@article {pmid42992196,
year = {2026},
author = {Pacheco-Valenciana, A and Milke, F and Wienhausen, G and Garcia, SL},
title = {Baltic Sea microbial cohorts exhibit catabolic specialization and anabolic interdependencies across environmental gradients.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21847},
pmid = {42992196},
issn = {2167-8359},
mesh = {*Seawater/microbiology ; *Microbiota/genetics ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Environment ; Oceans and Seas ; Salinity ; },
abstract = {Microbial communities are structured by environmental gradients and metabolic interactions, making the study of co-occurring populations essential for understanding emergent ecological properties. Here, we investigated microbial cohorts, recurring groups of co-occurring microorganisms shaped by shared environmental preferences and potential biotic interactions, across the Baltic Sea, a well-characterized region where microbial community composition and metabolic functions vary strongly across salinity, temperature, and oxygen gradients. We used a genomic catalog consisting of 701 species-representative genomes to recruit reads from 112 metagenomes and infer cohort structure, environmental distributions, and metabolic potential. We identified nine microbial cohorts that showed strong associations with environmental gradients, indicating deterministic assembly. Cohorts differed markedly in their genomic and functional characteristics. The most abundant and prevalent cohorts were dominated by taxa with smaller, streamlined genomes, whereas the low-oxygen cohort contained larger genomes and contributed disproportionately to nitrogen and sulfur transformations. Within cohorts, different biosynthetic pathways were consistently associated with different taxonomic groups. Complete amino acid biosynthesis pathways were common among individual genomes, whereas complete B-vitamin biosynthesis pathways were rare. The six biosynthetic pathways with the lowest completeness were consistently associated with different taxonomic groups across all cohorts, with individual genomes encoding only a subset of these pathways, consistent with widespread metabolic interdependencies. Together, these results show that Baltic Sea microbial cohorts are ecologically structured assemblages whose genomic repertoires reflect catabolic specialization and anabolic interdependencies.},
}

*Seawater/microbiology
*Microbiota/genetics
*Bacteria/metabolism/genetics/classification
Metagenome
Environment
Oceans and Seas
Salinity

@article {pmid42993179,
year = {2026},
author = {Scranton, C and Obergh, V and Goforth, M and Ravi, K and Jayakrishna, P and Khan, A and Boone, SA and Gerba, CP and Ijaz, MK and Xu, FY and Krupp, K and Madhivanan, P and Cooper, KK},
title = {Characterization of household microbiomes from three unique cities around the world.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
pmid = {42993179},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; Humans ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; India ; United Arab Emirates ; Cities ; United States ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; Family Characteristics ; Metagenome ; Housing ; },
abstract = {Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes to which a person is exposed every day in their home. Exploring household microbiomes in different countries around the world increases our understanding of the impact human behaviour might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome from ten locations around the house in ten different houses from three countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, USA). There was a significant difference in alpha diversity between the three countries (ANOVA, P<0.001), with homes in Mysuru, India, showing significantly higher bacterial diversity compared with those in Tucson, AZ, USA and Dubai, UAE. Beta diversity analysis of the homes found that bacterial communities differed significantly by geographic location [permutational multivariate analysis of variance (PERMANOVA), P=0.001] and, within cities, by household location (PERMANOVA, P=0.001), with geographic location explaining 5.3% and household location explaining 7.3% of variation. Household location was a strong driver of diversity within each of the three cities individually, accounting for 14-18% of microbiome variation. The highest levels of bacterial diversity across the three cities were found underneath the toilet rim and within bathroom and kitchen sinks. A core microbiome of classes Actinomycetota and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations. Many bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetota (e.g. genera Brevibacterium, Mycolicibacterium and Rhodococcus), Pseudomonadota (e.g. genera Acinetobacter, Moraxella, Paracoccus and Pseudomonas) and Bacillota (genus Streptococcus), which is comparable to previous studies. The household microbiome is variable across different locations within the house and on a global scale. Factors such as human activity, cultural practices, climate and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose.},
}

*Microbiota/genetics
Humans
Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
India
United Arab Emirates
Cities
United States
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing
Family Characteristics
Metagenome
Housing

@article {pmid42995195,
year = {2026},
author = {Qi, W and Chen, X and Guo, H and Zhu, S and Zhou, Z and Xu, L and Yan, Q and Gu, FF and Liu, JX and Sun, HZ},
title = {Microbiome-derived proline dipeptides underpin improved nitrogen utilization efficiency in dairy cattle.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42995195},
issn = {2041-1723},
support = {no. 32322077//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle ; *Dipeptides/metabolism ; *Nitrogen/metabolism ; *Proline/metabolism ; Rumen/microbiology/metabolism ; Female ; Fermentation ; Milk/metabolism ; *Microbiota ; Dairying ; Metagenomics ; Metabolomics ; *Gastrointestinal Microbiome ; },
abstract = {Dairy production is constrained by low nitrogen utilization efficiency (NUE; milk N/intake N), leading to nitrogen losses and environmental pollution. Although the rumen microbiome is central to nitrogen turnover, the role of small peptides, a critical nitrogen pool, remains poorly understood. Here, we constructed a genome-resolved atlas of predicted small-peptide metabolism and integrated high-performance chemical isotope-labeling metabolomics with metagenomics in 30 dairy cows. Among 349 detected small peptides, proline-containing dipeptides were associated with higher NUE, together with an S15 peptidyl-peptidase with Xaa-Pro dipeptide-generating activity. In vitro rumen fermentation, metatranscriptomics and targeted quantification showed that proline-dipeptide accumulation coincided with transcriptional patterns consistent with nitrogen assimilation and amino acid biosynthesis. Bacterial incubation and heterologous expression confirmed that S15.001 hydrolyzed Xaa-Pro substrates. These findings identify a microbial proline-dipeptide axis associated with NUE and provide a basis for precision nutrition strategies targeting ruminal peptide metabolism.},
}

Animals
Cattle
*Dipeptides/metabolism
*Nitrogen/metabolism
*Proline/metabolism
Rumen/microbiology/metabolism
Female
Fermentation
Milk/metabolism
*Microbiota
Dairying
Metagenomics
Metabolomics
*Gastrointestinal Microbiome

@article {pmid42995511,
year = {2026},
author = {Zhang, Q and Han, Z and Yin, B and Zhang, S and Lu, Y and Zang, Y and Zhou, X and Li, T and Salem, H and Zhang, Y},
title = {Microbial Life-History Strategies Shape Biocrusts Soil Multifunctionality Responses to Multi-Year Snow-Cover Change.},
journal = {Global change biology},
volume = {32},
number = {11},
pages = {},
doi = {10.1111/gcb.71194},
pmid = {42995511},
issn = {1365-2486},
support = {42471073//National Natural Science Foundation of China/ ; 2025B03021//Xinjiang Uygur Autonomous Region Key Research and Development Program/ ; 2022D01D083//Key Project of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; 42161144004//the Key Project of the UNEP-NSFC International Cooperation Project/ ; },
mesh = {*Snow ; *Soil Microbiology ; *Lichens/physiology ; *Cyanobacteria/physiology ; Seasons ; *Microbiota ; Soil/chemistry ; },
abstract = {Winter snowfall is a critical water source sustaining the survival and ecological functioning of biocrusts in desert ecosystems, yet how different biocrust types respond to altered snow-depth conditions and maintain soil multifunctionality (SMF) through microbial community adjustments and life-history strategies remains poorly understood. Based on a field snow-manipulation experiment, we compared SMF responses in cyanobacterial and lichen crusts under snow removal, ambient snow, and double-snow treatments across different treatment-duration categories and further explored the underlying microbial regulatory mechanisms. Cyanobacterial and lichen crusts exhibited contrasting SMF responses to altered snow conditions. SMF significantly increased in cyanobacterial crusts in the short-term treatment plots (1 year), whereas lichen crusts showed a significant decline only under short-term snow removal. In the medium- and long-term treatment plots (8 and 11 years), differences in SMF between altered-snow and ambient-snow conditions were reduced for both biocrust types. Lichen crusts mainly showed increases in bacterial and total microbial diversity under snow manipulation, whereas significant diversity responses in cyanobacterial crusts were primarily associated with fungi. Microbial life-history strategies showed clear but biocrust-type-specific associations with SMF. Random forest and structural equation modeling (SEM) analyses indicated that SMF in cyanobacterial crusts was strongly constrained by the S strategy, while Y-related metabolic pathways were positively associated with SMF; in contrast, SMF in lichen crusts was positively associated with the A strategy but negatively associated with the S strategy. Soil physicochemical properties also played an important role in regulating SMF, but their effects and interactions with microbial attributes differed between the two biocrust types. Overall, this study demonstrates that altered snow conditions regulate biocrust SMF through the coupling of soil environmental changes and microbial functional responses, with the underlying regulatory pathways strongly dependent on biocrust type.},
}

*Snow
*Soil Microbiology
*Lichens/physiology
*Cyanobacteria/physiology
Seasons
*Microbiota
Soil/chemistry

@article {pmid42827198,
year = {2026},
author = {Tawk, C and El Mouali, Y and Huang, KD and Valkiers, S and Heidrich, V and Gronow, A and Osbelt, L and Rapp, J and Link, H and Segata, N and Typas, A and Strowig, T},
title = {Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut.},
journal = {Nature microbiology},
volume = {11},
number = {11},
pages = {3074-3089},
pmid = {42827198},
issn = {2058-5276},
support = {390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/15-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1343/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Enterobacteriaceae/physiology/genetics ; Animals ; *Diet ; Mice ; *Gastrointestinal Microbiome/physiology ; *Bacteroidaceae/genetics/growth & development/isolation & purification/physiology/classification ; Metagenome ; Feces/microbiology ; Prevotella ; },
abstract = {Healthy human gut microbiota is dominated by Bacteroidaceae in industrialized populations and by Prevotellaceae in those with traditional lifestyles, but diet alone is insufficient to explain this dominance of different Bacteroidota. Here we screened 94 dietary components in synthetic gut communities and find that these two bacterial families compete for overlapping nutritional niches. Segatella copri, a key member of Prevotellaceae-rich communities, outcompeted Bacteroidaceae when preferred polysaccharides such as arabinan were available, but this advantage depended on community composition, particularly the presence of Enterobacteriaceae. Metatranscriptomics and targeted metabolomics further revealed that Enterobacteriaceae synergized with dietary components to promote Segatella dominance in human and mouse gut communities. These interactions were validated by using multiple E. coli and Segatella isolates. Analyses of global metagenomes also showed a positive correlation between Segatella-rich non-industrialized microbiomes and Enterobacteriaceae abundance. Our results establish an ecosystem-level dynamic interplay between dietary components and key gut commensals that favour the dominance of Prevotellaceae.},
}

