallo, D and Sene, O and Ngom, D and Khoulé, A and Faye, ET and Dieng, I and Ndione, MHD and Faye, O and Simon-Lorière, E and Diagne, MM and Diallo, M and Sakuntabhai, A and Fall, G},
title = {Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in southeastern and central Senegal, October 2022.},
journal = {Medical and veterinary entomology},
volume = {39},
number = {4},
pages = {863-874},
doi = {10.1111/mve.70017},
pmid = {41020558},
issn = {1365-2915},
support = {U01AI151758//National Institute of Allergy and Infectious Diseases, National Institues of Health/ ; },
mesh = {Animals ; Senegal ; *Arboviruses/isolation & purification/genetics ; *Culicidae/virology ; Phylogeny ; *Mosquito Vectors/virology ; *Virome ; },
abstract = {The knowledge of the distribution of viruses and their associated mosquito species is still incomplete in Senegal. Additionally, data on the genetic characterization of these viruses are limited. The aim was to update knowledge on the diversity, distribution and genetic relationships of mosquito-associated viruses in Senegal through entomological and molecular surveillance. Mosquitoes were collected in October 2022 across 10 districts in Senegal. Samples were identified morphologically and processed for virome characterization using qRT-PCR and next-generation sequencing. The most common species were Culex cinereus Theobald, 1901, Culex quinquefasciatus Say, 1823, Culex neavei Theobald, 1904, and Culex poicilipes Theobald, 1904 (Diptera: Culicidae). The number of mosquitoes collected varied by habitat and district. We detected 42 isolates of 7 viruses, including Bagaza (BAGV), Barkedji, Sindbis (SINV), Usutu (USUV), Dezidougou, Densovirus and Pestivirus A (PESVA), in 6 mosquito species (Mansonia uniformis, Cx. neavei Theobald, 1901, Anopheles coustani, Cx. cinereus Laveran, 1900, Aedes aegypti Linnaeus, 1762 and Aedes vexans Meigen, 1830) (Diptera: Culicidae). The viruses were mainly detected in mosquitoes collected near ponds (92.9%). BAGV and SINV were detected for the first time in southeastern Senegal. This is also the first association of PESVA with mosquitoes in the field. Phylogenetic analyses revealed that PESVA clustered with strains from Asia and Egypt, BAGV with strains from Senegal and Spain, USUV with strains from Senegal and SINV with strains from Spain and Kenya. This study expands the understanding of mosquito-virus associations in Senegal, revealing new geographic distributions and vectors for several viruses, with implications for arbovirus emergence and surveillance strategies.},
}

Animals
Senegal
*Arboviruses/isolation & purification/genetics
*Culicidae/virology
Phylogeny
*Mosquito Vectors/virology
*Virome

@article {pmid40998209,
year = {2025},
author = {Olsen, IA and Eggesbø, M and Trivedi, U and Timmermann, A},
title = {Per- and polyfluoroalkyl substances and the gut microbiota in infants: A scoping review.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122937},
doi = {10.1016/j.envres.2025.122937},
pmid = {40998209},
issn = {1096-0953},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Fluorocarbons/toxicity ; Infant ; *Environmental Pollutants/toxicity ; *Environmental Exposure ; Infant, Newborn ; Female ; },
abstract = {Per-and polyfluoroalkyl substances (PFASs) are persistent environmental chemicals associated with adverse health effects. Emerging evidence suggests PFAS exposure may influence gut microbiota composition, which is a critical determinant of health particularly during infancy. A systematic search was conducted in PubMed to identify epidemiological studies investigating PFAS exposure and infant gut microbiota. Seven studies met the inclusion criteria, examining a range of PFASs derived from either breast milk, maternal blood, or umbilical cord blood and including from 30 to 789 subjects. These studies used either 16S rRNA sequencing or shotgun metagenomics to assess microbiota changes. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the most frequently examined PFASs. Across studies, exposure to PFASs was associated with both increased and decreased α-diversity. β-diversity shifts were also observed in some studies, suggesting altered microbial structures. PFAS exposure was associated with changes in the abundance of specific taxa, such as increased Enterococcus and decreased Faecalibacterium and Phocaeicola vulgatus. Functional pathway alterations were also reported, including disrupted bile acid metabolism. Variation in study design, covariate adjustment, and methodological approaches likely contribute to the inconsistencies in the observed associations between PFAS exposure and the infant gut microbiota. In conclusion, current evidence suggests that PFAS exposure may influence infant gut microbiota, but more and larger longitudinal studies are needed to better understand whether PFAS exposure is associated with altered gut microbiota composition in infants. This review synthesizes existing evidence on associations between PFAS exposure and gut microbiota composition in infants.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Fluorocarbons/toxicity
Infant
*Environmental Pollutants/toxicity
*Environmental Exposure
Infant, Newborn
Female

@article {pmid40953724,
year = {2025},
author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W},
title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122845},
doi = {10.1016/j.envres.2025.122845},
pmid = {40953724},
issn = {1096-0953},
mesh = {*Soil Microbiology ; Oxidation-Reduction ; *Soil Pollutants/toxicity ; *Carbon/metabolism ; *Microbiota/drug effects ; *Hydrocarbons, Aromatic/toxicity ; Bacteria/drug effects ; Benzene Derivatives/toxicity ; },
abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03 % (±29.18 %) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P < 0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.},
}

*Soil Microbiology
Oxidation-Reduction
*Soil Pollutants/toxicity
*Carbon/metabolism
*Microbiota/drug effects
*Hydrocarbons, Aromatic/toxicity
Bacteria/drug effects
Benzene Derivatives/toxicity

