@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
doi = {10.4014/jmb.2506.06014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}

*Probiotics/pharmacology
*Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Humans
Fermentation
*Feces/microbiology
*Metabolome
Inflammatory Bowel Diseases/microbiology
Bifidobacterium/metabolism
Lactobacillus/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Streptococcus/metabolism

@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02595-0},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}

@article {pmid41306589,
year = {2025},
author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H},
title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1708266},
pmid = {41306589},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation & purification ; *Murinae/microbiology ; },
abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.

METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.

RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.

CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.},
}

Animals
*Enterocytozoon
*Gastrointestinal Microbiome/genetics
Metagenomics
*Microsporidiosis/microbiology/veterinary
Feces/microbiology
Mice
China
Animals, Wild/microbiology
Virome
Bacteria/classification/genetics/isolation & purification
*Murinae/microbiology

@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}

Humans
*Saliva/microbiology
*Obesity/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
*Mouth/microbiology
Male
Female
Biomarkers/analysis
Middle Aged
Adult
Dental Plaque/microbiology
*Bacteria/isolation & purification/classification/genetics
Metagenome

@article {pmid41305529,
year = {2025},
author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W},
title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111508},
pmid = {41305529},
issn = {1999-4915},
support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; },
abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Metagenomics
*Crows/virology
*Gastrointestinal Microbiome
*Virome
*Birds/virology
Genome, Viral
Tibet
Genetic Variation

@article {pmid41305373,
year = {2025},
author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH},
title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111136},
pmid = {41305373},
issn = {2076-0817},
support = {ĐTĐLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation & purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; },
abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
*Diarrhea/microbiology
Male
Female
Feces/microbiology
Child, Preschool
RNA, Ribosomal, 16S/genetics
Prospective Studies
*Bacteria/classification/genetics/isolation & purification
Vietnam
Biodiversity
DNA, Bacterial/genetics
Metagenomics/methods
Southeast Asian People

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41299634,
year = {2025},
author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V},
title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {241},
pmid = {41299634},
issn = {2049-2618},
support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; },
abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.

RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.

CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Adult
Metagenome
Female
Male

@article {pmid41299624,
year = {2025},
author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W},
title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {242},
pmid = {41299624},
issn = {2049-2618},
support = {81825019//National Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.

RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.

CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.},
}

Animals
*Virome/genetics
*Zoonoses/virology/transmission
Metagenomics/methods
Chiroptera/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Africa, Western
Humans
Shrews/virology
Genome, Viral
*Animals, Wild/virology
Disease Reservoirs/virology
*Mammals/virology
Rodentia/virology
*Viral Zoonoses/virology/transmission

@article {pmid41299512,
year = {2025},
author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B},
title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {23},
number = {1},
pages = {154},
pmid = {41299512},
issn = {1477-7827},
mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation & purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.

METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n = 15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n = 13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.

RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p = 0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.

CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.},
}

Humans
Male
Case-Control Studies
*Virome/genetics
Adult
*Semen/virology
Retrospective Studies
*Papillomavirus Infections/virology/complications
*Infertility, Male/virology
*Papillomaviridae/genetics/isolation & purification
*Fertility/physiology
Spermatozoa/virology
Human Papillomavirus Viruses

@article {pmid41298564,
year = {2025},
author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP},
title = {Laser-assisted microbial culturomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10614},
pmid = {41298564},
issn = {2041-1723},
support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Biofilms/growth & development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification/growth & development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; },
abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.},
}

Biofilms/growth & development
Humans
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification/growth & development
*Lasers
Dental Plaque/microbiology
Bioprinting/methods
Metagenomics/methods

@article {pmid41298409,
year = {2025},
author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS},
title = {National-scale biogeography and function of river and stream bacterial biofilm communities.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10571},
pmid = {41298409},
issn = {2041-1723},
support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Biofilms/growth & development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; },
abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.},
}

*Biofilms/growth & development
*Rivers/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
England
Ecosystem
Biodiversity
Metagenomics
Metagenome
Microbiota/genetics
Phylogeny

@article {pmid41148242,
year = {2025},
author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R},
title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {72},
number = {4},
pages = {296-312},
doi = {10.1556/030.2025.02725},
pmid = {41148242},
issn = {1588-2640},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases/diagnosis/microbiology ; *Artificial Intelligence ; Machine Learning ; Dysbiosis ; },
abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.},
}

Humans
*Gastrointestinal Microbiome
*Neurodegenerative Diseases/diagnosis/microbiology
*Artificial Intelligence
Machine Learning
Dysbiosis

@article {pmid41118252,
year = {2025},
author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z},
title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {72},
number = {4},
pages = {287-295},
doi = {10.1556/030.2025.02690},
pmid = {41118252},
issn = {1588-2640},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diarrhea/chemically induced/therapy/microbiology ; *Anti-Bacterial Agents/adverse effects ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Dysbiosis/chemically induced/therapy ; Animals ; },
abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Diarrhea/chemically induced/therapy/microbiology
*Anti-Bacterial Agents/adverse effects
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Dysbiosis/chemically induced/therapy
Animals

@article {pmid40783881,
year = {2025},
author = {Maldonado-Gómez, JC and Rincón-Molina, FA and Rincón-Rosales, R and Manzano-Gómez, LA and Gen-Jiménez, A and Rincón-Molina, CI},
title = {Diversity and plant growth-promoting properties of rhizospheric and endophytic bacteria associated with Agave americana.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {4},
pages = {2777-2790},
pmid = {40783881},
issn = {1678-4405},
support = {21914.25-P//Tecnológico Nacional de México/ ; 22004.25-P//Tecnológico Nacional de México/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; *Endophytes/classification/genetics/isolation & purification/metabolism ; *Agave/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; Biodiversity ; Indoleacetic Acids/metabolism ; Plant Growth Regulators/metabolism ; Phylogeny ; Plant Roots/microbiology/growth & development ; Plant Development ; },
abstract = {Plant-microbe interactions play a critical role in maintaining plant health, enhancing soil fertility, and sustaining ecosystem functionality. Agave americana (Asparagales, Asparagaceae, L.), a crassulacean acid metabolism (CAM) species known for its remarkable drought tolerance and diverse industrial uses, represents a valuable model for exploring the ecological and functional dynamics of these associations. This study explores the diversity and functional potential of bacterial communities associated with A. americana and their role in promoting plant growth. A combination of culture-dependent techniques and metagenomic sequencing was employed to isolate and characterize rhizospheric and endophytic bacteria. Prominent bacterial genera identified included Acinetobacter, Bacillus, Rhizobium/Mesorhizobium, and Microbacterium. Metagenomic analyses revealed a high abundance of Actinobacteria, Proteobacteria, and Chloroflexi, highlighting their roles in nutrient cycling and organic matter decomposition. Plant growth-promoting assays demonstrated that Rhizobium sp. 34 A produced significant levels of indole-3-acetic acid (IAA), enhancing nutrient availability and plant growth. Mesorhizobium sp. 28 A had the greatest overall impact, significantly increasing total fresh weight, chlorophyll content, and sugar profiles, surpassing the effects of chemical fertilizers. Furthermore, Bacillus sp. T12C12, in combination with other plant growth-promoting bacteria (PGPB), exhibited the highest nitrogenase activity, as measured through acetylene reduction assays (ARA). These findings suggest that bacterial inoculants can enhance the nutritional and agronomic value of Agave species, which are of significant agro-industrial and food importance, providing a sustainable alternative to chemical fertilizers. This study offers valuable insights into sustainable agricultural practices by leveraging microbial communities to enhance crop productivity and resilience.},
}

*Bacteria/classification/genetics/isolation & purification/metabolism
*Endophytes/classification/genetics/isolation & purification/metabolism
*Agave/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
Biodiversity
Indoleacetic Acids/metabolism
Plant Growth Regulators/metabolism
Phylogeny
Plant Roots/microbiology/growth & development
Plant Development

@article {pmid41298355,
year = {2025},
author = {Holcik, L and von Haeseler, A and Pflug, FG},
title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10523},
pmid = {41298355},
issn = {2041-1723},
mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; },
abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.},
}

*Metagenomics/methods
Humans
Algorithms
*Gastrointestinal Microbiome/genetics
Base Composition/genetics
Colorectal Neoplasms/microbiology
*Metagenome
Bacteria/genetics/classification
Microbiota/genetics

@article {pmid41298327,
year = {2025},
author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70229},
doi = {10.1111/1758-2229.70229},
pmid = {41298327},
issn = {1758-2229},
support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; },
mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; },
abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.},
}

China
*Oil and Gas Fields/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Petroleum/microbiology
Hydrocarbons/metabolism/analysis
*Microbiota
Phylogeny
Metagenomics

@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.

AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.

METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as ≥2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.

RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.

CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}

Humans
Female
*Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging
*Adverse Childhood Experiences
*Gastrointestinal Microbiome
Adult
*Brain/diagnostic imaging/physiopathology
Middle Aged
*Brain-Gut Axis
Magnetic Resonance Imaging
Young Adult
Multiomics

@article {pmid41290854,
year = {2025},
author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R},
title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41955},
pmid = {41290854},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.},
}

*Soil Microbiology
*Bacteria/genetics/classification
*Fungi/genetics/classification
*Soil Pollutants/analysis
Mercury/analysis
Ecosystem
*Microbiota
Soil/chemistry
Metagenomics
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid41164876,
year = {2025},
author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K},
title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {45},
number = {12},
pages = {e594-e607},
doi = {10.1161/ATVBAHA.125.322968},
pmid = {41164876},
issn = {1524-4636},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Plaque, Atherosclerotic ; *Carotid Artery Diseases/immunology/microbiology/diagnostic imaging/blood/genetics/epidemiology ; Biomarkers/blood ; Prospective Studies ; Aged ; China/epidemiology ; *Complement Pathway, Alternative/genetics ; *Inflammation Mediators/blood ; Mendelian Randomization Analysis ; Risk Factors ; Longitudinal Studies ; Complement C3 ; *Inflammation/blood ; },
abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.

METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age±SD, 57.75±5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3×. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.

RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (complement C3; odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.

CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.},
}

Humans
Female
Male
*Gastrointestinal Microbiome
Middle Aged
*Plaque, Atherosclerotic
*Carotid Artery Diseases/immunology/microbiology/diagnostic imaging/blood/genetics/epidemiology
Biomarkers/blood
Prospective Studies
Aged
China/epidemiology
*Complement Pathway, Alternative/genetics
*Inflammation Mediators/blood
Mendelian Randomization Analysis
Risk Factors
Longitudinal Studies
Complement C3
*Inflammation/blood

@article {pmid40816543,
year = {2025},
author = {Amarlapudi, MR and Balasubramaniam, C and Akash, and Singh, H and Yadav, A and Hirikyathanahalli Vishweswaraiah, R and Pradhan, D and Kumar, N and Dhotre, D and Kolte, AP and Hogarehalli Mallappa, R},
title = {Microbiome and antibiotic resistance profile of milk and faeces from cattle in an organized dairy production system.},
journal = {International journal of antimicrobial agents},
volume = {66},
number = {6},
pages = {107590},
doi = {10.1016/j.ijantimicag.2025.107590},
pmid = {40816543},
issn = {1872-7913},
mesh = {Animals ; Cattle ; *Feces/microbiology ; *Milk/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota ; Dairying ; Metagenomics ; Metagenome ; Microbial Sensitivity Tests ; Female ; },
abstract = {Antimicrobial resistance (AMR) represents a critical public health challenge, responsible for over one million fatalities each year. Livestock, particularly dairy cattle, significantly contribute to the AMR crisis due to the extensive use of antibiotics in the animal health sector. This study aimed to characterize the antibiotic resistome of dairy cattle by analyzing their fecal and milk metagenomes. We collected 36 milk and 36 fecal samples from three different organized dairy farms and extracted metagenomic DNA, yielding 2.58 and 2.81 billion total reads contributing 200.4 and 206.5 GB data, respectively. The majority of these reads mapped to bacterial genomes, revealing 37 bacterial phyla within the dairy production system, with greater phylum-level diversity observed in feces compared to milk. The predominant phyla identified were Bacillota (53.3%), Pseudomonadota (24.7%), Bacteroidota (11.0%), and Actinomycetota (8.4%). The most abundant genera found were Clostridium in milk and Bifidobacterium in feces. In total, we identified 290 distinct antibiotic-resistant genes spanning 27 diverse drug classes and 12 resistance mechanisms. The abundance of antibiotic-resistant genes was higher in feces than in milk, with 229 distinct antibiotic-resistant genes found in milk. Overall, aminoglycoside-resistant genes were the most prevalent and abundant in both fecal and milk metagenomes of cattle from organized dairy production systems.},
}

Animals
Cattle
*Feces/microbiology
*Milk/microbiology
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
*Microbiota
Dairying
Metagenomics
Metagenome
Microbial Sensitivity Tests
Female

@article {pmid40622282,
year = {2025},
author = {Ni, Z and Zhou, Y and Chang, M and Xia, T and Zhou, W and Gao, Y},
title = {High-Altitude Impacts on Gut Microbiota: Accelerated Aging and the Urgency for Targeted Health Interventions.},
journal = {High altitude medicine & biology},
volume = {26},
number = {4},
pages = {388-392},
doi = {10.1089/ham.2025.0016},
pmid = {40622282},
issn = {1557-8682},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Altitude ; Adult ; *Aging/physiology ; Male ; Female ; Feces/microbiology ; Middle Aged ; Young Adult ; Bacteroidetes/isolation & purification ; Aged ; Firmicutes/isolation & purification ; },
abstract = {Ni, Zhexin, Yongqiang Zhou, Mingyang Chang, Tiantian Xia, Wei Zhou, and Yue Gao. High-altitude impacts on gut microbiota: Accelerated aging and the urgency for targeted health interventions. High Alt Med Biol. 26:416-423, 2025.-The human gut microbiota is integral to the aging process, and its composition is notably influenced by the unique environmental pressures of high-altitude plateaus, characterized by hypobaric and hypoxic conditions. This study explores the correlation between physiological aging and gut microbiota among high-altitude plateau inhabitants, an essential aspect of health preservation in such regions. We conducted a metagenomic analysis of fecal samples from 105 individuals who migrated to high-altitude areas before the age of 20. Our results demonstrate that advancing age and prolonged high-altitude living significantly modify the gut microbiota, evidenced by reduced diversity and an elevated Firmicutes to Bacteroidetes (F/B) ratio in older subjects. Notably, the abundance of the anti-aging bacterium Akkermansia muciniphila (A. muciniphila) inversely correlates with age, showing a significant decline post the age of 25. A comparative analysis of 2,007 individuals from lower altitudes revealed a similar negative correlation between A. muciniphila and age, with a decline evident from age 38. These findings indicate that the high-altitude plateau environment may accelerate the decline of A. muciniphila by 10 years, underscoring the need for targeted health strategies for high-altitude populations.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Altitude
Adult
*Aging/physiology
Male
Female
Feces/microbiology
Middle Aged
Young Adult
Bacteroidetes/isolation & purification
Aged
Firmicutes/isolation & purification

@article {pmid41290836,
year = {2025},
author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS},
title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41935},
pmid = {41290836},
issn = {2045-2322},
mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.},
}

Animals
*Insemination, Artificial/veterinary/methods
*Semen/microbiology
Swine
Female
Male
Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Metagenomics

@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}

*Geologic Sediments/virology/microbiology
Genome, Viral/genetics
China
Virome/genetics
Metagenomics
Mining
Metagenome
Phylogeny
Ecosystem
Acids
*Host Microbial Interactions

@article {pmid41289388,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2523178122},
doi = {10.1073/pnas.2523178122},
pmid = {41289388},
issn = {1091-6490},
support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; K01DK134840/GF/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; },
abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Goblet Cells/metabolism/physiology
*Germ-Free Life
Female
Humans
*Malnutrition/microbiology
Child

@article {pmid41286929,
year = {2025},
author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM},
title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {401},
pmid = {41286929},
issn = {1474-760X},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; },
abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.},
}

Humans
*Gastrointestinal Microbiome
*Immunotherapy
*Neoplasms/therapy/microbiology
Metagenomics

@article {pmid41286799,
year = {2025},
author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K},
title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {1117},
pmid = {41286799},
issn = {1471-244X},
mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; },
abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.

METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13 years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.

RESULTS: Fifty-three participants (mean age = 10.2 years, SD = 1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M = 2.03, SE = 0.33 vs. 2.86, SE = 0.34), p = 0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M = 70.10, SE = 0.09) than the placebo group (M = 89.72, SE = 0.07), p = 0.04. However, the kefir group self-reported more sleep problems post-intervention (M = 39.81, SE = 0.75 vs. 37.40, SE = 0.65), p = 0.02. For Go/NoGo RT variance, a non-significant interaction (p = 0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.

CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.

ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.

TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.},
}

Humans
Child
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology
Male
Female
*Gastrointestinal Microbiome/physiology
Double-Blind Method
Adolescent
*Kefir
*Sleep
Attention
Severity of Illness Index

@article {pmid41285810,
year = {2025},
author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ},
title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {216},
pmid = {41285810},
issn = {2055-5008},
support = {F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; },
mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; },
abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.},
}

Humans
*Urinary Tract Infections/microbiology/urine/diagnosis
Female
*Microbiota
Biomarkers/urine
Recurrence
Metabolomics
*Urinary Tract/microbiology
Metagenomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Urine/microbiology/chemistry
Adult
Middle Aged
Deoxycholic Acid/urine

@article {pmid41183495,
year = {2025},
author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC},
title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish sauce.},
journal = {Letters in applied microbiology},
volume = {78},
number = {11},
pages = {},
doi = {10.1093/lambio/ovaf128},
pmid = {41183495},
issn = {1472-765X},
support = {112-2313-B-020-017-MY3//National Science and Technology Council of Taiwan/ ; NPUST-KMU-111-P009//National Pingtung University of Science and Technology/ ; },
mesh = {*Biogenic Amines/metabolism/analysis ; Fermentation ; *Enterococcaceae/metabolism/isolation & purification/genetics/classification ; *Fish Products/microbiology/analysis ; *Microbiota ; Animals ; *Fermented Foods/microbiology ; Food Microbiology ; Fishes ; Cadaverine/analysis/metabolism ; },
abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/l) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.},
}

*Biogenic Amines/metabolism/analysis
Fermentation
*Enterococcaceae/metabolism/isolation & purification/genetics/classification
*Fish Products/microbiology/analysis
*Microbiota
Animals
*Fermented Foods/microbiology
Food Microbiology
Fishes
Cadaverine/analysis/metabolism

@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {10},
number = {11},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
support = {R01AG079224-01/NH/NIH HHS/United States ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Mice ; *Genotype ; Mice, Inbred C57BL ; *Apolipoproteins E/genetics ; Feces/microbiology ; Humans ; Sex Factors ; Bacteria/classification/genetics/isolation & purification ; Mice, Transgenic ; Alzheimer Disease/microbiology/genetics ; Dysbiosis/microbiology ; },
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}

Animals
Male
Female
*Gastrointestinal Microbiome/genetics
Mice
*Genotype
Mice, Inbred C57BL
*Apolipoproteins E/genetics
Feces/microbiology
Humans
Sex Factors
Bacteria/classification/genetics/isolation & purification
Mice, Transgenic
Alzheimer Disease/microbiology/genetics
Dysbiosis/microbiology

@article {pmid41081506,
year = {2025},
author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W},
title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.},
journal = {mSphere},
volume = {10},
number = {11},
pages = {e0034825},
doi = {10.1128/msphere.00348-25},
pmid = {41081506},
issn = {2379-5042},
support = {41871198//National Natural Science Foundation of China/ ; 42471292//National Natural Science Foundation of China/ ; XRC-23078//Fuzhou University Reaserch Start-up Project/ ; },
mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Archaea/genetics/classification ; *Bacteria/genetics/classification/drug effects ; Ecosystem ; Fungi/genetics/classification ; Microbiota ; Biodiversity ; Metagenome ; China ; },
abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems. IMPORTANCE Currently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.},
}

*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Metagenomics
Archaea/genetics/classification
*Bacteria/genetics/classification/drug effects
Ecosystem
Fungi/genetics/classification
Microbiota
Biodiversity
Metagenome
China

@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}

Single-Cell Analysis/methods
Symbiosis/genetics
*Amoeba/virology/microbiology/genetics
*Microbiota/genetics
Metagenomics/methods
*Ciliophora/virology/microbiology/genetics
Bacteria/genetics/classification
Genomics/methods
Giant Viruses/genetics
Phylogeny
Viruses/genetics/classification

@article {pmid41282988,
year = {2025},
author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y},
title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20199},
pmid = {41282988},
issn = {2167-8359},
mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Archaea/genetics/isolation & purification ; },
abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.

METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.

RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.

CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.},
}

*Sewage/microbiology/virology
China
*Metagenomics
*Rain
Bacteria/genetics/classification/isolation & purification
*Microbiota
Archaea/genetics/isolation & purification

@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}

*Soil Microbiology
*Metagenome
China
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Metagenomics

@article {pmid41278541,
year = {2025},
author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T},
title = {MeTAline: enabling reproducible and scalable metagenomic analyses.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf158},
pmid = {41278541},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; },
abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.},
}

*Metagenomics/methods
*Software
Metagenome
Microbiota/genetics
Reproducibility of Results
Computational Biology/methods

@article {pmid41278154,
year = {2025},
author = {Zheng, L and Duan, SL and Wang, K},
title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {31},
number = {42},
pages = {113170},
pmid = {41278154},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; },
abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.},
}

Humans
*Gastrointestinal Microbiome/immunology/genetics
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Intestinal Mucosa/microbiology/immunology/pathology
*Crohn Disease/microbiology/therapy/immunology
*Colitis, Ulcerative/microbiology/therapy/immunology
Genetic Predisposition to Disease
Dysbiosis/microbiology/immunology/therapy
*Inflammatory Bowel Diseases/microbiology/therapy
Metagenomics
Animals
Metabolomics
Immunity, Mucosal

@article {pmid41271709,
year = {2025},
author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C},
title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10295},
pmid = {41271709},
issn = {2041-1723},
mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; },
abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.},
}

*Caves/microbiology
*Ecosystem
Carbon Dioxide/metabolism
Metagenome
Geologic Sediments/microbiology
Microbiota/genetics
Hydrogen/metabolism
Metagenomics
*Bacteria/genetics/metabolism/classification
Biodiversity
Carbon Monoxide/metabolism
Biofilms
Gammaproteobacteria/genetics/metabolism

@article {pmid41182235,
year = {2025},
author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E},
title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf247},
pmid = {41182235},
issn = {1751-7370},
support = {12T5622N//FWO/ ; G092619N//FWO/ ; },
mesh = {*Daphnia/microbiology/genetics/physiology ; Animals ; *Epigenesis, Genetic ; *Cyanobacteria/physiology ; DNA Methylation ; *Host Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Stress, Physiological ; Daphnia magna ; },
abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or nontoxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed nontoxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on nontoxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.},
}

*Daphnia/microbiology/genetics/physiology
Animals
*Epigenesis, Genetic
*Cyanobacteria/physiology
DNA Methylation
*Host Microbial Interactions
RNA, Ribosomal, 16S/genetics
*Microbiota
*Stress, Physiological
Daphnia magna

@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {89},
number = {12},
pages = {1931-1939},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; *Stroke/microbiology/mortality ; *Streptococcus anginosus/isolation & purification ; Prognosis ; Saliva/microbiology ; *Dysbiosis/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}

Humans
Male
Female
*Gastrointestinal Microbiome
Aged
Middle Aged
*Stroke/microbiology/mortality
*Streptococcus anginosus/isolation & purification
Prognosis
Saliva/microbiology
*Dysbiosis/microbiology
Aged, 80 and over

@article {pmid41138869,
year = {2025},
author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M},
title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.},
journal = {International journal of biological macromolecules},
volume = {332},
number = {Pt 2},
pages = {148387},
doi = {10.1016/j.ijbiomac.2025.148387},
pmid = {41138869},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/chemistry/pharmacology ; Humans ; *Fatty Acids, Volatile/biosynthesis ; *Selenium/chemistry/pharmacology ; *Nanoparticles/chemistry ; Antioxidants/pharmacology/chemistry ; Caco-2 Cells ; Prebiotics ; },
abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.},
}

*Gastrointestinal Microbiome/drug effects
*Polysaccharides/chemistry/pharmacology
Humans
*Fatty Acids, Volatile/biosynthesis
*Selenium/chemistry/pharmacology
*Nanoparticles/chemistry
Antioxidants/pharmacology/chemistry
Caco-2 Cells
Prebiotics