Humans
*Enterobacteriaceae/physiology/genetics
Animals
*Diet
Mice
*Gastrointestinal Microbiome/physiology
*Bacteroidaceae/genetics/growth & development/isolation & purification/physiology/classification
Metagenome
Feces/microbiology
Prevotella

@article {pmid42897202,
year = {2026},
author = {Zelik, L and Levin, Y and Sawaed, J and Telpaz, S and Zigdon, M and Nuriel-Ohayon, M and Rubin, E and Gordon, A and Mogilevski, Z and Yehuda, A and Awad, A and Shaalan, H and Ben-Simon, S and Modilevsky, S and Naama, M and Dalvi, J and Moadi, L and Kurtz, M and Perez, S and Turjeman, S and Werbner, M and Khatib, S and Koren, O and Erez, A and Bel, S},
title = {Disentangling microbiota-dependent and -independent impacts of antibiotics on host physiology.},
journal = {Nature microbiology},
volume = {11},
number = {11},
pages = {3268-3284},
pmid = {42897202},
issn = {2058-5276},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Circadian Rhythm/drug effects ; Germ-Free Life ; Colon/drug effects/microbiology ; Mice, Inbred C57BL ; Vancomycin/pharmacology ; *Microbiota/drug effects ; Glucose/metabolism ; Metagenomics ; Gene Expression Profiling ; },
abstract = {Antibiotics are believed to affect host physiology by altering the gut microbiota. However, it remains unclear which effects of antibiotics are microbiota dependent and which are microbiota independent. Here we present a resource encompassing host and microbiota responses to antibiotic treatment and a computational tool with which to analyse them. Metagenomic and transcriptomic analyses of conventional and germ-free mice revealed that antibiotic administration routes and their combinations affect host and microbiota responses. We developed CompoRes-a computational tool that distinguishes the microbiota-independent impact of antibiotic-induced perturbations, revealing that antibiotics directly impact host physiology. We found that diurnal expression of major histocompatibility complex class II in the mouse colon is controlled by glucose via feeding. This pattern was lost during antibiotic treatment as vancomycin altered feeding behaviour in a microbiota-independent and evolutionarily conserved manner. Together, our study establishes a direct, non-microbial pathway by which antibiotics reshape host immunity and circadian physiology.},
}

Animals
*Anti-Bacterial Agents/pharmacology/administration & dosage
Mice
*Gastrointestinal Microbiome/drug effects
Circadian Rhythm/drug effects
Germ-Free Life
Colon/drug effects/microbiology
Mice, Inbred C57BL
Vancomycin/pharmacology
*Microbiota/drug effects
Glucose/metabolism
Metagenomics
Gene Expression Profiling

@article {pmid42957850,
year = {2026},
author = {Roux, S and Neri, U and Bushnell, B and Fremin, BJ and George, NA and Gophna, U and Hug, LA and Camargo, AP and Wu, D and Ivanova, N and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems.},
journal = {Nature microbiology},
volume = {11},
number = {11},
pages = {3253-3267},
pmid = {42957850},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; ERC-AdG 787514//European Commission (EC)/ ; 2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
mesh = {*Metagenomics/methods ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Bacteriophages/genetics ; *Metagenome ; *Ecosystem ; Microbiota/genetics ; *CRISPR-Cas Systems ; Bacteria/genetics/virology ; Plasmids/genetics ; Viruses/genetics ; },
abstract = {Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth's biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus-host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes.},
}

*Metagenomics/methods
*Clustered Regularly Interspaced Short Palindromic Repeats/genetics
Bacteriophages/genetics
*Metagenome
*Ecosystem
Microbiota/genetics
*CRISPR-Cas Systems
Bacteria/genetics/virology
Plasmids/genetics
Viruses/genetics

@article {pmid42986536,
year = {2026},
author = {Jemaà, M and Chebbi, A},
title = {Microbiota-driven of chromosomal instability in colorectal cancer.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42986536},
issn = {1573-4978},
support = {FABA2025-MJ//Foundation Abdelwaheb Ben Ayed (FABA), Tunisia/ ; PEJC2025-D1P12//Tunisian Ministry of Higher Education and Scientific Research MES/ ; PEJC2025-D5P02//Tunisian Ministry of Higher Education and Scientific Research MES/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology ; *Chromosomal Instability/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Reactive Oxygen Species/metabolism ; Dysbiosis/genetics/microbiology ; Peptides ; Polyketides ; },
abstract = {Colorectal cancer (CRC) is the third most common malignancy worldwide and the second leading cause of cancer-related death, and chromosomal instability (CIN) underlies 65-70% of sporadic cases. Here we review the evidence that the gut microbiota acts as an environmental instigator of CIN through three mechanistically intertwined routes. The first is direct genotoxicity: pks+ Escherichia coli produce colibactin, which alkylates deoxyadenosine to form DNA interstrand cross-links whose repair generates double-strand break intermediates and the mutational signatures SBS88 and ID18; transient exposure of primary colon epithelial cells suffices to provoke chromosomal aberrations and malignant transformation. The second is community-level dysbiosis: the oncomicrobial community subtypes OCS2 and OCS3 are enriched in CIN-positive tumours and carry the reactive oxygen species-related signature SBS18, while at strain-level resolution Fusobacterium nucleatum subspecies animalis clade C2 shows the strongest association with the tumour niche, and Parvimonas micra and Peptostreptococcus stomatis contribute through WNT/β-catenin activation and Th17-skewed immunity. The third, advanced here as a working framework rather than an established mechanism, is the microbiota-induced bystander effect (MIBE), in which microbiota-driven para-inflammation creates a milieu rich in reactive oxygen and nitrogen species and inflammatory cytokines that damages DNA in neighbouring epithelial cells and establishes a field of cancerization. We integrate these routes into a three-stage model (initiation, propagation, perpetuation) linking microbial exposure to APC, KRAS and TP53 alterations, discuss translation towards risk stratification, faecal metagenomic diagnosis, OCS-based prognostication and targeted prevention, and delineate the limitations of the current evidence.},
}

Humans
*Colorectal Neoplasms/genetics/microbiology
*Chromosomal Instability/genetics
*Gastrointestinal Microbiome/genetics
Animals
Reactive Oxygen Species/metabolism
Dysbiosis/genetics/microbiology
Peptides
Polyketides

@article {pmid42986679,
year = {2026},
author = {Maloney, S and Folliard, NT and Karakaya, G and Waters, SM},
title = {Importance of rumen ciliated protozoa and current research techniques for their analysis.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {11},
pages = {},
pmid = {42986679},
issn = {1465-2080},
mesh = {Animals ; *Rumen/parasitology/microbiology ; *Ciliophora/genetics/classification/isolation & purification/physiology ; Ruminants/parasitology ; Methane/metabolism ; Microbiota ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Rumen protozoa are an integral component of the ruminant foregut microbiome, with a profound influence on feed digestion, microbial ecosystem dynamics and enteric methane emissions. Although they represent only a small proportion of species richness, protozoa contribute significantly to microbial biomass and functions in fibre degradation, volatile fatty acid production, microbial protein turnover, pH modulation and hydrogen-mediated methanogenesis. In addition to highlighting their importance to rumen function, this review summarizes classical and contemporary methodologies for enumerating, identifying and characterizing rumen protozoa. These methodologies include microscopy, fluorescent staining, flow cytometry and molecular approaches such as 18S rRNA, ITS and 28S rRNA amplicon sequencing. All major rRNA primers widely used over the last two decades are catalogued and their coverage is evaluated against current databases, highlighting the superior taxonomic resolution provided by ITS-based markers. The integration of single-cell sequencing and long-read platforms with multi-omics approaches (metagenomics, metatranscriptomics and metaproteomics) and advanced bioinformatic tools enables genome-resolved and functionally informed analyses of rumen protozoa. Methodological advances are integrated with functional insights to elucidate the contributions of protozoa to rumen ecology, feed efficiency and methane output. Key research gaps are also identified, including the need for improved microscopy techniques, automated image analysis, optimized cryopreservation protocols and robust culturing systems. This synthesis provides a comprehensive resource for researchers in microbial ecology, animal nutrition and environmental science, enabling precise protozoal profiling and informing strategies to enhance livestock productivity while mitigating environmental impacts.},
}

Animals
*Rumen/parasitology/microbiology
*Ciliophora/genetics/classification/isolation & purification/physiology
Ruminants/parasitology
Methane/metabolism
Microbiota
RNA, Ribosomal, 18S/genetics

@article {pmid42988813,
year = {2026},
author = {Brown, CL and Rumi, MA and McDaniel, L and Maile-Moskowitz, A and Sein, J and Nguyen, L and Choi, M and Hindi, F and Mullet, JI and Emon, M and Moumi, N and Blair, MF and Davis, BC and Rao, J and Baffoe-Bonnie, A and Vikesland, P and Pruden, A and Zhang, L},
title = {Resistance indicators in sewage microbiota mirror clinical antibiotic use with temporal lag linked to host.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42988813},
issn = {2041-1723},
support = {2125798//National Science Foundation (NSF)/ ; 1545756//National Science Foundation (NSF)/ ; },
mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Humans ; *Microbiota/drug effects/genetics ; *Bacteria/genetics/drug effects ; Enterobacteriaceae/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Seasons ; Wastewater/microbiology ; },
abstract = {Wastewater-based surveillance (WBS) offers a promising window into community pathogens but extending it to antibiotic resistance (AR) is complicated by ecological and physical processes within sewer systems. The epidemiological meaning of antibiotic resistance gene (ARG) abundances in sewage remains unclear because signals reflect both human-derived inputs and in-sewer microbial dynamics. Using a unique 5-year dataset of outpatient antibiotic prescriptions and a yearlong, twice-weekly metagenomic survey of a single wastewater treatment plant, we differentiate associations between sewage-borne antibiotic-resistant bacteria and community antibiotic use. We find that ARGs linked to Enterobacteriaceae track closely with antibiotic usage, while those associated with ecologically-distinct Pseudomonadaceae show lagged correlations of 1-3 months. Nested statistical modeling further links Pseudomonas MAG dynamics with lagged sulfamethoxazole/trimethoprim use after accounting for sewage characteristics and seasonality. Our results demonstrate that WBS can capture local patterns of epidemiologically relevant AR when microbial ecological factors shaping sewage signals are considered.},
}