@article {pmid40940422,
year = {2025},
author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL},
title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.},
journal = {The EMBO journal},
volume = {44},
number = {21},
pages = {6226-6252},
pmid = {40940422},
issn = {1460-2075},
support = {R35 GM136390/GM/NIGMS NIH HHS/United States ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; P30GM140963//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; },
mesh = {*Heme/metabolism ; *Iron/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Bacteroides thetaiotaomicron/metabolism/enzymology/genetics ; Humans ; *Gastrointestinal Microbiome ; Cryoelectron Microscopy ; Models, Molecular ; Protoporphyrins/metabolism ; *Lyases/metabolism/genetics/chemistry ; },
abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.},
}

*Heme/metabolism
*Iron/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
*Bacteroides thetaiotaomicron/metabolism/enzymology/genetics
Humans
*Gastrointestinal Microbiome
Cryoelectron Microscopy
Models, Molecular
Protoporphyrins/metabolism
*Lyases/metabolism/genetics/chemistry

@article {pmid40925458,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JW and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M},
title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122775},
doi = {10.1016/j.envres.2025.122775},
pmid = {40925458},
issn = {1096-0953},
mesh = {*Fertilizers/analysis ; *Manure/analysis ; Animals ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen Cycle ; Chickens ; Metagenomics ; Carbon ; *Diptera ; Nitrogen ; Microbiota ; },
abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1 % (p < 0.05) and total potassium by 11.0 % (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7 % (p < 0.01), 107.1 % (p < 0.001), and 14.6 % (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7 % (p < 0.001), and 25.9 % (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9 % higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.},
}

*Fertilizers/analysis
*Manure/analysis
Animals
*Soil Microbiology
*Soil/chemistry
*Nitrogen Cycle
Chickens
Metagenomics
Carbon
*Diptera
Nitrogen
Microbiota

@article {pmid40312036,
year = {2025},
author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C},
title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.},
journal = {Beneficial microbes},
volume = {16},
number = {6},
pages = {631-645},
doi = {10.1163/18762891-bja00075},
pmid = {40312036},
issn = {1876-2891},
mesh = {Humans ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant ; *Breast Feeding ; Milk, Human/microbiology ; Feces/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Time Factors ; Infant Formula ; Male ; *Feeding Behavior ; },
abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.},
}

Humans
*Gastrointestinal Microbiome
Pilot Projects
Infant
*Breast Feeding
Milk, Human/microbiology
Feces/microbiology
Female
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Time Factors
Infant Formula
Male
*Feeding Behavior

@article {pmid41182689,
year = {2025},
author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ},
title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {21},
pages = {e71207},
doi = {10.1096/fj.202502006RR},
pmid = {41182689},
issn = {1530-6860},
mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; },
abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.},
}

Humans
*Feces/microbiology
Infant, Newborn
RNA, Ribosomal, 16S/genetics
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Female
Male
Intensive Care Units, Neonatal
*Bacteria/genetics/classification

@article {pmid41181328,
year = {2025},
author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS},
title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660939},
pmid = {41181328},
issn = {2235-2988},
mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation & purification ; Haemophilus influenzae/isolation & purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Infant ; },
abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.

METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.

RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.

DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.},
}

Humans
*Otitis Media with Effusion/microbiology
Child
*Adenoids/microbiology
Male
Female
Child, Preschool
Age Factors
Chronic Disease
*Microbiota
Feces/microbiology
Streptococcus pneumoniae/isolation & purification
Haemophilus influenzae/isolation & purification
Gastrointestinal Microbiome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Infant

@article {pmid41181319,
year = {2025},
author = {Wang, Z and Song, L and Li, D and Jin, Y},
title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1693796},
pmid = {41181319},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; },
abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.},
}

Humans
*Virome
*Microbiota
*Symbiosis
*Respiratory System/virology/microbiology
Bacteriophages
*Viruses/classification/genetics
Animals
Metagenomics
Host-Pathogen Interactions
Respiratory Tract Infections/virology

@article {pmid41005405,
year = {2025},
author = {Gomes, BM and de Oliveira, GS and de Melo, VS and Rossini, NO and Adriani, PP and Dias, MVB and Chambergo, FS},
title = {Structural and functional characterization of a bifunctional GH43 α-L-arabinofuranosidase/β-xylosidase from the metagenome of Pseudacanthotermes militaris gut.},
journal = {International journal of biological macromolecules},
volume = {329},
number = {Pt 2},
pages = {147909},
doi = {10.1016/j.ijbiomac.2025.147909},
pmid = {41005405},
issn = {1879-0003},
mesh = {*Glycoside Hydrolases/chemistry/metabolism/genetics ; *Xylosidases/chemistry/metabolism/genetics ; Substrate Specificity ; *Metagenome ; Animals ; *Isoptera/enzymology/genetics/microbiology ; Kinetics ; *Gastrointestinal Microbiome ; Models, Molecular ; Catalytic Domain ; Amino Acid Sequence ; },
abstract = {The pursuit of sustainable energy has intensified the search for efficient biocatalysts to convert lignocellulosic biomass. In this context, we characterized a novel bifunctional enzyme, TerARA, identified from the gut metagenome of the termite Pseudacanthotermes militaris. Belonging to the glycoside hydrolase 43 (GH43) family, TerARA was heterologously expressed in E. coli BL21 and purified. The enzyme demonstrated bifunctional activity toward synthetic substrates p-nitrophenyl-α-L-arabinofuranoside (pNP-Araf) (387.22 ± 74.2 U/mg) and p-nitrophenyl-β-D-xylopyranoside (pNP-Xyl) (330.82 ± 31.2 U/mg), with higher catalytic efficiency for pNP-Araf (9.14 s[-1]·mM[-1]), suggesting functional preference as an α-L-arabinofuranosidase. Activity modulation by metal ions revealed that Ca[2+] slightly improved efficiency toward pNP-Araf (to 9.58 s[-1]·mM[-1] at 1 mM), while Zn[2+] reduced efficiency for pNP-Xyl except at 5 mM (6.65 s[-1]·mM[-1]). Zn[2+] also enhanced enzymatic stability, maintaining 80 % activity in pNP-Xyl hydrolysis. Crystallographic analysis at 2.0 Å resolution revealed a 43 Glycosyl Hydrolase catalytic domain with a five-bladed β-propeller fold and two Ca[2+] ions and a Carbohydrate-Binding Module (CBM) domain with a β-sandwich fold likely involved in substrate interaction. Conserved catalytic residues, binding sites, and Ca[2+] stabilizing effects were identified. TerARA's bifunctionality and structural features support its application in hemicellulose degradation and biomass conversion.},
}