@article {pmid41138860,
year = {2025},
author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S},
title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107295},
doi = {10.1016/j.mimet.2025.107295},
pmid = {41138860},
issn = {1872-8359},
mesh = {*Oryza/microbiology/chemistry ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/classification/genetics/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Food Microbiology ; Biodiversity ; *Fermented Foods/microbiology ; Phylogeny ; },
abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.},
}

*Oryza/microbiology/chemistry
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
*Fungi/classification/genetics/metabolism/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Food Microbiology
Biodiversity
*Fermented Foods/microbiology
Phylogeny

@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
mesh = {*Metagenomics/methods/trends ; Humans ; *Microbiota/genetics ; *Forensic Sciences/methods ; Bacteria/genetics/classification/isolation & purification ; *Forensic Genetics/methods ; },
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}

*Metagenomics/methods/trends
Humans
*Microbiota/genetics
*Forensic Sciences/methods
Bacteria/genetics/classification/isolation & purification
*Forensic Genetics/methods

@article {pmid41177025,
year = {2025},
author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S},
title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140254},
doi = {10.1016/j.jhazmat.2025.140254},
pmid = {41177025},
issn = {1873-3336},
mesh = {Animals ; *Benzhydryl Compounds/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Phenols/toxicity ; Mice ; Male ; *Cognition/drug effects ; Brain/drug effects/metabolism ; Maze Learning/drug effects ; *Cognitive Dysfunction/chemically induced ; Behavior, Animal/drug effects ; Dysbiosis ; Bisphenol A Compounds ; },
abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.},
}

Animals
*Benzhydryl Compounds/toxicity
*Gastrointestinal Microbiome/drug effects
*Phenols/toxicity
Mice
Male
*Cognition/drug effects
Brain/drug effects/metabolism
Maze Learning/drug effects
*Cognitive Dysfunction/chemically induced
Behavior, Animal/drug effects
Dysbiosis
Bisphenol A Compounds

@article {pmid41175752,
year = {2025},
author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H},
title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140318},
doi = {10.1016/j.jhazmat.2025.140318},
pmid = {41175752},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Heterocyclic Compounds/toxicity ; *Soil Pollutants/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Virulence Factors/genetics ; },
abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.},
}

*Soil Microbiology
*Microbiota/drug effects
*Heterocyclic Compounds/toxicity
*Soil Pollutants/toxicity
Drug Resistance, Microbial/genetics
Bacteria/drug effects/genetics
Virulence Factors/genetics

@article {pmid41172852,
year = {2025},
author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140283},
doi = {10.1016/j.jhazmat.2025.140283},
pmid = {41172852},
issn = {1873-3336},
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Female ; *Animal Feed ; Rumen/microbiology ; Feces/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.},
}

Animals
Cattle
*Gastrointestinal Microbiome
Female
*Animal Feed
Rumen/microbiology
Feces/microbiology
*Carbohydrate Metabolism
*Bacteria/metabolism/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid41135463,
year = {2025},
author = {Zhang, A and Pan, P and Zhou, NY and Li, T},
title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140176},
doi = {10.1016/j.jhazmat.2025.140176},
pmid = {41135463},
issn = {1873-3336},
mesh = {*Benzophenones/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Wastewater/microbiology ; *Sunscreening Agents/metabolism ; *Microbial Consortia ; Bacteria/metabolism/genetics ; },
abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.},
}

*Benzophenones/metabolism
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Wastewater/microbiology
*Sunscreening Agents/metabolism
*Microbial Consortia
Bacteria/metabolism/genetics

@article {pmid41130000,
year = {2025},
author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z},
title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140201},
doi = {10.1016/j.jhazmat.2025.140201},
pmid = {41130000},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects/genetics ; Trimethoprim/pharmacology ; Nitrogen/metabolism ; Lincomycin/pharmacology ; Carbon/metabolism ; *Genes, Bacterial ; Sulfur/metabolism ; Drug Resistance, Microbial/genetics ; *Water Microbiology ; *Bacteria/genetics/drug effects/metabolism ; },
abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.},
}

*Anti-Bacterial Agents/pharmacology/toxicity
*Water Pollutants, Chemical/toxicity
*Microbiota/drug effects/genetics
Trimethoprim/pharmacology
Nitrogen/metabolism
Lincomycin/pharmacology
Carbon/metabolism
*Genes, Bacterial
Sulfur/metabolism
Drug Resistance, Microbial/genetics
*Water Microbiology
*Bacteria/genetics/drug effects/metabolism

@article {pmid41110291,
year = {2025},
author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M},
title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109874},
doi = {10.1016/j.envint.2025.109874},
pmid = {41110291},
issn = {1873-6750},
mesh = {Animals ; *Copper/toxicity ; *Spodoptera/physiology/drug effects ; Risk Assessment ; *Metal Nanoparticles/toxicity ; Oxidative Stress/drug effects ; Gastrointestinal Microbiome/drug effects ; Nanoparticles/toxicity ; },
abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.},
}

Animals
*Copper/toxicity
*Spodoptera/physiology/drug effects
Risk Assessment
*Metal Nanoparticles/toxicity
Oxidative Stress/drug effects
Gastrointestinal Microbiome/drug effects
Nanoparticles/toxicity

@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
mesh = {Animals ; Chickens ; *Air Microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Farms ; *DNA/analysis ; Bacteria/genetics ; Metagenomics ; },
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}

Animals
Chickens
*Air Microbiology
Microbiota
*Drug Resistance, Microbial/genetics
Farms
*DNA/analysis
Bacteria/genetics
Metagenomics

@article {pmid41086989,
year = {2026},
author = {Zheng, L and Yao, L and Zhu, B and Chen, S and Qian, J and Liu, S and Zhao, J and Chen, Z and Xiang, S and Xie, Z and Zhu, J and Wang, S and Wu, K and Chen, J and Zhang, S and Lu, X},
title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.},
journal = {Journal of affective disorders},
volume = {394},
number = {Pt A},
pages = {120399},
doi = {10.1016/j.jad.2025.120399},
pmid = {41086989},
issn = {1573-2517},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Adolescent ; *Bipolar Disorder/microbiology ; Male ; Female ; Child ; Phenotype ; Feces/microbiology ; Archaea/genetics ; Bacteria ; Case-Control Studies ; },
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Adolescent
*Bipolar Disorder/microbiology
Male
Female
Child
Phenotype
Feces/microbiology
Archaea/genetics
Bacteria
Case-Control Studies

@article {pmid40910191,
year = {2025},
author = {Yehezkel-Cortes, AM and Ruiz-Ordaz, N and Galíndez-Mayer, J and González-Juárez, S and Gómez-Murcia, V},
title = {Modeling and simulation of a modified Ludzack-Ettinger wastewater treatment bioprocess based on the concept of multifunctional microbiota.},
journal = {Environmental technology},
volume = {46},
number = {28},
pages = {5680-5694},
doi = {10.1080/09593330.2025.2551907},
pmid = {40910191},
issn = {1479-487X},
mesh = {*Wastewater/microbiology ; *Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism/analysis ; Biological Oxygen Demand Analysis ; Models, Theoretical ; Biomass ; },
abstract = {This research investigates the behavior of key components within aerobic and anoxic bioreactors in Biological Nitrogen Removal (BNR) bioprocesses. A mathematical model based on the Modified Ludzack-Ettinger (MLE) configuration is proposed. The model comprises an ensemble of ten differential equations derived from mass balances in the MLE system, complemented with a set of biokinetic models. To reduce complexity and enhance applicability, the model treats all nitrogen and phosphorus compounds as atomic N and P, and aggregates carbon sources as Chemical Oxygen Demand (COD), eliminating the need for tuning complex compound-specific parameters. The model was calibrated and validated using analytical determinations of nitrogen, phosphorus, COD, dissolved oxygen, and biomass concentrations from experiments conducted with synthetic wastewater in aerobic and anoxic reactors. Complementing this, a metagenomic study characterized the diversity and relative abundance of taxonomic groups involved in nitrogen and phosphorus metabolism within the microbial communities. Utilizing biokinetic and stoichiometric parameters for the entire microbiota, the model can be solved for both transient and steady-state conditions across a range of operational variables. It enables the estimation of bioprocess resilience following disturbances and the subsequent recovery time to a new steady state. A one-at-a-time (OAT) sensitivity analysis identified the parameters most significantly affecting state variables. The experimental results confirm the model's validity and reliability in simulating BNR processes.},
}