*Sewage/microbiology
*Anti-Bacterial Agents/pharmacology/therapeutic use
Humans
*Microbiota/drug effects/genetics
*Bacteria/genetics/drug effects
Enterobacteriaceae/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Seasons
Wastewater/microbiology

@article {pmid42989112,
year = {2026},
author = {Liang, T and Cao, L and Cheng, A and Cheng, Z and Ou, D and Gu, X and Song, X and Yang, J},
title = {Effects of monensin residues on microbial community and the attenuation of antibiotic resistance genes during chicken manure composting.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989112},
issn = {1471-2180},
support = {Leading Group 2024-12//Guizhou University Natural Sciences Project for Special Post/ ; BQW2025-004//Hundred Thousand Million Leading Talent Teams of Guizhou Province/ ; QKHJC-MS-2025-586//Guizhou Provincial Basic Research Program (Natural Science)/ ; },
mesh = {*Monensin/pharmacology ; Animals ; *Manure/microbiology ; Chickens ; *Composting/methods ; *Bacteria/genetics/drug effects/classification ; *Genes, Bacterial ; *Microbiota/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics/drug effects ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; },
abstract = {BACKGROUND: Monensin is a polyether ionophore antibiotic widely used to prevent coccidiosis and inhibit Gram-positive bacteria. Composting is widely regarded as an effective strategy for reducing the abundance of antibiotic resistance genes (ARGs) in manure. However, the long half-life of monensin may impose selective pressure on ARG attenuation, while its potential ecological risk remains unclear.

RESULTS: In this study, metagenomics was used to analyze the effect of monensin residues on microbial communities during chicken manure composting (1, 15, and 45 days). Results showed that monensin significantly changed the structure of microbial communities during composting. It suppressed functional groups within Firmicutes and Actinobacteria, particularly the genera Bacillus and Streptomyces. Simultaneously, it promoted tolerant taxa, including Proteobacteria and the genus Halomonas. The results of qPCR for six representative ARGs (aadD, ant2-I, sul1, sul2, tetZ, and tetL) revealed that monensin could reduce the attenuation of some ARGs. Furthermore, monensin increased the abundance of several mobile genetic elements (MGEs) during the middle composting phase, especially the integron intI1 and transposase tnpA. Co-occurrence network analysis suggested stronger associations among specific ARGs, MGEs, and tolerant bacteria under monensin exposure, indicating a potential increase risk of ARG dissemination.

CONCLUSIONS: Monensin may suppress ARGs attenuation during manure composting by changing microbial communities and increasing the potential risk of ARG dissemination via MGEs. This study will provide a theoretical basis for the treatment of livestock waste and ecological risk assessment of monensin.},
}

*Monensin/pharmacology
Animals
*Manure/microbiology
Chickens
*Composting/methods
*Bacteria/genetics/drug effects/classification
*Genes, Bacterial
*Microbiota/drug effects/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics/drug effects
Metagenomics
Drug Resistance, Bacterial/genetics
Soil Microbiology

@article {pmid42989121,
year = {2026},
author = {Suchet, M and Pannetier, P and Danion, M and Braunbeck, T and Alves Gomes, P and Cachot, J and Bellec, L},
title = {Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989121},
issn = {1471-2180},
support = {ANSES-22-EST-050//French National Research Program for Environmental and Occupational Health of ANSES/ ; },
mesh = {Animals ; *Oncorhynchus mykiss/microbiology ; *Gills/microbiology/drug effects ; *Triazoles/toxicity/adverse effects/pharmacology ; *Fluorides/adverse effects/pharmacology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology/drug effects ; *Water Pollutants, Chemical ; Skin Microbiome ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Fluoride and tebuconazole are two compounds widely used in industrial processes and agriculture, respectively, and are regularly detected in surface waters. Therefore, there is an urgent need to characterise their effects on aquatic organisms. In this context, adopting a holistic approach that integrates the host and its associated microbiomes, the holobiont, is particularly relevant. In this study, rainbow trout were exposed from 6 days post-fertilisation for 7 months to a daily 7-hour pulsed regime of two concentrations of fluoride (6.8 or 24.7 mg/L, representing environmentally relevant levels for contaminated hotspots), to tebuconazole (51.7 µg/L, within the range of agricultural runoff peaks), or maintained in control conditions. At the end of the exposure period, gill, skin and intestine microbiomes were characterized using 16 S rRNA gene metabarcoding.

RESULTS: Fluoride and tebuconazole significantly affected the bacterial alpha diversity in gill and skin tissues. Beta diversity was significantly affected in gill and skin tissues, whereas the intestine exhibited a weak overall treatment effect without significant pairwise differences. If compared to the control treatment, fluoride exposure altered microbial co-occurrence networks, affecting bacterial interconnections in a tissue-specific manner, with reduced interconnections in gills and increased interconnections in skin and intestine compared to the control treatment. Shifts in taxonomical composition were present following exposure to both pollutants, and notably increases in the relative abundance of fish pathogens such as Candidatus Piscichlamydia, Flavobacterium and Aeromonas were observed. Increased abundance of Aeromonas (gill, skin and intestine) and Acidovorax (gill), along with functional predictions, suggested potential alterations in pathways related to antibiotic resistance, warranting further metagenomic investigation.

CONCLUSIONS: These results highlight alterations of gill, skin and intestine microbiomes in the rainbow trout following chronic exposure to fluoride and tebuconazole, with distinct and tissue-specific microbial responses. Beyond taxonomical shifts, the observed alterations of bacterial co-occurrence networks, enrichment of pathogenic bacteria, and antibiotic-resistant taxa, indicating that the fish microbiome is a sensitive bioindicator of chronical chemical stress. Whether these microbial shifts translate into adverse host health outcomes remains to be investigated in future studies.},
}

Animals
*Oncorhynchus mykiss/microbiology
*Gills/microbiology/drug effects
*Triazoles/toxicity/adverse effects/pharmacology
*Fluorides/adverse effects/pharmacology
*Bacteria/classification/genetics/drug effects/isolation & purification
*Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Skin/microbiology/drug effects
*Water Pollutants, Chemical
Skin Microbiome
*Microbiota/drug effects

@article {pmid42989617,
year = {2026},
author = {Sommer, AJ and Kiudeliene, E and Lauridsen, M and Torre, A and Fagan, A and Skieceviciene, J and Jonasson, E and Obolewicz, H and Sikaroodi, M and Kupcinskas, J and Khoruts, A and Gillevet, PM and Bajaj, JS},
title = {Gut‒liver‒brain axis signature of cirrhosis-related cognitive impairment is consistent across multi-national cohorts.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2753908},
doi = {10.1080/19490976.2026.2753908},
pmid = {42989617},
issn = {1949-0984},
mesh = {Humans ; Female ; Middle Aged ; *Liver Cirrhosis/complications/microbiology/psychology ; Male ; Hepatic Encephalopathy/microbiology ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/etiology/physiopathology ; *Liver/metabolism/microbiology/physiopathology ; *Brain/metabolism/physiopathology ; Lithuania ; Mexico ; United States ; Denmark ; Feces/microbiology ; Aged ; Cohort Studies ; Bacteria/classification/isolation & purification/genetics ; *Brain-Gut Axis ; },
abstract = {Cognitive impairment in cirrhosis is associated with an altered gut‒liver‒brain axis, but geographic variations in diet and clinical practices may limit generalizability. We investigated consistency of microbial signatures for cirrhosis-related cognitive impairment across four countries. We enrolled outpatients with cirrhosis from USA, Denmark, Lithuania, and Mexico who underwent Psychometric Hepatic Encephalopathy Score (PHES) testing for covert hepatic encephalopathy (CHE), and stool shotgun metagenomic sequencing. Taxonomic and functional associations with PHES were evaluated after adjustment for MELD, country, demographics, sex, proton pump inhibitor (PPI), lactulose, and rifaximin use. We enrolled 221 patients (median age 58 y, 57.9% men, median MELD 12). Cognitive performance varied by country despite adjustment for clinical covariates. Lithuania demonstrated greater microbial richness and better cognition despite higher MELD, accompanied by distinct dietary patterns including greater yogurt and tea consumption. In the entire cohort, increasing MELD was associated with reduced microbial richness and depletion of commensals. Worse PHES performance, however, showed a distinct microbiome signature with increased Streptococcus abundance independent of MELD, country, PPI use, and HE therapies. Twenty-two microbial pathways were associated with PHES, mostly related to amino-acid biosynthesis and nitrogen metabolism. Of these, ornithine degradation and heme B biosynthesis II were uniquely enriched with worse PHES and CHE, which mapped onto Enterobacteriaceae. We conclude that across four geographically and culturally disparate countries, cirrhosis-related cognitive impairment was associated with consistent microbial compositional and functional alterations distinct from advancing liver disease. These findings support a consistent gut‒liver‒brain axis signature involving oral-gut translocation and altered nitrogen metabolism.},
}

Humans
Female
Middle Aged
*Liver Cirrhosis/complications/microbiology/psychology
Male
Hepatic Encephalopathy/microbiology
*Gastrointestinal Microbiome
*Cognitive Dysfunction/microbiology/etiology/physiopathology
*Liver/metabolism/microbiology/physiopathology
*Brain/metabolism/physiopathology
Lithuania
Mexico
United States
Denmark
Feces/microbiology
Aged
Cohort Studies
Bacteria/classification/isolation & purification/genetics
*Brain-Gut Axis