*Glycoside Hydrolases/chemistry/metabolism/genetics
*Xylosidases/chemistry/metabolism/genetics
Substrate Specificity
*Metagenome
Animals
*Isoptera/enzymology/genetics/microbiology
Kinetics
*Gastrointestinal Microbiome
Models, Molecular
Catalytic Domain
Amino Acid Sequence

@article {pmid40722249,
year = {2025},
author = {Hilberath, J and Busch, A and Schoppmeier, U and Schmauder, K and Oberhettinger, P and Marschal, M and Slavetinsky, C and Sturm, E and Peter, S and D'Alvise, P},
title = {Small intestinal bacterial overgrowth and dysbiosis in children with intestinal failure: A descriptive cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {49},
number = {8},
pages = {964-974},
doi = {10.1002/jpen.2808},
pmid = {40722249},
issn = {1941-2444},
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Intestine, Small/microbiology ; Child, Preschool ; Child ; *Gastrointestinal Microbiome ; Infant ; Prospective Studies ; Cohort Studies ; *Intestinal Failure/microbiology/complications ; Bacteria/growth & development ; Short Bowel Syndrome/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is a clinical and diagnostic challenge in pediatric intestinal failure. This study aimed to assess SIBO and dysbiosis in children with intestinal failure and to analyze clinical characteristics as well as cultural and metagenomic sequencing results from different sampling methods.

METHODS: Descriptive, single-center cohort study in intestinal failure patients with prospective collection of intraluminal aspirate, epithelial brush swab, mucosal biopsy, and small bowel stoma stool for SIBO diagnosis, defined as ≥10[3] CFU/ml of enteric, colonic-type bacteria, and microbiome analysis via whole-genome sequencing. Statistical testing included receiver operating characteristic analysis, chi-square test, and independent samples t test.

RESULTS: Forty-four children with intestinal failure were analyzed (median age 58 months; female 48%; short bowel syndrome 70%). Sixty-six percent of samples were positive for SIBO. In 93%, all three endoscopic sampling methods showed congruent results. SIBO-positive cases were associated (P < 0.05) with small bowel dilatation, proton pump inhibitor use, intestinal inflammation, elevated direct bilirubin and hepatocellular enzyme levels, and a history of liver fibrosis and central venous catheter infections. Metagenomic sequencing revealed microbial dysbiosis in intestinal failure patients, with SIBO-positive cases showing higher microbial reads, lower alpha diversity, and increased abundance of Enterobacteriaceae and enteric anaerobes.

CONCLUSION: SIBO and dysbiosis are common in children with intestinal failure and associated with liver injury, central line-associated bloodstream infections, and intestinal inflammation. Cultural diagnosis of SIBO using mucosal biopsies or brush swabs are alternatives to small bowel aspirates. Metagenomic sequencing is feasible, and high microbial read numbers are indicative of SIBO.},
}

Humans
*Dysbiosis/microbiology
Female
Male
*Intestine, Small/microbiology
Child, Preschool
Child
*Gastrointestinal Microbiome
Infant
Prospective Studies
Cohort Studies
*Intestinal Failure/microbiology/complications
Bacteria/growth & development
Short Bowel Syndrome/microbiology
Feces/microbiology

@article {pmid41177609,
year = {2026},
author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W},
title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {300-307},
doi = {10.1016/j.jes.2025.04.024},
pmid = {41177609},
issn = {1001-0742},
mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; },
abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.},
}

*Fluorocarbons/analysis/toxicity
*Water Pollutants, Chemical/analysis/toxicity
*Geologic Sediments/microbiology/chemistry
Rivers/microbiology/chemistry
*Drug Resistance, Microbial/genetics
China
*Environmental Monitoring
Metagenomics
*Microbiota/drug effects
Caprylates/toxicity

@article {pmid39756573,
year = {2025},
author = {Shen, H and Li, Y and Pi, Q and Tian, J and Xu, X and Huang, Z and Huang, J and Pian, C and Mao, S},
title = {Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate.},
journal = {Journal of advanced research},
volume = {77},
number = {},
pages = {821-835},
doi = {10.1016/j.jare.2025.01.005},
pmid = {39756573},
issn = {2090-1224},
mesh = {Animals ; *Methicillin-Resistant Staphylococcus aureus/drug effects ; *Deep Learning ; *Antimicrobial Peptides/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; Molecular Dynamics Simulation ; *Ruminants/microbiology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Staphylococcal Infections/drug therapy/microbiology ; Computational Biology/methods ; },
abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.

OBJECTIVES: The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.

METHODS: We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.

RESULTS: The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.