*Wastewater/microbiology
*Bioreactors/microbiology
*Waste Disposal, Fluid/methods
*Microbiota
Nitrogen/metabolism
Phosphorus/metabolism/analysis
Biological Oxygen Demand Analysis
Models, Theoretical
Biomass

@article {pmid40553742,
year = {2025},
author = {Aharoni-Frutkoff, Y and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole Food Diet Induces Remission in Children and Young Adults With Mild to Moderate Crohn's Disease and Is More Tolerable Than Exclusive Enteral Nutrition: A Randomized Controlled Trial.},
journal = {Gastroenterology},
volume = {169},
number = {7},
pages = {1462-1474.e2},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
mesh = {Humans ; *Crohn Disease/diet therapy/microbiology/diagnosis/blood/therapy ; Male ; Female ; Adolescent ; *Enteral Nutrition/adverse effects/methods ; Young Adult ; Remission Induction ; Adult ; Child ; Treatment Outcome ; Gastrointestinal Microbiome ; Severity of Illness Index ; Feces/microbiology ; Leukocyte L1 Antigen Complex/blood ; C-Reactive Protein/metabolism ; Blood Sedimentation ; Time Factors ; *Diet, Healthy/adverse effects ; },
abstract = {BACKGROUND & AIMS: Tasty&Healthy (T&H) is a whole food diet for Crohn's disease (CD) that excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized controlled trial comparing tolerability and effectiveness of T&H vs exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naïve mild to moderate CD and aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires, and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Noninvasive index, calprotectin, C-reactive protein, and erythrocyte sedimentation rate. Fecal microbiome was analyzed by metagenomics at baseline, week 4, and week 8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (n = 41 T&H, n = 42 EEN; mean ± SD age, 14.5 ± 3.7 years), 88% tolerated T&H vs 52% for EEN (adjusted odds ratio [aOR], 7.7; 95% CI, 2.4-25; P < .001). Calprotectin, C-reactive protein, and erythrocyte sedimentation rate decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of the T&H group vs 38% of the EEN group (aOR, 2.5; 95% CI, 0.98-6.3; P = .1; per-protocol: 67% vs 76%; P = .47). Calprotectin <250 μg/g was achieved in 34% vs 33% (aOR, 0.97; 95% CI, 0.37-2.6; P = .84) and Mucosal-Inflammation Noninvasive index score <8 in 44% vs 31% (aOR, 1.8; 95% CI, 0.7-4.5; P = .33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week 4 and week 8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q < .001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild to moderate CD, while positively affecting the microbiome.

CLINICALTRIALS: gov, Number: NCT04239248.},
}

Humans
*Crohn Disease/diet therapy/microbiology/diagnosis/blood/therapy
Male
Female
Adolescent
*Enteral Nutrition/adverse effects/methods
Young Adult
Remission Induction
Adult
Child
Treatment Outcome
Gastrointestinal Microbiome
Severity of Illness Index
Feces/microbiology
Leukocyte L1 Antigen Complex/blood
C-Reactive Protein/metabolism
Blood Sedimentation
Time Factors
*Diet, Healthy/adverse effects

@article {pmid41269405,
year = {2025},
author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q},
title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {102},
pmid = {41269405},
issn = {1559-0267},
support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; },
abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.},
}

Humans
*Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology
*Skin/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
Precision Medicine
Animals
Dysbiosis
Disease Susceptibility
Probiotics
Cellular Microenvironment/immunology

@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism
Male
Female
*Metabolome
Adult
Middle Aged
*Diet, High-Protein Low-Carbohydrate
*Diet, High-Protein

@article {pmid41267624,
year = {2025},
author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J},
title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70234},
doi = {10.1111/1758-2229.70234},
pmid = {41267624},
issn = {1758-2229},
support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; },
mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; },
abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.},
}

*Eutrophication
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota
RNA, Ribosomal, 16S/genetics
Ecosystem
Metagenomics
Phylogeny

@article {pmid41267035,
year = {2025},
author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z},
title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {236},
pmid = {41267035},
issn = {2049-2618},
support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; },
abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.

RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.

CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Mammals/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Altitude
Tibet
Symbiosis

@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}

*Metagenomics/methods
*Genome, Bacterial
*Metagenome
*Microbiota/genetics
Humans

@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}

Animals
*Enterococcus faecalis/physiology/genetics
Bees/virology/microbiology
*Symbiosis
Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Larva/virology/microbiology
Apoptosis

@article {pmid41151484,
year = {2025},
author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J},
title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.},
journal = {International immunopharmacology},
volume = {167},
number = {},
pages = {115730},
doi = {10.1016/j.intimp.2025.115730},
pmid = {41151484},
issn = {1878-1705},
mesh = {*Melatonin/pharmacology/therapeutic use ; *NF-kappa B/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bronchopulmonary Dysplasia/drug therapy/chemically induced/metabolism/pathology ; *Fatty Acids, Volatile/metabolism ; Mice ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Bleomycin ; Cell Line ; Lung/pathology/drug effects/metabolism ; Male ; },
abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).

METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-κB signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.

RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-κB pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-κB pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-κB activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-κB and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.

CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-κB pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.},
}

*Melatonin/pharmacology/therapeutic use
*NF-kappa B/metabolism
Animals
*Gastrointestinal Microbiome/drug effects
Humans
*Bronchopulmonary Dysplasia/drug therapy/chemically induced/metabolism/pathology
*Fatty Acids, Volatile/metabolism
Mice
Signal Transduction/drug effects
Mice, Inbred C57BL
Disease Models, Animal
Bleomycin
Cell Line
Lung/pathology/drug effects/metabolism
Male

@article {pmid40900671,
year = {2025},
author = {Day, AS and Slater, R and Young, RB and Wheeler, RZ and Marcelino, VR and Maddigan, NK and Forster, SC and Costello, SP and Uylaki, W and Probert, CSJ and Andrews, JM and Yao, CK and Gibson, PR and Bryant, RV},
title = {Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {11},
pages = {3160-3171},
doi = {10.1093/ibd/izaf177},
pmid = {40900671},
issn = {1536-4844},
support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; //Gastrointestinal Society of Australia FICE/ ; //European Crohn's Colitis/ ; //Commonwealth Research Stipend/ ; },
mesh = {Humans ; *Colitis, Ulcerative/diet therapy/metabolism/microbiology ; *Hydrogen Sulfide/metabolism ; Male ; Female ; Adult ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; *Diet ; *Sulfides/metabolism ; Volatile Organic Compounds/analysis ; },
abstract = {BACKGROUND: As a dietary approach to reducing inflammation in ulcerative colitis, the 4-SURE (4 Strategies to Sulfide Reduction) diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulfide (H2S) production in the distal colon. We aimed to perform a deep functional analysis (microbial and metabolomic) of the feces of 28 adults with mild-moderately active ulcerative colitis who adhered to the 4-SURE diet over 8 weeks to explore whether the 4-SURE diet could modulate the intraluminal environment as intended.

METHODS: Fecal samples were collected at week 0 and 8 of dietary intervention, processed and aliquoted. Metagenomic sequencing was undertaken to identify changes in H2S-metabolizing genes, while gas chromatography-mass spectrometry was used to analyze fecal volatile organic compounds and H2S production.

RESULTS: The 4-SURE diet significantly increased alpha diversity between weeks 0 and 8. By random forest plot classifier, the abundance of taxonomic groups comprising known H2S-producing genera were markedly lower at week 8, specifically Odoribacter and Peptostreptococcaceae, and were of highest importance in discriminating between before- and after-diet samples. The capacity for bacterial H2S metabolism was altered with diet, with differences in 12 of 67 analyzed sulfur-metabolizing genes identified. H2S production and indole, a specific marker of protein fermentation, were significantly decreased due to the diet.