@article {pmid42244179,
year = {2026},
author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H},
title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.},
journal = {The New phytologist},
volume = {252},
number = {5},
pages = {2070-2087},
doi = {10.1111/nph.71330},
pmid = {42244179},
issn = {1469-8137},
support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; },
mesh = {Seashore ; *Microbiota/genetics ; *Desiccation ; *Glycerophosphates/metabolism ; *Rhodophyta/microbiology/physiology/metabolism ; Symbiosis ; Stress, Physiological ; Adaptation, Physiological ; },
abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.},
}

Seashore
*Microbiota/genetics
*Desiccation
*Glycerophosphates/metabolism
*Rhodophyta/microbiology/physiology/metabolism
Symbiosis
Stress, Physiological
Adaptation, Physiological

@article {pmid42436183,
year = {2026},
author = {Liu, Z and Wu, H and Howe, S and Zuo, B and Tian, Y and Wang, X and Assress, HA and Shang-Lun Lan, R and Mu, C and Xiao, Y and Huang, Y and Looper, M and Tsai, T and Zhao, J},
title = {Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42436183},
issn = {2055-5008},
support = {Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; USDA-ARS 6026-10700-001-000D//USDA/ ; USDA-ARS 6026-10700-001-000D//Food and Nutrition Service/ ; 2023YFE0124400//National Key Research and Development Program of China/ ; 2025-WPY-00-001//the Guangdong Provincial Special Fund Project for Seed Industry Revitalization/ ; },
mesh = {Animals ; *Cell Differentiation ; Signal Transduction ; Swine ; *Goblet Cells/cytology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; *Indoles/metabolism ; Ileum/cytology/metabolism/microbiology ; *Gastrointestinal Microbiome ; Mucin-2/metabolism/genetics ; Cell Proliferation ; Organoids ; },
abstract = {The swine intestinal microbiota dynamically remodels during development and supports gut homeostasis. However, whether stage-specific microbial shifts, are associated with epithelial development remains poorly understood. Here, longitudinal metagenomic profiling of the swine gut microbiome identified Lactiplantibacillus plantarum as a transiently enriched nursery-stage bacterium positively associated with goblet cell numbers. Dietary supplementation with L. plantarum validated this association, showing increased goblet cell numbers and MUC2 expression in the ileum of nursery piglets. Co-culture with porcine ileum organoids further demonstrated that L. plantarum cell-free supernatant promoted ileal organoid growth and goblet cell differentiation. Integrated untargeted metabolomic analyses of ileal samples and bacterial culture supernatants identified indole-3-lactic acid (ILA) as a potential key microbial metabolite from L. plantarum. Mechanistically, ILA promoted intestinal stem cell proliferation and MUC2 expression, accompanied by increased expression of aryl hydrocarbon receptor (AHR) and its downstream target CYP1A1 in ileal organoids. Consistently, activation of AHR using FICZ increased MUC2 expression, whereas inhibition with CH-223191 suppressed MUC2 expression in ileal organoids. Collectively, these findings uncover a L. plantarum-ILA-AHR signaling axis that promotes intestinal goblet cell differentiation, providing mechanistic insight into microbial metabolite-mediated regulation of epithelial homeostasis during post-weaning period in pigs.},
}

Animals
*Cell Differentiation
Signal Transduction
Swine
*Goblet Cells/cytology/metabolism
*Receptors, Aryl Hydrocarbon/metabolism/genetics
*Indoles/metabolism
Ileum/cytology/metabolism/microbiology
*Gastrointestinal Microbiome
Mucin-2/metabolism/genetics
Cell Proliferation
Organoids

@article {pmid42493609,
year = {2026},
author = {Yang, Y and Li, N and Zhou, L and Gong, S and He, Z and Tang, S and Ni, J and Liu, Y and Chan, JWY and Or, BPN and Lam, SP and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Lai, CKC and Scheperjans, F and Wang, J and Huang, B and Wing, YK},
title = {Gut Microbiome in Depression with and without REM Sleep Behavior Disorder.},
journal = {Molecular psychiatry},
volume = {31},
number = {12},
pages = {7208-7218},
pmid = {42493609},
issn = {1476-5578},
support = {18190221//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 05162876//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; C4044-21G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
mesh = {Humans ; *REM Sleep Behavior Disorder/microbiology/metabolism/physiopathology/complications ; Female ; *Major Depressive Disorder/microbiology/physiopathology/metabolism/complications ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Case-Control Studies ; Middle Aged ; Aged ; Dysbiosis ; Depression/microbiology ; Adult ; Feces/microbiology ; },
abstract = {Major depressive disorder (MDD) is a risk factor for neurodegeneration, yet its heterogeneity makes identifying at-risk subtype challenging. Notably, MDD frequently co-occurs with REM sleep behavior disorder (RBD), a specific prodrome of α-synucleinopathy. It remains unclear whether comorbid MDD + RBD reflects a benign antidepressant effect, or higher neurodegenerative risk. Given growing recognition of gut-brain axis in neuropsychiatry, we aimed to delineate microbial signatures of MDD + RBD. We employed a four-group case-control design (N = 420) comprising 124 healthy controls (HC); 80 MDD without RBD features (MDD-only); 82 MDD + RBD; and 134 iRBD without psychiatric disease. All participants underwent clinical evaluation and provided fecal samples for metagenomic sequencing. Random Forest model was used to distinguish MDD + RBD, and further assessed in a validation dataset of 65 participants with MDD + RBD (n = 31) and MDD-only (n = 34). MDD + RBD exhibited prodromal neurodegenerative features, including elevated total likelihood ratio of prodromal Parkinson's Disease, olfactory deficits, and subtle motor signs. The microbial composition in MDD + RBD differed from HC and MDD-only, while resembling iRBD. Taxonomically, MDD + RBD exhibited an iRBD-like dysbiosis (e.g., enriched Akkermansia muciniphila, Ruthenibacterium lactatiformans; depleted Faecalibacterium prausnitzii), alongside depression-associated shifts (e.g., Streptococcus parasanguinis and Actinomyces oris). Functionally, MDD + RBD showed attenuated capacity of B‑vitamin biosynthesis and polysaccharides degradation, mirroring iRBD. The Random Forest machine-learning model distinguished MDD + RBD in older adults from MDD-only with an AUC of 0.73 in cross-validation and 0.79 in the validation dataset. MDD + RBD may represent a biologically distinct depression subtype associated with potential neurodegenerative risk. Gut microbiome provides a candidate approach for potential risk stratification in psychiatric populations.},
}

Humans
*REM Sleep Behavior Disorder/microbiology/metabolism/physiopathology/complications
Female
*Major Depressive Disorder/microbiology/physiopathology/metabolism/complications
*Gastrointestinal Microbiome/physiology/genetics
Male
Case-Control Studies
Middle Aged
Aged
Dysbiosis
Depression/microbiology
Adult
Feces/microbiology

@article {pmid42880389,
year = {2026},
author = {Yang, Z and Zhang, X and Zheng, S and Huang, Y and Wei, X and Zhang, Y},
title = {Gut microbiota remodeling correlates with pentose phosphate pathway activation and steroid hormone biosynthesis dysregulation in polystyrene nanoplastic-induced hepatic lipotoxicity.},
journal = {Chemico-biological interactions},
volume = {440},
number = {},
pages = {112378},
doi = {10.1016/j.cbi.2026.112378},
pmid = {42880389},
issn = {1872-7786},
mesh = {Animals ; Female ; *Pentose Phosphate Pathway/drug effects ; *Liver/drug effects/metabolism/pathology ; *Gastrointestinal Microbiome/drug effects ; *Polystyrenes/toxicity/chemistry ; Rats, Sprague-Dawley ; Rats ; Lipid Metabolism/drug effects ; },
abstract = {Polystyrene nanoplastics (PS-NPs) have been detected in human tissues, but the systemic consequences of chronic oral exposure remain unclear. Female Sprague-Dawley rats received environmentally relevant PS-NP concentrations of 5 or 50 mg/L in drinking water for 42 days. Gut-liver-endocrine interactions were assessed by 16S rRNA sequencing, shotgun metagenomics, fecal metabolomics, hepatic transcriptomics, and biochemical validation of selected nodes. PS-NP exposure caused notable dysregulation of serum and hepatic lipids and produced histopathological damage in the liver. The exposure was also associated with gut dysbiosis dominated by Bacteroidia, along with hepatic glucose-6-phosphate dehydrogenase (G6PD) upregulation and pentose phosphate pathway (PPP) activation, as well as NADPH accumulation. Low-dose exposure was associated with adaptive redox response (elevated hepatic superoxide dismutase (SOD)) and lipid clearance signatures, whereas high-dose exposure correlated with glutathione peroxidase (GSH-PX) depletion, elevated 8-iso-prostaglandin (8-iso-PG), and transcriptomic evidence of mitochondrial impairment and ferroptosis vulnerability. Steroid hormone biosynthesis (SHB) disruption-declining estradiol and rising cortisol-was observed across both doses, with ovarian Cyp19a1/Cyp11a1 downregulation at low dose and additional adrenal Cyp21a2 upregulation at high dose. Multi-omics integration linked Bacteroidia enrichment to the PPP intermediate deoxyribose 5-phosphate and estrogen metabolites. Collectively, these findings outline a Gut Microbiota-PPP-SHB (GMPS) axis as a candidate integrative framework for understanding PS-NP-associated hepatic lipotoxicity. This work offers an integrative resource that identifies candidate pathways and testable hypotheses for future investigation of metabolic risks from chronic nanoplastic exposure.},
}

Animals
Female
*Pentose Phosphate Pathway/drug effects
*Liver/drug effects/metabolism/pathology
*Gastrointestinal Microbiome/drug effects
*Polystyrenes/toxicity/chemistry
Rats, Sprague-Dawley
Rats
Lipid Metabolism/drug effects