CONCLUSION: This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.},
}

Animals
*Methicillin-Resistant Staphylococcus aureus/drug effects
*Deep Learning
*Antimicrobial Peptides/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Mice
Molecular Dynamics Simulation
*Ruminants/microbiology
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Staphylococcal Infections/drug therapy/microbiology
Computational Biology/methods

@article {pmid41175763,
year = {2025},
author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X},
title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140321},
doi = {10.1016/j.jhazmat.2025.140321},
pmid = {41175763},
issn = {1873-3336},
abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.},
}

@article {pmid41175161,
year = {2025},
author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV},
title = {Gellan gum-based media recover more diverse microbial communities from soil material.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {338},
pmid = {41175161},
issn = {1432-072X},
support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation & purification/classification/genetics/growth & development ; *Microbiota ; },
abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.},
}

*Polysaccharides, Bacterial/chemistry
*Soil Microbiology
*Culture Media/chemistry
*Bacteria/isolation & purification/classification/genetics/growth & development
*Microbiota

@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, MÀ and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
doi = {10.1111/liv.70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}

Humans
*Liver Cirrhosis/complications/therapy/microbiology
*Frailty/therapy/microbiology
Male
Metagenomics
*Gastrointestinal Microbiome
Female
*Probiotics/therapeutic use
Middle Aged
Aged
Feces/microbiology
Amino Acids, Branched-Chain/therapeutic use

@article {pmid41174518,
year = {2025},
author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B},
title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {704},
pmid = {41174518},
issn = {1471-2180},
mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; },
abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.

RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.

CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.},
}

*Lakes/microbiology/chemistry
*Metagenomics/methods
India
*Bacteria/genetics/metabolism/classification/isolation & purification
*Xenobiotics/metabolism
Microbiota
Metagenome
Inactivation, Metabolic

@article {pmid41174459,
year = {2025},
author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C},
title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117386},
doi = {10.1016/j.foodres.2025.117386},
pmid = {41174459},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.},
}

*Metabolomics/methods
*Citrullus/microbiology
*Metagenomics/methods
*Glycine max/microbiology
*Taste
Fermentation
*Microbiota
Food Microbiology
Flavoring Agents/metabolism
Bacteria/metabolism/classification/genetics

@article {pmid41174397,
year = {2025},
author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C},
title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117319},
doi = {10.1016/j.foodres.2025.117319},
pmid = {41174397},
issn = {1873-7145},
mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; },
abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.},
}

*Citrullus/microbiology/chemistry
*Fermentation
*Taste
*Fermented Foods/microbiology/analysis
Volatile Organic Compounds/analysis
*Microbiota
Acetic Acid/analysis
Odorants/analysis
Cresols/analysis
*Food Microbiology
Flavoring Agents/analysis
Bacteria/classification/metabolism/genetics
Gas Chromatography-Mass Spectrometry
China

@article {pmid41173910,
year = {2025},
author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW},
title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9658},
pmid = {41173910},
issn = {2041-1723},
support = {R01NS055349//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32GM148382//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation & purification/genetics ; Metagenome ; Enterobacteriaceae/isolation & purification/genetics ; Patient Discharge ; },
abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.},
}

*Dysbiosis/microbiology/mortality/complications
Humans
*Gastrointestinal Microbiome/genetics
Child, Preschool
*Malaria/mortality/microbiology/complications
Female
Male
Infant
Feces/microbiology
Child
Escherichia coli/isolation & purification/genetics
Metagenome
Enterobacteriaceae/isolation & purification/genetics
Patient Discharge

@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}

India
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification
RNA, Ribosomal, 16S/genetics
*Ecosystem
*Drug Resistance, Bacterial/genetics
beta-Lactamases/genetics/metabolism
Gastrointestinal Microbiome
Metagenomics/methods
Humans
Microbiota
Metagenome

@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Bacteria/classification

@article {pmid41172529,
year = {2025},
author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ},
title = {Biological dynamics of no-tillage soils in the western region of Paraná.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e298630},
doi = {10.1590/1519-6984.298630},
pmid = {41172529},
issn = {1678-4375},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; },
abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.},
}

*Soil Microbiology
*Soil/chemistry
Brazil
Nitrogen/analysis
*Agriculture/methods
Biomass
Biodiversity
Fungi/classification
Carbon/analysis

@article {pmid41168432,
year = {2025},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, Â and Castrillo, G and Wagner, MR},
title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2823-2844},
pmid = {41168432},
issn = {2058-5276},
support = {IOS-2016351//National Science Foundation (NSF)/ ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Droughts ; *Soil Microbiology ; *Microbiota/genetics ; Zea mays/physiology/genetics/microbiology ; Soil/chemistry ; *Rain ; Kansas ; Plant Roots/microbiology/genetics ; Stress, Physiological ; Metagenome ; Adaptation, Physiological ; Water/metabolism ; *Plants/microbiology/genetics ; Bacteria/classification/genetics ; },
abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.},
}

*Droughts
*Soil Microbiology
*Microbiota/genetics
Zea mays/physiology/genetics/microbiology
Soil/chemistry
*Rain
Kansas
Plant Roots/microbiology/genetics
Stress, Physiological
Metagenome
Adaptation, Physiological
Water/metabolism
*Plants/microbiology/genetics
Bacteria/classification/genetics

@article {pmid41168431,
year = {2025},
author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ},
title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2720-2735},
pmid = {41168431},
issn = {2058-5276},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Uganda ; Alkynes ; Metagenomics ; Benzoxazines/therapeutic use/adverse effects ; Male ; Female ; Feces/microbiology ; Cyclopropanes ; Adult ; Botswana ; *Anti-Retroviral Agents/therapeutic use ; Middle Aged ; United States ; Reverse Transcriptase Inhibitors/therapeutic use ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/drug effects/isolation & purification ; },
abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*HIV Infections/drug therapy/microbiology
Uganda
Alkynes
Metagenomics
Benzoxazines/therapeutic use/adverse effects
Male
Female
Feces/microbiology
Cyclopropanes
Adult
Botswana
*Anti-Retroviral Agents/therapeutic use
Middle Aged
United States
Reverse Transcriptase Inhibitors/therapeutic use
*Anti-HIV Agents/therapeutic use
Bacteria/classification/genetics/drug effects/isolation & purification