CONCLUSIONS: Here, we demonstrate that the objectives of the 4-SURE diet were fulfilled. This application of deep functional analysis to a dietary intervention study is novel and highlights an exemplar framework for including microbial and metabolomic biomarkers of pathogenic relevance in the analysis of therapeutic diet strategies. (Australian New Zealand Clinical Trials Registry, Number: ACTRN12619000063112).},
}

Humans
*Colitis, Ulcerative/diet therapy/metabolism/microbiology
*Hydrogen Sulfide/metabolism
Male
Female
Adult
Feces/microbiology/chemistry
Middle Aged
*Gastrointestinal Microbiome
*Diet
*Sulfides/metabolism
Volatile Organic Compounds/analysis

@article {pmid40038232,
year = {2025},
author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M},
title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {6},
pages = {5326-5344},
pmid = {40038232},
issn = {1867-1314},
support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; *Geotrichum/physiology/classification ; Mice ; Mice, Inbred BALB C ; },
abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.},
}

Animals
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
*Geotrichum/physiology/classification
Mice
Mice, Inbred BALB C

@article {pmid39441337,
year = {2025},
author = {Shi, J and Lei, Y and Li, Z and Jia, L and He, P and Cheng, Q and Zhang, Z and Lei, Z},
title = {Alteration of Cecal Microbiota by Antimicrobial Peptides Enhances the Rational and Efficient Utilization of Nutrients in Holstein Bulls.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {6},
pages = {4491-4507},
pmid = {39441337},
issn = {1867-1314},
support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GSSLCSX-2020-1//the local funding/ ; },
mesh = {Animals ; *Cecum/microbiology/metabolism ; Cattle/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Antimicrobial Peptides/pharmacology/administration & dosage ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation & purification ; *Nutrients/metabolism ; Dietary Supplements/analysis ; },
abstract = {We previously observed that supplementation with antimicrobial peptides facilitated the average daily weight gain, net meat, and carcass weights of Holstein bulls. To expand our knowledge of the possible impact of antimicrobial peptides on cecum microbiota, further investigations were conducted. In this study, 18 castrated Holstein bulls with insignificant weight differences and 10 months of age were split randomly into two groups. The control group (CK) was fed a basic diet, whereas the antimicrobial peptide group (AP) was supplemented with 8 g of antimicrobial peptides for 270 days. After slaughter, metagenomic and metabolomic sequencing analyses were performed on the cecum contents. The results showed significantly higher levels of amylase, cellulase, protease, and lipase in the CK than in the AP group (P ≤ 0.05). The levels of β-glucosidase and xylanase (P ≤ 0.05), and acetic and propionic acids (P ≤ 0.01), were considerably elevated in the AP than in the CK group. The metagenome showed variations between the two groups only at the bacterial level, and 3258 bacteria with differences were annotated. A total of 138 differential abundant genes (P < 0.05) were identified in the CAZyme map, with 65 genes more abundant in the cecum of the AP group and 48 genes more abundant in the cecum of the CK group. Metabolomic analysis identified 68 differentially expressed metabolites. Conjoint analysis of microorganisms and metabolites revealed that Lactobacillus had the greatest impact on metabolites in the AP group and Brumimicrobium in the CK group. The advantageous strains of the AP group Firmicutes bacterium CAG:110 exhibited a strong symbiotic relationship with urodeoxycholic acid and hyodeoxycholic acid. This study identified the classification characteristics, functions, metabolites, and interactions of cecal microbiota with metabolites that contribute to host growth performance. Antimicrobial peptides affect the cecal microorganisms, making the use of nutrients more efficient. The utilization of hemicellulose in the cecum of ruminants may contribute more than cellulose to their production performance.},
}

Animals
*Cecum/microbiology/metabolism
Cattle/microbiology
Male
*Gastrointestinal Microbiome/drug effects
*Antimicrobial Peptides/pharmacology/administration & dosage
Animal Feed/analysis
Bacteria/classification/genetics/isolation & purification
*Nutrients/metabolism
Dietary Supplements/analysis

@article {pmid39313703,
year = {2025},
author = {Talib, N and Mohamad, NE and Ho, CL and Masarudin, MJ and Alitheen, NB},
title = {Modulatory Effects of Isolated Lactobacillus paracasei from Malaysian Water Kefir Grains on the Intestinal Barrier and Gut Microbiota in Diabetic Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {6},
pages = {4224-4236},
pmid = {39313703},
issn = {1867-1314},
support = {FRGS/1/2017/SKK10/UPM/02/4 and FRGS-MRSA/1/2018/SKK10/UPM/02/1//Ministry of Education, Government of Malaysia./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Kefir/microbiology ; *Lacticaseibacillus paracasei/isolation & purification/physiology ; *Probiotics/administration & dosage ; Male ; *Diabetes Mellitus, Type 2/microbiology ; Malaysia ; *Diabetes Mellitus, Experimental/microbiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {Type 2 diabetes (T2DM) is one of the four major types of non-communicable diseases that have become a global health concern. Water kefir is a product of a brown sugar solution fermented with kefir grains which comprises around 30 microbial species in its grains. Water kefir possesses a wide range of health benefits, including anti-hyperlipidemic effects, and reduces hypertension and blood glucose levels in animal models. Reportedly, consuming water kefir containing probiotics may enhance the intestinal barrier and positively influence the composition of the intestinal microflora. The present study aimed to evaluate the regulatory effects of Lactobacillus paracasei isolated from Malaysian water kefir grains (MWKG) on the alterations of intestinal barrier and gut microbiota in diabetic mice via histopathological analysis of the distal colon and 16S rRNA gene sequencing on fecal microbiome. Results indicated that the administration of isolated Lactobacillus paracasei from MWKG to diabetic mice ameliorated the dominant probiotic phyla in the gut microbiota. Results showed that lower dose (LD) and high dose (HD) treatments of the isolated Lactobacillus paracasei could significantly reduce inflammatory cell infiltration in the distal colon of diabetic mice. The treatments revealed a significant decrease in the relative abundance of Firmicutes in the gut, 0.27 ± 0.06% for LD and 0.34 ± 0.04% for HD, compared to untreated (UN) diabetic mice, 0.40 ± 0.02%. These results suggest that L. paracasei isolated from MWKG could serve as a potential dietary supplement against intestinal inflammation and modify gut microbiota composition in patients with T2DM.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Kefir/microbiology
*Lacticaseibacillus paracasei/isolation & purification/physiology
*Probiotics/administration & dosage
Male
*Diabetes Mellitus, Type 2/microbiology
Malaysia
*Diabetes Mellitus, Experimental/microbiology
Mice, Inbred C57BL
Bacteria/classification/isolation & purification/genetics

@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {1OT3HL14715//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Humans ; *Asthma/genetics/microbiology/epidemiology/ethnology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Adult ; Female ; Male ; Middle Aged ; Obesity/microbiology/genetics/complications ; Cross-Sectional Studies ; United States/epidemiology ; Feces/microbiology ; Risk Factors ; Body Mass Index ; White ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}

Humans
*Asthma/genetics/microbiology/epidemiology/ethnology
*Gastrointestinal Microbiome/genetics
*Hispanic or Latino/genetics
Adult
Female
Male
Middle Aged
Obesity/microbiology/genetics/complications
Cross-Sectional Studies
United States/epidemiology
Feces/microbiology
Risk Factors
Body Mass Index
White

@article {pmid41262425,
year = {2025},
author = {Morelle-Hungría, E},
title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {244},
doi = {10.12688/openreseurope.21126.2},
pmid = {41262425},
issn = {2732-5121},
abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.},
}

@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics/methods
Proteomics/methods
*Snails/microbiology
Phylogeny
Metagenome
Multiomics

@article {pmid41192424,
year = {2025},
author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z},
title = {Assessment of enzyme diversity in the fermented food microbiome.},
journal = {Cell systems},
volume = {16},
number = {11},
pages = {101430},
doi = {10.1016/j.cels.2025.101430},
pmid = {41192424},
issn = {2405-4720},
mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Fermentation ; Food Microbiology/methods ; Metagenome/genetics ; Machine Learning ; *Enzymes/genetics/metabolism ; },
abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.},
}

*Fermented Foods/microbiology
*Microbiota/genetics
Fermentation
Food Microbiology/methods
Metagenome/genetics
Machine Learning
*Enzymes/genetics/metabolism

@article {pmid41259660,
year = {2025},
author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A},
title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf620},
pmid = {41259660},
issn = {1367-4811},
abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.

RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.

raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.},
}

@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}

Humans
*Dental Caries/microbiology
Adolescent
Male
*Microbiota/genetics
Female
Child
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
DMF Index
Reference Values

@article {pmid41258552,
year = {2025},
author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK},
title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1354},
pmid = {41258552},
issn = {1573-2959},
support = {core funding//Zoological Survey of India/ ; },
mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; },
abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.},
}

*Environmental Monitoring/methods
Public Health
*Eukaryota/classification/genetics
RNA, Ribosomal, 18S/genetics
Metagenomics
*Metagenome
Biodiversity

@article {pmid41258100,
year = {2025},
author = {Wang, C and Zheng, R and Sun, C},
title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10134},
pmid = {41258100},
issn = {2041-1723},
mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; },
abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.},
}

*Seawater/virology/microbiology
*Viruses/genetics/classification/metabolism
Virome/genetics
Metagenomics
Geologic Sediments/virology/microbiology
*Host Microbial Interactions
Genome, Viral
Oceans and Seas
Ecosystem
RNA Viruses/genetics/classification
Microbiota
Biodiversity
Carbon Cycle
Transcriptome

@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetic Neuropathies/microbiology/therapy/metabolism
*Dysbiosis/microbiology
Animals
Probiotics/therapeutic use

@article {pmid41250240,
year = {2025},
author = {Gwak, HJ and Rho, M},
title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {393},
pmid = {41250240},
issn = {1474-760X},
support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; },
abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Electron Transport Complex IV/genetics
*Software
Biodiversity
Large Language Models

@article {pmid41218604,
year = {2025},
author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O},
title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {6},
number = {11},
pages = {102426},
doi = {10.1016/j.xcrm.2025.102426},
pmid = {41218604},
issn = {2666-3791},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/pharmacology/administration & dosage ; Adult ; Biomarkers/metabolism ; Young Adult ; Prednisolone/pharmacology/administration & dosage ; Healthy Volunteers ; Insulin Resistance ; Methylprednisolone/pharmacology/analogs & derivatives/administration & dosage ; Feces/microbiology ; },
abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Glucocorticoids/pharmacology/administration & dosage
Adult
Biomarkers/metabolism
Young Adult
Prednisolone/pharmacology/administration & dosage
Healthy Volunteers
Insulin Resistance
Methylprednisolone/pharmacology/analogs & derivatives/administration & dosage
Feces/microbiology

@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; },
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}

Humans
*Microbiota
*Software
*Gastrointestinal Microbiome
Algorithms
*Computational Biology/methods
*Metagenomics/methods
Phylogeny

@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {6},
number = {11},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
mesh = {Humans ; *Microbiota/genetics ; *Oral Health ; *Esophageal Squamous Cell Carcinoma/microbiology ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Risk Factors ; *Mouth/microbiology ; Aged ; Saliva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}

Humans
*Microbiota/genetics
*Oral Health
*Esophageal Squamous Cell Carcinoma/microbiology
*Esophageal Neoplasms/microbiology
Male
Female
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Middle Aged
Risk Factors
*Mouth/microbiology
Aged
Saliva/microbiology
Bacteria/genetics/classification

@article {pmid41189540,
year = {2026},
author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S},
title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70066},
doi = {10.1111/1755-0998.70066},
pmid = {41189540},
issn = {1755-0998},
support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project ‛Ocean DNA'/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; },
abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
*Biodiversity
Internet
*DNA, Environmental/genetics
*Computational Biology/methods
*Aquatic Organisms/classification/genetics
*Metagenomics/methods
*Software

@article {pmid41168956,
year = {2026},
author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD},
title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70069},
doi = {10.1111/1755-0998.70069},
pmid = {41168956},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; },
abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Fishes/genetics/classification
*Electron Transport Complex IV/genetics
Benchmarking
*Metagenomics/methods
*DNA, Environmental/genetics
Cluster Analysis
Biodiversity
Computational Biology/methods

@article {pmid41104935,
year = {2025},
author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF},
title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {11},
pages = {e0150825},
doi = {10.1128/aem.01508-25},
pmid = {41104935},
issn = {1098-5336},
support = {https://doi.org/10.54499/2022.11916.BD//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04292/2020, http://doi.org/10.54499/UIDP/04292/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04046/2020, http://doi.org/10.54499/UIDP/04046/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/UIDB/00329/2020, http://doi.org/10.54499/UIDP/00329/2020//Fundação para a Ciência e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0121/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Seafood/microbiology/analysis ; *Gastrointestinal Microbiome ; *Sea Bream/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Portugal ; },
abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.},
}

Animals
*Seafood/microbiology/analysis
*Gastrointestinal Microbiome
*Sea Bream/microbiology
*Bacteria/classification/genetics/isolation & purification
Machine Learning
Portugal

@article {pmid41094135,
year = {2025},
author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ},
title = {Isolation, engineering and ecology of temperate phages from the human gut.},
journal = {Nature},
volume = {647},
number = {8090},
pages = {698-705},
pmid = {41094135},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Prophages/genetics/isolation & purification/classification/physiology ; *Bacteriophages/isolation & purification/genetics/classification/physiology ; Caco-2 Cells ; Lysogeny/genetics ; Virus Activation ; *Bacteria/virology/isolation & purification ; Genome, Viral/genetics ; },
abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Prophages/genetics/isolation & purification/classification/physiology
*Bacteriophages/isolation & purification/genetics/classification/physiology
Caco-2 Cells
Lysogeny/genetics
Virus Activation
*Bacteria/virology/isolation & purification
Genome, Viral/genetics

@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {60},
number = {12},
pages = {1481-1495},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Male ; Middle Aged ; Female ; *Neuroendocrine Tumors/microbiology/pathology ; *Gastrointestinal Microbiome ; *Gastric Mucosa/microbiology/pathology ; Adult ; Aged ; *Autoimmune Diseases/microbiology/pathology/complications ; *Gastritis, Atrophic/microbiology ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Stomach Neoplasms/microbiology ; Metabolome ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}

Humans
Male
Middle Aged
Female
*Neuroendocrine Tumors/microbiology/pathology
*Gastrointestinal Microbiome
*Gastric Mucosa/microbiology/pathology
Adult
Aged
*Autoimmune Diseases/microbiology/pathology/complications
*Gastritis, Atrophic/microbiology
Case-Control Studies
RNA, Ribosomal, 16S/genetics
*Stomach Neoplasms/microbiology
Metabolome

@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}

Animals
Freezing
*Amphibians/physiology
Skin/microbiology
Cold Temperature
Acclimatization
Microbiota

@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {5},
number = {11},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
mesh = {Humans ; *Metagenomics/methods ; *Benchmarking/methods ; Microbiota/genetics ; Genome, Human/genetics ; *Viruses/genetics ; Polymorphism, Single Nucleotide/genetics ; Metagenome ; },
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}

Humans
*Metagenomics/methods
*Benchmarking/methods
Microbiota/genetics
Genome, Human/genetics
*Viruses/genetics
Polymorphism, Single Nucleotide/genetics
Metagenome

@article {pmid41147731,
year = {2025},
author = {Jones, JA and Moczek, AP and Newton, ILG},
title = {The dung beetle microbiome complements host metabolism and nutrition.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0117225},
doi = {10.1128/msystems.01172-25},
pmid = {41147731},
issn = {2379-5077},
support = {2243725//National Science Foundation/ ; 1901680//National Science Foundation/ ; 2141416//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism ; *Microbiota ; Amino Acids/metabolism/biosynthesis ; Bacteria/genetics/metabolism/classification ; },
abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.},
}

Animals
*Coleoptera/microbiology/metabolism
*Microbiota
Amino Acids/metabolism/biosynthesis
Bacteria/genetics/metabolism/classification

@article {pmid41128541,
year = {2025},
author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S},
title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0095625},
doi = {10.1128/msystems.00956-25},
pmid = {41128541},
issn = {2379-5077},
support = {2023YFD1702200//National Key Research and Development Program of China/ ; 42277357//National Natural Science Foundation of China/ ; 2022RC3057//Science and technology innovation Program of Hunan Province/ ; YLS-2025-ZY02039//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Composting/methods ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Hot Temperature ; Soil Microbiology ; Metagenome ; Metagenomics ; Transcriptome ; },
abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.

IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.},
}

*Composting/methods
*Microbiota
*Bacteria/metabolism/genetics/classification
Hot Temperature
Soil Microbiology
Metagenome
Metagenomics
Transcriptome

@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
support = {№ 0088-2024-0009//IDB RAS Government basic research program/ ; № 0088-2024-0009//IDB RAS Government basic research program/ ; },
mesh = {*Symbiosis ; Animals ; *Porifera/microbiology/physiology/classification ; *Microbiota ; Arctic Regions ; Phylogeny ; Sympatry ; Bacteria/classification/genetics ; Gammaproteobacteria/genetics/classification ; },
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}

*Symbiosis
Animals
*Porifera/microbiology/physiology/classification
*Microbiota
Arctic Regions
Phylogeny
Sympatry
Bacteria/classification/genetics
Gammaproteobacteria/genetics/classification

@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0164224},
doi = {10.1128/msystems.01642-24},
pmid = {41055333},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; *Machine Learning ; Microbiota/genetics ; Humans ; Metagenome ; },
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}

*Metagenomics/methods
*Machine Learning
Microbiota/genetics
Humans
Metagenome

@article {pmid41014671,
year = {2025},
author = {Zhao, Y and Song, T and Ren, P and Wu, X and Luo, Q and Xie, J and Lai, H and Li, X and Wen, Y and Liao, X and Zhou, J},
title = {Integrating metagenomics, lipidomics and proteomics to explore the effect and mechanism of ginsenoside Rb1 on atherosclerosis co-depression disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157301},
doi = {10.1016/j.phymed.2025.157301},
pmid = {41014671},
issn = {1618-095X},
mesh = {Animals ; *Ginsenosides/pharmacology ; *Atherosclerosis/drug therapy/complications ; Proteomics ; Mice ; Lipidomics ; Male ; Gastrointestinal Microbiome/drug effects ; *Depression/drug therapy/complications ; Metagenomics ; Lipid Metabolism/drug effects ; Panax/chemistry ; Mice, Inbred C57BL ; Diet, High-Fat ; Disease Models, Animal ; },
abstract = {BACKGROUND: The comorbidity of atherosclerosis (AS) and depression presents a significant clinical challenge. Its pathogenesis entails complex abnormalities in inflammatory responses, lipid metabolism, and gut microbiota homeostasis. Ginsenoside Rb1 (GRb1)-a bioactive compound derived from the dried roots of Panax ginseng (Araliaceae)-demonstrates anti-inflammatory, antioxidant, lipid-lowering, and neuroprotective properties. However, GRb1's therapeutic potential and underlying mechanisms in AS co-depression remain inadequately characterized.

PURPOSE: This study aims to elucidate the mechanism of GRb1 in AS co-depression disease, identify potential therapeutic targets, and thereby develop novel therapeutic strategies for this condition.

METHODS: An AS co-depression comorbidity model was established using ApoE[⁻/⁻] mice fed a high-fat diet and subjected to chronic restraint stress. To evaluate GRb1's therapeutic efficacy, we assessed serum lipid profiles, performed aortic Oil Red O staining, and conducted behavioral tests for depressive-like phenotypes. Furthermore, we employed an integrated multi-omics approach-combining metagenomics, targeted lipid metabolomics, and proteomics-to identify key alterations in gut microbiota, lipid metabolites, and proteins, with subsequent correlation analysis. Key differential proteins and associated pathways identified through multi-omics were validated using both in vivo (AS co-depression mouse model) and in vitro (HT22 cells) experiments. Finally, GRb1's effects on ferroptosis and specific signaling pathways (CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/GPX4) were examined via Western blotting, immunofluorescence, and transmission electron microscopy in both mouse tissues and HT22 cells.

RESULTS: Proteobacteria, Helicobacter, and Helicobacter_typhlonius represent significant intestinal microbiota components. Their primary differential lipids include phosphatidylethanolamine (PE), phosphatidylcholine (PC), and lysophosphatidylcholine (LPC), while key differential proteins encompass CD44, Gls2, and Snrpf. Notably, a strong correlation exists among Helicobacter_typhlonius, PE, and CD44. GRb1 modulates PE metabolic dysregulation by reducing the relative abundance of Helicobacter_typhlonius, thereby inhibiting lipid peroxidation and ameliorating oxidative stress. Furthermore, GRb1 suppresses the CD44/Gls2 axis, ACSL4/LPCAT3/ALOX15 pathway, and activates the SLC7A11/GPX4-mediated ferroptosis pathway, thereby exerting its anti-AS co-depression effects through these multi-target mechanisms.

CONCLUSION: GRb1 regulates the intestinal microbiota, abnormal lipid metabolism, modulates protein function, inhibits lipid peroxidation, improves oxidative stress, inhibits ferroptosis, regulates the CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/ GPX4 signaling pathways, and prevents the progression of AS co-depression disease.},
}

Animals
*Ginsenosides/pharmacology
*Atherosclerosis/drug therapy/complications
Proteomics
Mice
Lipidomics
Male
Gastrointestinal Microbiome/drug effects
*Depression/drug therapy/complications
Metagenomics
Lipid Metabolism/drug effects
Panax/chemistry
Mice, Inbred C57BL
Diet, High-Fat
Disease Models, Animal

@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth & development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}

Animals
*Soil Microbiology
*Cucumis sativus/parasitology/growth & development
*Microbiota/drug effects
*Nitrification/drug effects
Plant Roots/parasitology
*Tylenchoidea
Soil/chemistry
*Plant Diseases/parasitology/prevention & control
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Brachyura/chemistry

@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41243436,
year = {2025},
author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A},
title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2576657},
doi = {10.1080/19490976.2025.2576657},
pmid = {41243436},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; },
abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Multiple Sclerosis/metabolism/microbiology/therapy
*Lipid Metabolism
Animals

@article {pmid41110566,
year = {2025},
author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y},
title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.},
journal = {International journal of biological macromolecules},
volume = {331},
number = {Pt 2},
pages = {148390},
doi = {10.1016/j.ijbiomac.2025.148390},
pmid = {41110566},
issn = {1879-0003},
mesh = {*Dendrobium/chemistry ; *Polysaccharides/metabolism/chemistry/pharmacokinetics/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; *Intestinal Absorption ; Male ; *Intestinal Mucosa/metabolism ; Bacteroides/metabolism/genetics ; *Intestines/microbiology ; },
abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.},
}

*Dendrobium/chemistry
*Polysaccharides/metabolism/chemistry/pharmacokinetics/pharmacology
Gastrointestinal Microbiome/drug effects
Animals
*Intestinal Absorption
Male
*Intestinal Mucosa/metabolism
Bacteroides/metabolism/genetics
*Intestines/microbiology

@article {pmid40626932,
year = {2025},
author = {Talwar, C and Guria, A and Hoffman, K and Biest, S and Jimenez, P and Kommagani, R},
title = {A role for gut mycobiome and altered fungal-bacterial interactions in women with endometriosis†.},
journal = {Biology of reproduction},
volume = {113},
number = {5},
pages = {1155-1169},
doi = {10.1093/biolre/ioaf148},
pmid = {40626932},
issn = {1529-7268},
mesh = {Female ; *Endometriosis/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; *Mycobiome/physiology ; Animals ; Mice ; *Fungi/physiology ; *Bacteria ; Adult ; },
abstract = {Endometriosis is a gynecological pathology prevalent in reproductive age women in which the inner uterine wall (endometrium) grows outside as ectopic lesions. The inflammation resulting from these growing implants closely associates with disease severity, causing chronic pain and infertility. Emerging studies have found altered bacterial communities in endometriosis and a causal role for gut bacteria in endometriosis. However, the role of the gut mycobiome, i.e., the fungal component of the microbiome in endometriosis is a current knowledge gap that needs to be addressed. In this study, utilizing the stool samples from women with endometriosis, we found that the gut fungal communities are altered in women with endometriosis. By integrating the bacterial microbiota and studying the co-occurring relationships between fungi and bacteria, we identify the altered fungal-bacterial community interactions in endometriosis. In addition, we studied the microbial interactions with the host and identified the bacterial taxa as "microbiome-associated host genetic variants" in endometriosis. By determining their interactions with fungi, we highlight the fungal taxa as underlying regulators of the disease. Experimentally, we demonstrate that the progression of endometriosis in mice is significantly impeded by the depletion of fungi, revealing a role for the gut mycobiome in endometriosis. Our results highlight the positive- and negative-co-abundance relationships shared between bacteria-fungi, bacteria-bacteria, and microbes-host in the disease pathogenesis. These findings could help shape future experimental research on bacterial-fungal interactions, which should be considered when designing microbiome-based therapies that use antifungal agents.},
}

Female
*Endometriosis/microbiology
*Gastrointestinal Microbiome/physiology
Humans
*Mycobiome/physiology
Animals
Mice
*Fungi/physiology
*Bacteria
Adult

@article {pmid39617895,
year = {2024},
author = {Perrin, AJ and Dorrell, RG},
title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {279},
pmid = {39617895},
issn = {1741-7007},
mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; },
abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.},
}

*Climate Change
*Eukaryota/physiology
*Ecosystem
Biodiversity