@article {pmid42981365,
year = {2026},
author = {Mogire, DB and Neondo, J and Muhonja, C and Awuor, C and Mureithi, D and Ogada, S and Wekesa, TB},
title = {Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362106},
pmid = {42981365},
issn = {1932-6203},
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Kenya ; *Bacteriophages/genetics ; *Soil Microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Ralstonia/virology/genetics ; Phylogeny ; Metagenome ; *Ralstonia solanacearum/virology ; Agriculture ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum species complex is a major constraint in tomato production in Kenya, resulting in yield losses of up to 100% in heavily infested fields. This study used high-throughput shotgun metagenomic sequencing approach to characterize the rhizosphere microbiomes of tomato plants in three of the major production areas in Kenya (Kirinyaga, Kiambu, and Laikipia counties) focusing on detecting Ralstonia phage sequences. Soil samples were collected from the rhizosphere of bacterial wilt-infected tomato plants, and microbial DNA was extracted using a modified phenol-chloroform protocol and sequenced using Illumina NovaSeq platform. Taxonomic profiling revealed diverse microbial communities dominated by Actinobacteria and Proteobacteria. Four Ralstonia species were confirmed (R. insidiosa, R. pickettii, R. mannitolilytica and R. wenshanensis). Sequences similar to the R. solanacearum species complex were also detected but were too short for species-level confirmation. Metagenomic analysis detected sequences matching four previously described Ralstonia phages (RSL1, RSIBR3, Anchaing, and Cimandef). Functional annotation demonstrated abundant metabolic pathways, energy production systems, and stress response mechanisms, indicating highly adaptive microbial communities in the tomato rhizosphere. This study provides baseline data on rhizosphere microbiome composition in Kenyan tomato production systems and identifies Ralstonia phage sequences that could guide future isolation and host-range studies. If future work shows that these phages are active against Ralstonia, they could contribute to locally adapted biocontrol approaches that reduce reliance on chemical pesticides.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Kenya
*Bacteriophages/genetics
*Soil Microbiology
*Microbiota/genetics
*Metagenomics/methods
*Ralstonia/virology/genetics
Phylogeny
Metagenome
*Ralstonia solanacearum/virology
Agriculture

@article {pmid42982592,
year = {2026},
author = {Hessels, EW and Montoya, JV and Yuen, C and Valdiviezo-Rivera, J and Rios-Touma, B and Echevarría, G and Lujan, NK},
title = {A Museum-Curated, Voucher-Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon.},
journal = {Molecular ecology resources},
volume = {26},
number = {8},
pages = {},
pmid = {42982592},
issn = {1755-0998},
support = {//Belgian Development Cooperation/ ; //World Wildlife Fund/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Herbert A. Fritch Family Foundation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Ecuador ; *Fishes/genetics/classification ; Museums ; Biodiversity ; DNA, Environmental/genetics ; Metagenomics/methods ; Gene Library ; },
abstract = {Environmental DNA (eDNA) metabarcoding is an emerging method that promises to expedite and improve biodiversity surveys by identifying species from the genetic material they shed into the environment. eDNA methods offer many advantages over conventional specimen-based surveys, but their effectiveness hinges on reference libraries, which for highly biodiverse regions such as the Ecuadorian Amazon are too often incomplete, inconsistently curated and disconnected from morphological voucher specimens needed to reliably identify and revise taxa. To address this gap, we collected approximately 5000 fish specimens and 1500 tissues of an estimated 311 morphologically defined species from Ecuador's Aguarico, Napo and Pastaza river basins, and built a new, rigorously curated, museum voucher-backed 12S reference library spanning 748 barcodes from over 303 species across 12 orders, 46 families and 171 genera. When tested against unknown haplotypes from concurrently collected eDNA samples, the library nearly doubled the proportion identified to species (40.0%, vs. 21.3% using GenBank). It also enabled the empirical estimation of new species-level barcode thresholds: 0.4% for the full-length barcode, 0.9% for a general vertebrate mini-barcode, and 0.6% for a fish-specific mini-barcode. By linking museum vouchers, updated taxonomy, and operational scalability, this reference library helps transform eDNA metabarcoding from an exciting possibility to a practical tool for understanding, monitoring and safeguarding Amazonian freshwater biodiversity.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Ecuador
*Fishes/genetics/classification
Museums
Biodiversity
DNA, Environmental/genetics
Metagenomics/methods
Gene Library

@article {pmid42982859,
year = {2026},
author = {Whang, SN and Wang, X and Thomas-White, KJ and Olmschenk, G and Garza, JE and Navarro, P and Gilbert, NM},
title = {Large-scale metagenomic characterization of the vaginal microbiome and uropathogens in women with recent bacterial vaginosis and urinary tract infections.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42982859},
issn = {2041-1723},
support = {R01DK137964//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/epidemiology ; *Urinary Tract Infections/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota/genetics ; Metagenomics ; Adult ; Cross-Sectional Studies ; *Metagenome ; Young Adult ; Gardnerella/genetics/isolation & purification ; United States/epidemiology ; Escherichia coli/genetics/isolation & purification ; },
abstract = {The vaginal microbiome (VMB) influences susceptibility to urogenital infections, yet large-scale, population-based species-level metagenomic studies are rare. We analyzed cross-sectional shotgun metagenomic profiles and linked clinical metadata from 10,003 women across the United States who self-reported recent bacterial vaginosis (BV), urinary tract infection (UTI), both, or neither. Here we show that women reporting recent BV or UTI displayed distinct community structures, including higher prevalence of VALENCIA CST-IV subtypes and significantly elevated alpha diversity compared with women who reported no prior diagnosis. Species-level Gardnerella profiling revealed that multiple Gardnerella species were enriched in the recent BV group but did not differ significantly between UTI and non-UTI groups, refining prior mechanistic hypotheses. Uropathogens such as E. coli, E. faecalis, and S. saprophyticus were detectable at higher prevalence and relative abundance in women who recently experienced UTI, including among participants who reported recent antibiotic use, consistent with the possibility of residual or recurrent vaginal colonization. These findings demonstrate that microbial signatures associated with recent BV and UTI remain detectable at population scale, provide a high-resolution reference for human vaginal metagenomics, and offer new directions for prevention strategies that consider the vaginal reservoir in recurrent urogenital infections.},
}

Humans
Female
*Vaginosis, Bacterial/microbiology/epidemiology
*Urinary Tract Infections/microbiology/epidemiology
*Vagina/microbiology
*Microbiota/genetics
Metagenomics
Adult
Cross-Sectional Studies
*Metagenome
Young Adult
Gardnerella/genetics/isolation & purification
United States/epidemiology
Escherichia coli/genetics/isolation & purification

@article {pmid42983427,
year = {2026},
author = {Smoglica, C and Angelucci, S and Di Tana, F and Antonucci, A and Marsilio, F and Di Francesco, CE},
title = {Fecal microbiome and resistome in the long-term care of an Apennine wolf (Canis lupus italicus).},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42983427},
issn = {1746-6148},
mesh = {Animals ; *Wolves/microbiology ; Male ; *Feces/microbiology ; *Microbiota/genetics ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; },
abstract = {The Apennine wolf (Canis lupus italicus) increasingly inhabits human modified landscapes, where exposure to anthropogenic environments may influence microbial circulation and antimicrobial resistance. Wildlife Rehabilitation Centers provide opportunities to describe microbial and resistance gene profiles in animals at the human-wildlife interface; however, longitudinal shotgun metagenomic data from this subspecies during rehabilitation remain scarce. A juvenile male wolf admitted to a Wildlife Rehabilitation Center after traumatic injury and treated with multiple antibiotics was sampled at admission (T0) and after 11 months of rehabilitation (T1) in this case report. Fecal shotgun metagenomic sequencing was used to describe microbial communities, reads assigned to taxa of veterinary or public health interest, and antimicrobial resistance genes. Bacterial diversity increased from T0 to T1 with a shift from an Enterobacterales dominated profile to more diverse communities. Reads assigned to bacterial and viral taxa of potential health relevance were detected at both time points. The tools CARD-RGI identified 444 antibiotic resistance genes at T0 and 417 ARGs at T1, mainly associated with efflux pumps and β-lactamases. Genes related to Highest Priority Critically Important Antimicrobials-including mcr variants, van clusters, and oxazolidinone resistance determinants-were identified. This single-animal report provides baseline information on microbiome and resistome modification during wolf rehabilitation and suggests larger longitudinal studies and biosecurity awareness in Wildlife Rehabilitation Centers.},
}

Animals
*Wolves/microbiology
Male
*Feces/microbiology
*Microbiota/genetics
Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial/genetics
Bacteria/drug effects/genetics/classification

@article {pmid42983896,
year = {2026},
author = {Nofinska, BA and Mizutani, S and Salim, F and Sunakawa, H and Obana, N and Shiba, S and Shinmura, K and Kotani, D and Yachida, T and Takamaru, H and Kawazoe, A and Saito, Y and Ikematsu, H and Fukuda, S and Yachida, S and Yamada, T},
title = {Gut microbial and metabolic biomarkers for early-onset colorectal cancer.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42983896},
issn = {2049-2618},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Female ; Metabolomics/methods ; China ; Male ; Japan ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Biomarkers ; Cohort Studies ; Biomarkers, Tumor/metabolism ; Age of Onset ; },
abstract = {BACKGROUND: Early-onset colorectal cancer (EO-CRC) is a growing global health challenge with poorly understood etiology. While gut microbiota and metabolites are implicated in colorectal carcinogenesis, EO-CRC-associated signatures remain poorly characterized. This study presents the first large-scale multi-omics analysis in Japan cohort to characterize gut microbial and metabolic features of EO-CRC, with cross-cohort validation in an independent China cohort.