@article {pmid41131367,
year = {2025},
author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C},
title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2686-2701},
pmid = {41131367},
issn = {2058-5276},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; },
mesh = {*Hydrogenase/metabolism/genetics ; Humans ; Hydrogen/metabolism ; *Gastrointestinal Microbiome ; Fermentation ; *Bacteria/genetics/enzymology/classification/growth & development/metabolism/isolation & purification ; Metagenomics ; Feces/microbiology ; Bacteroidetes/growth & development/metabolism/genetics ; Firmicutes/growth & development/genetics/metabolism/enzymology ; Crohn Disease/microbiology ; *Gastrointestinal Tract/microbiology ; Iron-Sulfur Proteins/metabolism/genetics ; Healthy Volunteers ; },
abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.},
}

*Hydrogenase/metabolism/genetics
Humans
Hydrogen/metabolism
*Gastrointestinal Microbiome
Fermentation
*Bacteria/genetics/enzymology/classification/growth & development/metabolism/isolation & purification
Metagenomics
Feces/microbiology
Bacteroidetes/growth & development/metabolism/genetics
Firmicutes/growth & development/genetics/metabolism/enzymology
Crohn Disease/microbiology
*Gastrointestinal Tract/microbiology
Iron-Sulfur Proteins/metabolism/genetics
Healthy Volunteers

@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2797-2807},
pmid = {41073663},
issn = {2058-5276},
support = {K01-DK102771//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Mice ; *Bacteroides fragilis/genetics/metabolism/immunology ; *Glycolipids/immunology/chemistry/metabolism/biosynthesis ; Natural Killer T-Cells/immunology ; Galactosyltransferases/metabolism/genetics ; Symbiosis ; Mice, Inbred C57BL ; Colon/immunology/microbiology ; Infant ; Galactosylceramides/metabolism/biosynthesis ; Female ; *Bacteria/metabolism/classification/genetics ; Lymphocyte Activation ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
Mice
*Bacteroides fragilis/genetics/metabolism/immunology
*Glycolipids/immunology/chemistry/metabolism/biosynthesis
Natural Killer T-Cells/immunology
Galactosyltransferases/metabolism/genetics
Symbiosis
Mice, Inbred C57BL
Colon/immunology/microbiology
Infant
Galactosylceramides/metabolism/biosynthesis
Female
*Bacteria/metabolism/classification/genetics
Lymphocyte Activation

@article {pmid40972730,
year = {2026},
author = {Wang, X and Chen, M and Su, Y and Zhang, X and Chen, J and Huang, Z and Xie, J and Xie, Q and He, L and Su, L and Su, Z and Wang, H and Li, Y},
title = {A novel cholesterol-reducing mechanism of polygonati rhizoma: Dual action via Bacteroides-mediated cholesterol sulfonation and feedback inhibition of ACAT2 by sulfated metabolite.},
journal = {Journal of ethnopharmacology},
volume = {355},
number = {Pt A},
pages = {120619},
doi = {10.1016/j.jep.2025.120619},
pmid = {40972730},
issn = {1872-7573},
mesh = {Animals ; Mice ; Male ; *Cholesterol/metabolism/blood ; *Polygonatum/chemistry ; *Hypercholesterolemia/drug therapy ; Gastrointestinal Microbiome/drug effects ; Molecular Docking Simulation ; *Bacteroides/metabolism/drug effects ; *Anticholesteremic Agents/pharmacology/isolation & purification ; *Phosphatidylcholine-Sterol O-Acyltransferase/antagonists & inhibitors/metabolism ; Rhizome ; Disease Models, Animal ; *Plant Extracts/pharmacology ; Animals, Outbred Strains ; },
abstract = {Polygonati Rhizoma (PR) has the function of "invigorating spleen and tonifying kidney", and is historically applied as a homology of medicine and food to prevent and treat dyslipidemia in China. However, there is limited experimental evidence to support this application, and the underlying mechanism has not been fully deciphered.

AIM OF THE STUDY: To analyze the composition and illuminate the cholesterol-lowering potential and molecular mechanism of PR's aqueous extract (PRE) in high-fat emulsion (HFE)-induced hypercholesterolemia mouse model.

MATERIALS AND METHODS: Ion chromatograph was employed to determine the monosaccharide composition of PRE. HFE-induced Kunming mouse model was constructed to evaluate the anti-hypercholesterolemia effect of PRE. Metagenomic sequences and liquid chromatography-mass spectrometry (LC-MS) analysis were performed to elucidate the mechanism through which PR regulated cholesterol metabolism. Antibiotic cocktail (ABX) intervention and fecal microbiota transplantation (FMT) were used to validate whether PRE regulated cholesterol metabolism through the intestinal microbiota. The cholesterol-reducing effect of cholesterol sulfate (CS) was explored in poloxamer 407 (P407)-induced mouse model of dyslipidemia. Molecular docking and molecular dynamics (MD) simulation were also employed to elucidate the underlying mechanisms. Furthermore, a combination of qRT-PCR, Western blot, and surface plasmon resonance (SPR) were employed to delineate its mechanism.

RESULTS: Our study indicated that the polysaccharides of PRE were mainly composed of fructose (92.33 %) and glucose (5.25 %). PRE treatment effectively blocked body weight gain, significantly decreased serum and hepatic levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C), and increased high-density lipoprotein cholesterol (HDL-C) level. Additionally, PRE ameliorated hepatic lipid accumulation in mice with HFE-elicited hypercholesterolemia. Notably, metagenomic sequencing and LC-MS analysis indicated that PRE markedly increased the abundance of intestinal genera Bacteroides and significantly elevated the fecal CS concentration in HFE mice. Genome-based functional analysis further indicated that cofactors of sulfonation (ATP sulfurylase CysD and CysN, BT0414-BT0415) were significantly upregulated after treatment with PRE. The cholesterol-lowering effect of PRE was largely contingent upon microbial conversion of cholesterol-to-CS mediated by Bacteroides, as validated by antibiotics-induced intestinal microbiota depletion in pseudo-germ-free model and restoration of gut microbiota through FMT. In vitro study also showed that PRE promoted the growth of Bacteroides thetaiotaomicron. Furthermore, CS markedly alleviated serum, hepatic, bile, and fecal levels of TG, TC, LDL-C, HDL-C, and TBA, indicative of appreciable lipid-lowering effect. MD simulation and SPR results indicated that CS directly bound to ACAT2. Consistent with this interaction, CS greatly downregulated the mRNA and protein expression of ACAT2 in small intestinal tissue.