RESULTS: We enrolled 510 participants (EO-CRC n = 120, late-onset CRC [LO-CRC] n = 282, young healthy controls [yHC] n = 59, old healthy controls [oHC] n = 49); after age- and sex-matching, 324 samples were analyzed using metagenomics, metabolomics, and quantitative polymerase chain reaction (qPCR). Fourteen species formed a shared CRC-associated microbiome core enriched in both EO-CRC and LO-CRC relative to age-matched controls, of which seven were reproducible across both Japan and China cohorts. Beyond this core, 34 and 21 species were enriched exclusively in EO-CRC and LO-CRC, respectively. Among EO-CRC-specific virulence findings, the bft gene of enterotoxigenic Bacteroides fragilis, fadA of Fusobacterium nucleatum, and bai operon genes were enriched in EO-CRC, with cross-cohort validation for fadA and bai operon, and stage-specific enrichement of deoxycholic acid at Stage 0 providing preliminary metabolomic support. Targeted clbP qPCR revealed enrichment of colibactin-producing Escherichia coli specifically in EO-CRC against a background of age-increasing carriage. Metabolomic profiling identified kynurenine enrichment and depletion of vitamin B-related metabolites (pyridoxine, riboflavin, and nicotinamide) as EO-CRC-specific findings; LO-CRC showed distinct enrichment of carnitine, succinate, and spermine with relative butyrate depletion. The choline degradation pathway was enriched specifically in EO-CRC based on Enteropathway analysis. Species-based random forest classifiers distinguished EO-CRC from controls (AUPRC = 0.828; SD = 0.013; 95% CI 0.739-0.909) and generalized robustly to an independent cohort (AUPRC = 0.817; 95% CI 0.717-0.894), substantially outperforming functional gene profiles in cross-cohort settings. Within the Japan cohort, adding metabolomics provided modest additional discriminative value.

CONCLUSIONS: These findings identify a shared CRC microbiome core reproducible across age groups and cohorts, alongside EO-CRC-specific signatures encompassing enrichment of virulence-associated genes (bft, fadA), colibactin-producing E. coli (clbP), secondary bile acid biosynthetic genes (bai operon), and choline degradation capacity, as well as distinct metabolic perturbations including kynurenine enrichment and vitamin B-related metabolite depletion. Species-based classifiers generalize well across age groups and cohorts, with metabolomics providing complementary discriminatory value. All findings represent cross-sectional associations; longitudinal studies are needed to establish temporal ordering and evaluate clinical utility as non-invasive biomarkers for EO-CRC. Video Abstract.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism
*Gastrointestinal Microbiome/genetics
Multiomics
Female
Metabolomics/methods
China
Male
Japan
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
Adult
Biomarkers
Cohort Studies
Biomarkers, Tumor/metabolism
Age of Onset

@article {pmid42985544,
year = {2026},
author = {Zhao, T and Sun, Y and Jiang, X and Feng, Y and Ding, J and Li, X and Deng, A},
title = {Structural characteristics and regulatory mechanisms of the ocular surface microbiota and their relationship with ocular surface health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938863},
pmid = {42985544},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Eye/microbiology/immunology ; Host Microbial Interactions ; Animals ; RNA, Ribosomal, 16S/genetics ; Meibomian Glands/microbiology ; },
abstract = {This review delineates the spatial distribution of ocular surface microbiota (OSM) and its dynamic interplay with ocular health. Culture-independent surveys employing 16S rRNA and metagenomic sequencing reveal an ultra-low-biomass ecosystem characterized by restricted α-diversity. Firmicutes, Actinobacteria and Proteobacteria are the dominant phyla. Corynebacterium, coagulase-negative staphylococci, Propionibacterium and Streptococcus show high prevalence and temporal stability. These four genera form a conserved core. Their relative abundance is continuously reshaped by geography, lifestyle, age, sex, delivery mode, contact lens wear and systemic diseases such as dry eye and diabetes. Emerging evidence implicates host-microbe crosstalk, encompassing Toll-like receptor (TLR) and NOD-like receptor (NLR) mediated sensing of pathogen-associated molecular patterns (PAMPs), secretory immunoglobulin A (SIgA) neutralization, and a putative gut-eye immunoregulatory axis, in ocular immune maturation and the maintenance of immune homeostasis, although direct causal relationships remain to be established. Under physiological conditions, competitive exclusion and negative feedback maintain microbial equilibrium. However, surgical trauma, antibiotics or corticosteroids have been associated with destabilization of this niche, under which commensals may acquire virulence genes, form biofilms and transition into opportunistic pathogens implicated in infectious keratitis, exacerbation of meibomian gland dysfunction and increased dry eye severity. Consequently, high-resolution profiling of OSM composition and function may help clarify disease mechanisms and holds promise for furnishing microbial biomarkers for precision diagnosis and personalized therapeutic intervention.},
}

Humans
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Eye/microbiology/immunology
Host Microbial Interactions
Animals
RNA, Ribosomal, 16S/genetics
Meibomian Glands/microbiology

@article {pmid42986108,
year = {2026},
author = {Xu, Y and Zhang, C and Wu, Y and Zhuo, J and Shen, X and Zhou, Y and Jin, J},
title = {Metagenomic insights into the avian gut microbiome: novel viruses, antimicrobial resistance, and beyond.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234326},
doi = {10.1128/mbio.02343-26},
pmid = {42986108},
issn = {2150-7511},
abstract = {Birds play crucial roles in shaping ecosystems, and their gut microbiomes significantly influence host physiology and pathology. Understanding the composition, functions, and dynamics of avian gut microbiomes is therefore essential. Recent advances in metagenomic and metatranscriptomic sequencing have greatly increased our ability to characterize the avian gut microbiome. This review presents a systematic summary of the current knowledge regarding the composition of the avian gut microbiome as revealed through high-throughput sequencing technologies. It provides a statistical overview of the predominant bacterial and viral taxa present in the gut microbiomes of 195 bird species, revealing a persistent trend toward the discovery of novel viruses, and gives insight into the gene functions of these taxa. Interestingly, in terms of both antimicrobial resistance and multidrug resistance, wild birds harbor a greater diversity of resistance types than poultry. This review also presents a discussion of the relationships of avian life stages and the living conditions of birds with the gut microbiome and highlights practical applications of microbiome regulation in poultry production. Building on this foundation, future research priorities are outlined, such as the study of archaea, fungi, protists, and novel viruses, ways of improving methods to reduce costs and standardize protocols, and the development of more extensive metagenomic and metatranscriptomic data resources. Ultimately, these efforts could provide a holistic understanding of the avian gut microbiome.},
}

@article {pmid42237575,
year = {2026},
author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT},
title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.},
journal = {American journal of epidemiology},
volume = {195},
number = {11},
pages = {2719-2729},
pmid = {42237575},
issn = {1476-6256},
support = {R01 HL166473/HL/NHLBI NIH HHS/United States ; 25CDA1447396//American Heart Association/ ; R01HL166473//National Heart, Lung and Blood Institute (N.T.M.)/ ; R01AG050507/AG/NIA NIH HHS/United States ; //Intramural Research Program of the NIH, National Institute on Aging/ ; },
mesh = {Humans ; *Vascular Stiffness/physiology ; *Gastrointestinal Microbiome/physiology ; Female ; Longitudinal Studies ; Male ; Baltimore ; Aged ; *Aging/physiology ; Middle Aged ; Pulse Wave Analysis ; Feces/microbiology ; Carotid-Femoral Pulse Wave Velocity ; },
abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013 and 2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.},
}

Humans
*Vascular Stiffness/physiology
*Gastrointestinal Microbiome/physiology
Female
Longitudinal Studies
Male
Baltimore
Aged
*Aging/physiology
Middle Aged
Pulse Wave Analysis
Feces/microbiology
Carotid-Femoral Pulse Wave Velocity

@article {pmid42617883,
year = {2026},
author = {Kim, M and Huang, CY and Sun, Y and Cunningham, A and Tisza, MJ and Gold, DR and Koutrakis, P and Phipatanakul, W and Lai, PS},
title = {Classroom microbiome signatures of pest management associate with reduced asthma symptoms.},
journal = {The Journal of allergy and clinical immunology},
volume = {158},
number = {5},
pages = {1252-1265},
pmid = {42617883},
issn = {1097-6825},
support = {U01 AI110397/AI/NIAID NIH HHS/United States ; K24 AI199258/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; K24 AI106822/AI/NIAID NIH HHS/United States ; R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI178155/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Asthma/microbiology/epidemiology/prevention & control/immunology ; *Microbiota ; Female ; Animals ; Male ; Child ; Mice ; Schools ; *Pest Control/methods ; Allergens/immunology ; Dust ; },
abstract = {BACKGROUND: Integrated pest management (IPM) is thought to improve asthma symptoms through reduced mouse allergen exposure. Whether IPM acts through changes in mouse-associated microbes remains unknown.

OBJECTIVES: We examined the effects of school-based IPM on the classroom microbiome and sought to determine the association between intervention microbiome signatures and student asthma morbidity.

METHODS: In this ancillary study based on a randomized placebo-controlled clinical trial of school IPM and classroom high-efficiency air purifiers (ClinicalTrials.gov NCT02291302), we performed deep metagenomics sequencing of longitudinally collected dust samples from 208 classrooms in 41 schools of 236 children with active, physician-diagnosed asthma with prospective follow-up of asthma severity during the school year. We assessed the effect of the interventions on classroom microbial communities in intention-to-treat analyses. Sparse partial least squares models were used to identify microbial signatures of the interventions, and the association between these microbial signatures and asthma morbidity was assessed by mixed-effects models, controlling for covariates including mouse allergen exposure.

RESULTS: IPM significantly altered classroom bacterial and phage community structure and increased bacterial, archaeal, and fungal diversity. A classroom microbiome signature of IPM was identified (area under the curve = 0.84) and was associated with lower odds of any asthma symptom days in the past 2 weeks (odds ratio = 0.47; 95% confidence interval, 0.22, 0.97; P = .043) and lower Composite Asthma Severity Index (β = -0.92; 95% confidence interval, -1.51, -0.33; P = .002), adjusting for mouse allergen levels and student characteristics.