CONCLUSION: These findings for the first time suggested that PR acted as a prebiotic agent to ameliorate hypercholesterolemia, at least in part, via dual mechanism involving modulation of Bacteroides-mediated sulfonation metabolic pathway and feedback inhibition of ACAT2 by CS, highlighting its therapeutic potential for cholesterol-related disorders. This work might also offer novel mechanistic insight and further buttressed the ethnopharmacological application of PR in the therapy of hypercholesterolemia.},
}

Animals
Mice
Male
*Cholesterol/metabolism/blood
*Polygonatum/chemistry
*Hypercholesterolemia/drug therapy
Gastrointestinal Microbiome/drug effects
Molecular Docking Simulation
*Bacteroides/metabolism/drug effects
*Anticholesteremic Agents/pharmacology/isolation & purification
*Phosphatidylcholine-Sterol O-Acyltransferase/antagonists & inhibitors/metabolism
Rhizome
Disease Models, Animal
*Plant Extracts/pharmacology
Animals, Outbred Strains

@article {pmid40812707,
year = {2025},
author = {Wu, J and Chen, Y and Zhao, J and O'Brien, JW and Coin, L and Hai, FI and Sanderson-Smith, M and Jiang, G},
title = {Impact of human lifestyle on the pathogenic potential of urban wastewater.},
journal = {Environmental research},
volume = {286},
number = {Pt 1},
pages = {122591},
doi = {10.1016/j.envres.2025.122591},
pmid = {40812707},
issn = {1096-0953},
mesh = {*Wastewater/microbiology ; Humans ; *Life Style ; Australia ; Virulence Factors/genetics ; *Bacteria/pathogenicity/genetics ; Cities ; *Microbiota ; },
abstract = {Domestic wastewater has been known for its pathogenic potential including the presence of pathogenic bacteria, virulence factor genes (VFGs) and antibiotic resistance genes (ARGs). While previous studies have investigated regional differences in microbial communities, the influence of population lifestyle factors on the pathogenic potential of wastewater microbiomes remains poorly understood. In this study, we analyzed ten Australian wastewater treatment plants (WWTPs) using Nanopore metagenomic sequencing to profile pathogens, ARGs, and VFGs, and examined their associations with health-related behaviors such as smoking, alcohol consumption, and obesity. A total of 196 pathogenic species, 951 ARG subtypes, and 380 VFGs were detected. Staphylococcus aureus was the most abundant pathogen, macB the dominant ARG, and lipooligosaccharides (LOS) the most prevalent VFG. While pathogen and ARG profiles were relatively stable across sites and showed limited association with lifestyle variables, VFG profiles demonstrated significant correlations with smoking rates, alcohol consumption, and nicotine levels in wastewater. Co-occurrence network analysis revealed strong interconnectivity among VFGs and between VFGs and ARGs, suggesting potential co-selection. Principal component analysis and diversity metrics further confirmed distinct patterns in VFG distribution across sites. These findings suggest VFGs as potentially sensitive indicators of behavioral health risks in wastewater-based epidemiology.},
}

*Wastewater/microbiology
Humans
*Life Style
Australia
Virulence Factors/genetics
*Bacteria/pathogenicity/genetics
Cities
*Microbiota

@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.

METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.

CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
Biodiversity
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny

@article {pmid41171126,
year = {2025},
author = {She, J and Qian, PY and Wu, L},
title = {DOO: integrated multi-omics resources for deep ocean organisms.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1096},
pmid = {41171126},
issn = {1362-4962},
support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; },
abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth & development/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.

RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (> 23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2 days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15 days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.

CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}

*Groundwater/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/growth & development/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Adaptation, Physiological
Sequence Analysis, DNA

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168702,
year = {2025},
author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML},
title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {64},
pmid = {41168702},
issn = {1297-9686},
support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.

RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.

CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.},
}

Animals
Cattle/genetics/physiology
*Rumen/microbiology
*Metagenome
*Weight Gain/genetics
*Eating/genetics
Metagenomics/methods
Animal Feed
Phenotype
Genomics/methods
Diet/veterinary
Gastrointestinal Microbiome

@article {pmid41168291,
year = {2025},
author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM},
title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37987},
pmid = {41168291},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; },
abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Metagenome
*Microbiota/genetics
*Citrus sinensis/microbiology
*Rhizobiaceae
Plant Roots/microbiology
Soil Microbiology
*Bacteria/genetics/classification
Phylogeny
*Liberibacter
High-Throughput Nucleotide Sequencing

@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology ; *Bacteriophages/genetics/physiology ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Sputum/microbiology/virology ; Lung/microbiology/virology ; Severity of Illness Index ; },
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology
*Bacteriophages/genetics/physiology
*Microbiota
Female
Male
Middle Aged
Aged
Sputum/microbiology/virology
Lung/microbiology/virology
Severity of Illness Index

@article {pmid40966087,
year = {2025},
author = {Pu, Y and Qi, X and Huang, L and Wu, W and Zhou, X and Li, W and Yang, Z and Kong, M and Shen, J and Qi, W and Sun, Z and Mei, Z and Wang, Q and Yang, W and Gao, X and Wang, X and Liu, Z and Yuan, C and Zheng, Y},
title = {Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116297},
doi = {10.1016/j.celrep.2025.116297},
pmid = {40966087},
issn = {2211-1247},
mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; *Metabolome ; Male ; Middle Aged ; Aged, 80 and over ; *Metagenome ; *Sleep/physiology ; *Frailty/blood/microbiology/metabolism ; *Pyruvic Acid/metabolism ; },
abstract = {Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.},
}

Humans
Aged
*Gastrointestinal Microbiome/genetics/physiology
Female
*Metabolome
Male
Middle Aged
Aged, 80 and over
*Metagenome
*Sleep/physiology
*Frailty/blood/microbiology/metabolism
*Pyruvic Acid/metabolism

@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}

*Wastewater/microbiology
Animals
*Abattoirs
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Poultry
Genes, Bacterial
Waste Disposal, Fluid
RNA, Ribosomal, 16S
Environmental Monitoring
Anti-Bacterial Agents
*Water Microbiology
Microbiota

@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
doi = {10.1002/alz.70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Genève/ ; //Fondation Segré, Genève/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Genève/ ; //Fondation Edmond J. Safra, Genève/ ; //Fondation Minkoff, Genève/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et René Keller, Genève/ ; //Fondation AETAS, Genève/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //Hôpitaux Universitaires de Genève/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.

METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.

RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from < 2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.

DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.

HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology/chemistry
Male
Female
*Dysbiosis/metabolism
*Cognitive Dysfunction/metabolism/microbiology
Aged
*Inflammation/metabolism
*Brain/metabolism
Cytokines/blood
Multiomics

@article {pmid41163852,
year = {2025},
author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H},
title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660970},
pmid = {41163852},
issn = {2235-2988},
mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation & purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.

METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.

RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.

DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.},
}

Humans
*Autism Spectrum Disorder/virology
Feces/virology
*Gastrointestinal Microbiome
Child
Phylogeny
*Viruses/classification/genetics/isolation & purification
Male
*Virome
Female
Metagenomics
Child, Preschool
Case-Control Studies

@article {pmid41163226,
year = {2025},
author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {350},
pmid = {41163226},
issn = {1743-422X},
support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; },
mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.

RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n = 1), Paramyxoviridae (n = 1), Polyomaviridae (n = 1), Parvoviridae (n = 7), Circoviridae (n = 6), and Genomoviridae (n = 1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.

CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.},
}

Dogs
Animals
*Lymph Nodes/virology
Phylogeny
*Virome
*Zoonoses/virology
Genome, Viral
China
Humans
*Viruses/genetics/classification/isolation & purification
*Dog Diseases/virology
Metagenomics
*Viral Zoonoses/virology/transmission

@article {pmid41163171,
year = {2025},
author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z},
title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {59},
pmid = {41163171},
issn = {1476-0711},
support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&D Program of the China Ministry of Science and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.

METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.

RESULTS: No significant differences were observed in age (62.22 ± 5.74 vs. 58.23 ± 7.55, p = 0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p = 0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p < 0.05) and distinct beta diversity clustering (p < 0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p < 0.0001). Neutral modeling indicated stochastic assembly (R² >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.

CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.},
}

Humans
Female
*Vagina/microbiology
*Diabetes Mellitus, Type 2/microbiology
Middle Aged
*Postmenopause
*Microbiota
*Perimenopause
Aged
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Dysbiosis/microbiology

@article {pmid41163130,
year = {2025},
author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD},
title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {967},
pmid = {41163130},
issn = {1471-2164},
support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; },
abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.

RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.

CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.},
}

*Mycorrhizae/genetics/physiology
*Symbiosis/genetics
*Plant Roots/microbiology
Phylogeny
*Endophytes/genetics
*Genomics
*Metagenome
*Genome, Fungal
Glomeromycota/genetics

@article {pmid41162595,
year = {2025},
author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L},
title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37813},
pmid = {41162595},
issn = {2045-2322},
support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation & purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; },
abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.},
}

Humans
*COVID-19/microbiology/virology/diagnosis
Middle Aged
Male
Female
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Aged
SARS-CoV-2/isolation & purification
Adult
*Respiratory Tract Infections/microbiology
*Microbiota/genetics

@article {pmid41086517,
year = {2026},
author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q},
title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.},
journal = {Virology},
volume = {613},
number = {},
pages = {110712},
doi = {10.1016/j.virol.2025.110712},
pmid = {41086517},
issn = {1096-0341},
mesh = {*Extracellular Vesicles/virology/metabolism ; *Phosphatidylserines/metabolism ; Humans ; Feces/virology ; Metagenomics ; Gastrointestinal Microbiome ; Virome ; *Viruses/genetics/classification/isolation & purification/metabolism ; },
abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.},
}

*Extracellular Vesicles/virology/metabolism
*Phosphatidylserines/metabolism
Humans
Feces/virology
Metagenomics
Gastrointestinal Microbiome
Virome
*Viruses/genetics/classification/isolation & purification/metabolism

@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The sex related differences in health and Disease: A systematic review of sex-specific gut microbiota and Possible implications for microbial pathogenesis.},
journal = {Microbial pathogenesis},
volume = {209},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Female ; Male ; Sex Factors ; Mice ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Sex Characteristics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
Female
Male
Sex Factors
Mice
Bacteria/classification/genetics/isolation & purification
Biodiversity
Sex Characteristics
High-Throughput Nucleotide Sequencing

@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
mesh = {*Rhizosphere ; *Cadmium/metabolism ; *Microbiota/drug effects ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Iron/metabolism ; Manganese/metabolism ; Oryza/microbiology ; Sulfur/metabolism ; Bacteria ; Environmental Restoration and Remediation/methods ; },
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems (1) iron/manganese oxidation (e.g., feoB): associated with iron-manganese plaque (IP) formation (2) sulfate reduction (e.g., dsrA); linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}