CONCLUSION: IPM-associated changes in the classroom microbiome are associated with lower asthma morbidity independent of mouse allergen exposure.},
}

Humans
*Asthma/microbiology/epidemiology/prevention & control/immunology
*Microbiota
Female
Animals
Male
Child
Mice
Schools
*Pest Control/methods
Allergens/immunology
Dust

@article {pmid42765727,
year = {2026},
author = {Karačić, J and Singer, L and Bierbaum, G and Parčina, M and Zilles, J and Palmer, B and Karačić, S},
title = {Dental spittoon biofilms as reservoirs of antimicrobial resistance: a longitudinal multi-omics study.},
journal = {Microbiology spectrum},
volume = {14},
number = {11},
pages = {e0088326},
pmid = {42765727},
issn = {2165-0497},
support = {O-151.0084//BONFOR-Forschungsförderungsprogramm of the Medical Faculty of the University of Bonn/ ; },
mesh = {*Biofilms/drug effects/growth & development ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Multiomics ; Humans ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; Longitudinal Studies ; Metagenomics ; *Dental Equipment/microbiology ; Microbiota ; },
abstract = {Dental chair spittoons are chronically exposed to saliva, aerosols, intermittent water flow, and chemical disinfectants, yet their biofilm ecology and antimicrobial resistance (AMR) dynamics remain poorly defined. We applied longitudinal 16S rRNA gene sequencing, shotgun metagenomics, and culture-based antimicrobial susceptibility testing to biofilms collected across four dental departments at three time points. Community analyses revealed significant temporal succession and department-specific structuring, indicating the establishment of stable, ecologically differentiated biofilm systems. Null-model analysis (Raup-Crick) indicated that community assembly remained predominantly stochastic, although later sampling periods showed modest evidence of increasing ecological filtering. Shotgun metagenomics identified metabolically versatile communities enriched in disinfectant-tolerant environmental taxa, with resistomes dominated by β-lactamases and aminoglycoside-modifying enzymes. Clinically associated plasmid replicons, including IncFII and Col440I, were detected in metagenomically analyzed samples. Culture-based testing of 162 isolates confirmed that 21.7% expressed phenotypic resistance to at least one antimicrobial agent, including multidrug- and carbapenem-resistant representatives of Pseudomonas and Acinetobacter. Together, these findings position dental spittoons as structured aquatic biofilm ecosystems that maintain viable antimicrobial-resistant populations and clinically relevant plasmid replicons under recurrent disturbance, highlighting their ecological role within the broader built-water resistome.IMPORTANCEBiofilms in healthcare environments can act as reservoirs of antimicrobial resistance, yet some potential niches remain poorly studied. Dental chair spittoons are continuously exposed to oral fluids, aerosols, water flow, disinfectants, and residual antimicrobial compounds, creating conditions that may favor biofilm formation and microbial selection. Despite this unique combination of ecological pressures, the microbial communities inhabiting these systems have received little attention. Using a longitudinal multi-omics approach combined with culture-based phenotypic testing, we show that spittoon biofilms harbor diverse microbial communities enriched in antimicrobial resistance determinants, including multidrug-resistant and carbapenem-resistant bacteria. These findings suggest that dental spittoons may represent previously overlooked reservoirs of antimicrobial resistance within clinical environments.},
}

*Biofilms/drug effects/growth & development
RNA, Ribosomal, 16S/genetics
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Multiomics
Humans
Microbial Sensitivity Tests
*Drug Resistance, Bacterial
Longitudinal Studies
Metagenomics
*Dental Equipment/microbiology
Microbiota

@article {pmid42784973,
year = {2027},
author = {Groff, JM and Khrongsee, P and Armien, AG and de Oliveira Viadanna, PH and Subramaniam, K},
title = {Characterization of a novel poxvirus associated with an epidermal keratinocytic dermatopathy in a captive population of the endangered Knysna seahorse Hippocampuscapensis.},
journal = {Virology},
volume = {625},
number = {},
pages = {111083},
doi = {10.1016/j.virol.2026.111083},
pmid = {42784973},
issn = {1096-0341},
mesh = {Animals ; *Poxviridae/genetics/classification/isolation & purification ; *Poxviridae Infections/veterinary/virology/pathology ; Phylogeny ; *Fish Diseases/virology/pathology ; DNA, Viral/genetics/chemistry ; *Smegmamorpha/virology ; Molecular Sequence Data ; Endangered Species ; Sequence Analysis, DNA ; },
abstract = {The poxviruses are large, epitheliotropic, double-stranded DNA viruses that are pathogens of invertebrates and the mammalian, avian and reptilian vertebrate taxa including the familiar poxviruses of humans and domestic animals such as the variola virus or smallpox virus and the related vaccinia virus used for the live smallpox vaccine, mpox virus (formerly monkeypox virus), cowpox virus of rodents, and orf virus of sheep and goats. Poxviruses have also previously been described from teleost fishes including the common carp Cyprinus carpio, ayu Plecoglossus altivelis, Atlantic salmon Salmo salar, Atlantic cod Gadus morhua, red or Japanese seabream Pagrus major, and black bullhead Ameiurus melas. This report documents a novel poxvirus infection in a captive population of the endangered Knysna seahorse Hippocampus capensis. Histopathological examination revealed an epidermal keratinocytic dermatopathy with hypertrophy and subsequent progressive degeneration and necrosis of the affected cells; karyomegaly with a prominent nucleolus was also a feature of the affected cells. Ultrastructural examination of the affected keratinocytes revealed large and complex, intracytoplasmic virions with elliptical to discoid profiles and an average size of 548.5 nm (SD = 100.58) by 205.65 nm (SD = 21.19) consistent with a typical poxvirus morphology. Furthermore, metagenomic analysis revealed distinct genomic features, whereas phylogenetic analysis of nine core poxvirus genes demonstrated that the seahorse poxvirus forms a unique branch within the teleost poxvirus clade supporting its classification as a novel poxvirus with a proposed species name of Syngnathid cutaneouspox virus. Finally, this study confirms the utility of next-generation sequencing as a methodology for obtaining phylogenetically useful genomic sequences from archival formalin-fixed paraffin-embedded tissues.},
}

Animals
*Poxviridae/genetics/classification/isolation & purification
*Poxviridae Infections/veterinary/virology/pathology
Phylogeny
*Fish Diseases/virology/pathology
DNA, Viral/genetics/chemistry
*Smegmamorpha/virology
Molecular Sequence Data
Endangered Species
Sequence Analysis, DNA

@article {pmid42803159,
year = {2026},
author = {Merkesvik, J and Langa, J and Pietroni, C and Alberdi, A and Poulsen, LL and Bojesen, AM and Meuronen, T and Turunen, S and Kärkkäinen, O and Westereng, B and Pope, PB and Hvidsten, TR},
title = {Integrative holo-omic data analysis predicts interactions across the host-microbiome axis.},
journal = {Microbiology spectrum},
volume = {14},
number = {11},
pages = {e0026326},
doi = {10.1128/spectrum.00263-26},
pmid = {42803159},
issn = {2165-0497},
support = {101000309//Horizon 2020 Framework Programme/ ; POS_2022_1_0011//Basque Government/ ; },
mesh = {Animals ; Multiomics ; *Host Microbial Interactions ; Swine/microbiology ; *Gastrointestinal Microbiome/physiology ; Metagenome ; Cecum/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Microbiota ; },
abstract = {Understanding the interplay between host organisms and their microbiomes is central to the development of sustainable food systems. However, high dimensionality and spurious associations remain major obstacles to extracting meaningful biological insight from multi-omic host-associated microbiome data; a challenge further exacerbated when "holo-omic" analyses across the host-microbiome boundary are considered. Here, we show that a computational method designed for multi-omic analysis in eukaryotes can be leveraged to integrate and analyze five layers of holo-omic data from porcine hosts and their gut microbiomes. We collected caecal tissue and digesta samples during a feeding trial that tested the impact of microbiota-directed fibers (acetylated galactoglucomannan) at critical developmental stages. From 800,000 features including microbial and host genes, metagenome-assembled genomes, and metabolites from caecal tissue and digesta, we used multiset correlation and factor analysis to select the most relevant features for capturing coordinated patterns across omic layers. From these features, we predicted over 2,000 putative host-microbiome interactions based on co-occurrence. Some interactions reflected previously known relationships between animal and microbiome features, such as microbial genes for carbohydrate metabolism being linked to glycoside abundances in host tissue. Other predicted co-occurrences included features that were not detected in single-omic analysis and offer new hypotheses of host-microbiome interactions that warrant future investigation. Hence, we showcase an application of holo-omic analysis that avoids common pitfalls in high-dimensional data analysis, identifies known interactions as a form of validation, and most importantly, predicts new leads for understanding host-microbiome symbiosis.IMPORTANCEWhile study systems involving mammalian hosts and their microbiomes are inherently complex, multi- and holo-omic analyses promise to provide interpretable results with translational value for the animal production industry. Unfortunately, computational methods capable of this kind of integration are currently scarce, as most existing multi-omics approaches have been developed for analysis of data layers within a single multicellular organism. We propose to adapt existing multi-omic methods for holo-omics by combining feature selection and interaction inference. This two-step analysis approach addresses common challenges in data-driven studies and can be implemented with a variety of tools for feature selection and interaction modeling. Through this holistic approach, we show that both known and novel relationships across the holobiont axis can be identified in a data-driven manner, offering new targets for the continued study and experimental validation of host-microbiome interactions and the effect of dietary interventions on production animals.},
}

Animals
Multiomics
*Host Microbial Interactions
Swine/microbiology
*Gastrointestinal Microbiome/physiology
Metagenome
Cecum/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
Microbiota