*Rhizosphere
*Cadmium/metabolism
*Microbiota/drug effects
*Soil Pollutants/metabolism
*Soil Microbiology
Iron/metabolism
Manganese/metabolism
Oryza/microbiology
Sulfur/metabolism
Bacteria
Environmental Restoration and Remediation/methods

@article {pmid41015172,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C},
title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122952},
doi = {10.1016/j.envres.2025.122952},
pmid = {41015172},
issn = {1096-0953},
mesh = {*Wetlands ; *Phosphorus/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Carbon/metabolism ; Soil/chemistry ; China ; *Bacteria/metabolism ; Water/analysis ; Droughts ; Microbiota ; },
abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10 % SWC), and high SWC (50 % SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50 % SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50 % SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.},
}

*Wetlands
*Phosphorus/metabolism
*Soil Microbiology
*Nitrogen/metabolism
*Carbon/metabolism
Soil/chemistry
China
*Bacteria/metabolism
Water/analysis
Droughts
Microbiota

@article {pmid41162178,
year = {2025},
author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H},
title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506012},
doi = {10.4014/jmb.2506.06012},
pmid = {41162178},
issn = {1738-8872},
mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.},
}

*Milk, Human/microbiology
Humans
Female
*Microbiota/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
Adult
Metagenome
Sequence Analysis, DNA
Archaea/genetics/classification/isolation & purification
Phylogeny
DNA, Bacterial/genetics

@article {pmid41162143,
year = {2025},
author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R},
title = {Taxonomy is a foundation of marine science, and it is in trouble.},
journal = {Advances in marine biology},
volume = {101},
number = {},
pages = {197-212},
doi = {10.1016/bs.amb.2025.08.003},
pmid = {41162143},
issn = {2162-5875},
mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; },
abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.},
}

*Classification/methods
Animals
Conservation of Natural Resources
*Aquatic Organisms/classification
Biodiversity
*Marine Biology/education
Australia

@article {pmid41161821,
year = {2025},
author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L},
title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {10},
pages = {},
doi = {10.1136/jitc-2025-012444},
pmid = {41161821},
issn = {2051-1426},
mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.

METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.

RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).

CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.},
}

Humans
Male
Female
Prospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Immune Checkpoint Inhibitors/adverse effects/pharmacology
Middle Aged
*Metagenomics/methods
*Microbiota
*Pneumonia/chemically induced/microbiology/diagnosis
Aged
*Lung/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid41160250,
year = {2025},
author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y},
title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {543},
pmid = {41160250},
issn = {1436-3771},
support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; },
mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; },
abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.

MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.

RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.

CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.

CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.

TRIAL REGISTRATION: ITMCTR2024000616.},
}

Humans
Pilot Projects
*Tongue/microbiology
*Microbiota
Adult
Male
Female
*Specimen Handling/methods
Reproducibility of Results
Biofilms

@article {pmid41160143,
year = {2025},
author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM},
title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {183},
pmid = {41160143},
issn = {1572-9699},
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.},
}

*Anti-Bacterial Agents/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Metagenomics/methods
*Bacteria/classification/genetics/drug effects/isolation & purification
Phylogeny
Aquaculture
*Catfishes/microbiology
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests

@article {pmid41159034,
year = {2025},
author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN},
title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655428},
pmid = {41159034},
issn = {1664-3224},
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.

METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.

RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.

DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.},
}

Animals
*Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Autoimmunity
Mice
Mice, Inbred C57BL
*Central Nervous System/immunology/microbiology
*Multiple Sclerosis/immunology/microbiology
Female
Akkermansia
*Verrucomicrobia/immunology
Disease Models, Animal

@article {pmid41157632,
year = {2025},
author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K},
title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101362},
pmid = {41157632},
issn = {1999-4915},
support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; },
mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation & purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; },
abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.},
}

*Ixodes/virology
Animals
Phylogeny
*Genome, Viral
Siberia
*Virome/genetics
Encephalitis Viruses, Tick-Borne/genetics/isolation & purification/classification
Metagenomics
Genomics
Humans
Encephalitis, Tick-Borne/virology

@article {pmid41157620,
year = {2025},
author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ},
title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101349},
pmid = {41157620},
issn = {1999-4915},
support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation & purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; },
abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.},
}

Animals
*Chiroptera/virology
*Feces/virology
*Adenoviridae/genetics/classification/isolation & purification
*Virome
New Mexico/epidemiology
Phylogeny
Dogs
COVID-19/epidemiology/virology
Adenoviridae Infections/veterinary/virology/epidemiology
Metagenomics
SARS-CoV-2
Humans

@article {pmid41157605,
year = {2025},
author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J},
title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101334},
pmid = {41157605},
issn = {1999-4915},
support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; },
mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation & purification ; Genotype ; Genetic Variation ; },
abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.},
}

*Solanum lycopersicum/virology
*Virome/genetics
*Metagenomics
Phylogeny
*Plant Diseases/virology
Genome, Viral
*Plant Viruses/genetics/classification/isolation & purification
Genotype
Genetic Variation

@article {pmid41157584,
year = {2025},
author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS},
title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/v17101312},
pmid = {41157584},
issn = {1999-4915},
support = {202271250010//Parliamentary Amendment from the São Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; },
mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; },
abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.},
}

Animals
*Weevils/virology
Brazil
*Genome, Viral
Saccharum/parasitology
*Virome
Metagenomics
Phylogeny

@article {pmid41156832,
year = {2025},
author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P},
title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102373},
pmid = {41156832},
issn = {2076-2607},
support = {1671/22-03-2023//Green Fund/ ; },
abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.},
}