@article {pmid42836610,
year = {2026},
author = {Ruth, N and Shakya, M and Lewis, CD and Erickson, CE and Dolinski, A and Jankowski, M and Fair, JM and Owen, JC and Bartlow, AW},
title = {Mallard super-shedders of avian influenza exhibit distinct cloacal microbial abundance profiles.},
journal = {Microbiology spectrum},
volume = {14},
number = {11},
pages = {e0208926},
doi = {10.1128/spectrum.02089-26},
pmid = {42836610},
issn = {2165-0497},
mesh = {Animals ; *Cloaca/microbiology/virology ; *Influenza in Birds/virology/microbiology ; *Microbiota ; *Influenza A virus/physiology/genetics ; *Ducks/virology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Virus Shedding ; Metagenome ; Animals, Wild ; Metagenomics ; },
abstract = {In many infectious disease systems, a small fraction of hosts accounts for a disproportionate share of transmission, but the biological basis of this heterogeneity remains poorly resolved. In avian influenza, mallards show substantial variation in viral shedding, raising the possibility that only a subset of individuals contributes strongly to environmental contamination and onward spread. To examine whether host microbiome structure is associated with this variation, we experimentally infected wild, captive mallards with low-pathogenic avian influenza virus. We characterized cloacal microbiomes across control, low-shedding, and high-shedding birds using shotgun metagenomic sequencing combined with read-based taxonomic profiling and co-assembled metagenome-assembled genome (MAG) reconstruction. Although infected and uninfected birds were highly similar in species presence-absence, abundance-based analyses showed clear differences in shared taxa, particularly in high-shedding birds relative to controls. Differentially abundant taxa were dominated by taxa that belonged to groups that include host-associated opportunists, consistent with compositional imbalance rather than complete community restructuring. The phylum Pseudomonadota, especially the families Enterobacteriaceae and Moraxellaceae, is well represented. Together, these findings suggest that avian influenza infection is associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in species membership and that microbiome structure is associated with heterogeneity in shedding in a key wildlife reservoir.IMPORTANCEA small fraction of infected hosts often accounts for a disproportionate share of pathogen shedding, but the biological factors underlying this variation remain poorly understood. In experimentally infected mallards, a key wildlife reservoir for avian influenza A viruses, we found that high viral shedding was associated with shifts in the abundance of cloacal bacterial taxa rather than broad changes in microbial species membership. These results suggest that host-associated microbiome structure may be linked to shedding heterogeneity and could help explain why some individuals contribute more strongly to environmental contamination and onward transmission.},
}

Animals
*Cloaca/microbiology/virology
*Influenza in Birds/virology/microbiology
*Microbiota
*Influenza A virus/physiology/genetics
*Ducks/virology/microbiology
*Bacteria/classification/genetics/isolation & purification
*Virus Shedding
Metagenome
Animals, Wild
Metagenomics

@article {pmid42976950,
year = {2026},
author = {Yang, S and Jin, L and Deng, W and Xiao, H and Yao, Y and Xie, M and Xu, H and Zou, L},
title = {An integrated gut phage catalogue of nonhuman primates reveals functional adaptation to host ecology and evolutionary link to humans.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2082},
pages = {},
pmid = {42976950},
issn = {1471-2954},
support = {2024NSFSC1284//Sichuan Science and Technology Program/ ; 031-2222996053//Scientific Research Foundation from Sichuan Agricultural University/ ; },
mesh = {Animals ; *Bacteriophages/physiology/genetics ; Humans ; *Biological Evolution ; *Gastrointestinal Microbiome ; *Primates/virology ; Metagenome ; },
abstract = {Nonhuman primates (NHPs), the closest evolutionary relatives of humans, are pivotal models for biomedical and ecological research. Gut phage are recognized as critical modulators of gut microbial communities; however, comprehensive insight into gut phage of NHPs is lacking. We used gut metagenomes spanning 25 NHP species and constructed an integrated gut phage catalogue (IGPC) comprising 11 389 nonredundant phage genomes. Our results revealed that the composition and function of NHP gut phage were significantly influenced by host clade, dietary niche and lifestyle. Host clade exerted a stronger influence than dietary niche on gut phage diversity. The lifestyle of NHPs influenced gut phage diversity and altered auxiliary metabolic gene profiles for different NHP species. Comparatively, 78.5% of IGPC phages were detected in human guts, with higher prevalence in nonindustrialized human guts. crAss-like phage-the most prevalent human-associated phage-were abundant in NHP guts, while exhibiting distinct evolutionary differences from crAss-like phage of humans. These findings comprehensively characterize the gut phageome of NHPs, revealing NHP host-driven and environment-driven functional adaptations, and provide an evolutionary understanding of the gut phageome between NHPs and humans.},
}

Animals
*Bacteriophages/physiology/genetics
Humans
*Biological Evolution
*Gastrointestinal Microbiome
*Primates/virology
Metagenome

@article {pmid42977442,
year = {2026},
author = {Li, Z and Li, B and Sun, X and Cao, Y and Peng, K and Shoaib, M and Yang, B and Wang, J and Ma, Y and Wang, Z and Bai, L and Li, R},
title = {Metagenomics reveals potential risks of antibiotic and metal resistance genes in agricultural production systems.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 5},
pages = {120990},
doi = {10.1016/j.foodres.2026.120990},
pmid = {42977442},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Agriculture ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Metagenome ; *Metals ; Microbiota/genetics ; Vegetables/microbiology ; Agricultural Irrigation ; },
abstract = {Agricultural environments harbor diverse microbiomes and serve as key reservoirs of resistance genes, yet their influence on fresh produce remains unclear. In this study, metagenomics was employed to reveal the microbiome and resistome in soil, irrigation water, and fresh produce surfaces in production settings. The results revealed that soil harbored the greatest microbial diversity along with the highest abundance and diversity of antibiotic resistance genes (ARGs). Fresh produce harbored diverse ARGs of potential relevance to food-chain resistance surveillance. Among the 528 bacterial metagenome-assembled genomes (MAGs) retained for genome-resolved analysis, Pseudomonadota were the predominant carriers of ARGs, including those conferring resistance to tetracyclines, aminoglycosides, and β-lactams. Interestingly, similar contigs containing rep22_1b and tet(L) were found in MAGs obtained from irrigation water and vegetable samples, indicating a high level of conservation in the genetic environment. In addition, irrigation water harbored the most abundant mobile genetic elements (MGEs), found to be significantly associated with ARG profiles. Copper (Cu) resistance genes were predominant among the detected metal resistance genes (MRGs), indicating widespread genetic potential for copper resistance across the sampled agricultural environments. Overall, these findings reveal distinct but interconnected resistome profiles across soil, irrigation water, and fresh produce and identify resistance-associated genetic features of potential relevance to food safety surveillance.},
}

*Metagenomics/methods
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
*Agriculture
*Drug Resistance, Bacterial/genetics
*Genes, Bacterial
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
Metagenome
*Metals
Microbiota/genetics
Vegetables/microbiology
Agricultural Irrigation

@article {pmid42978014,
year = {2026},
author = {Park, K and Lee, J and Hyun, D and Kim, SG and Kim, J and Hilbe, M and Gu, SH and Lim, BK and Kadjo, B and Ohdachi, SD and Truong, T and Truong, N and Palacios, G and Yanagihara, R and Song, JW},
title = {Detection and whole-genome characterisation of Regana virus in the bicoloured shrew (Crocidura leucodon) from Graubünden, Switzerland.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {42978014},
issn = {1348-8945},
support = {RS-2026-25593026//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; },
abstract = {BACKGROUND: Orthonairoviruses are of medical and veterinary importance, but the genetic diversity and geographic distribution of shrew-associated orthonairoviruses remain unclear. Shrews are increasingly recognised as hosts for diverse orthonairoviruses, including Regana virus (REGV), which has been reported in the bicoloured white-toothed shrew (Crocidura leucodon) in Germany and the Czech Republic.

METHODS: We examined archived shrew specimens collected in Graubünden Canton, Switzerland, between 2005 and 2006 using nested reverse transcription-polymerase chain reaction, metagenomic next-generation sequencing, phylogenetic analysis, pairwise sequence comparison, and protein feature annotation.

RESULTS: Nairoviral RNA was detected in three C. leucodon from Luzein and Malans, whereas four Sorex araneus and one Neomys anomalus tested negative. Complete or near-complete REGV genome sequences were recovered from the three positive animals. Swiss REGV variants clustered with REGV from Germany and the Czech Republic across the S, M, and L segments. RdRp amino acid identities were 98.8-98.9% among Swiss variants and 92.1-95.6% between REGV Np12 and German or Czech variants. Comparative protein analyses identified conserved viral ovarian tumour protease catalytic residues, similar glycoprotein precursor organisations, and nairovirus-like nucleoprotein motifs.

CONCLUSIONS: These findings document REGV in C. leucodon in Switzerland and expand the known geographical and genetic ranges of REGV in European shrew populations.},
}

@article {pmid42978490,
year = {2026},
author = {Sheng, Y and Dai, X and Lu, J and Zhang, H and Cai, P},
title = {The Potential Role of Gut Microbiome Dysbiosis and Functional Reprogramming in Colorectal Liver Metastasis via the Gut-Liver Axis.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {11},
pages = {},
pmid = {42978490},
issn = {2573-8348},
support = {2024KY1551//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2025KY1386//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2025KY1503//Medical Scientific Research Foundation of Zhejiang Province, China/ ; 2024Z229//Science and Technology Innovation Yongjiang 2035 Key Research and Development Project of Ningbo/ ; 2022E50008//Zhejiang Provincial Clinical Research Center for CANCER/ ; 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; },
mesh = {Humans ; *Liver Neoplasms/secondary/microbiology ; *Colorectal Neoplasms/pathology/microbiology ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Feces/microbiology ; Middle Aged ; Aged ; Liver/pathology/microbiology ; Case-Control Studies ; Metagenomics ; Biomarkers, Tumor ; },
abstract = {BACKGROUND: Colorectal liver metastasis (CRLM) is a leading cause of mortality in colorectal cancer (CRC), yet current surveillance often misses occult micrometastases, underscoring an urgent need for early non-invasive biomarkers and mechanistic insights.

AIMS: This study aimed to investigate gut microbiota dysbiosis and functional alterations associated with CRLM and explore potential non-invasive biomarkers.

METHODS AND RESULTS: Fecal metagenomic sequencing was performed in 60 participants, comprising healthy controls, patients with non-metastatic CRC, and patients with synchronous CRLM (n = 20 per group). Microbial composition, functional pathways, co-occurrence networks, and clinical associations were systematically analyzed, and a random forest model was constructed to identify potential diagnostic biomarkers. Results showed that gut microbiota dysbiosis intensified as CRC progressed toward CRLM, characterized by the depletion of commensal flora and significant enrichment of specific genera, such as Eikenella and Porphyromonas. Functionally, the gut microbiome displayed stage-specific remodeling, shifting from infection- and virulence-related pathways in CRC to functions associated with microbial secondary metabolism and stress adaptation in CRLM. Furthermore, SPIEC-EASI-based network analysis revealed a sparser and more compartmentalized microbial ecological structure in CRLM, with [Clostridium] symbiosum, Campylobacter concisus, and Coprococcus eutactus emerging as module hubs. A random forest model integrating nine core taxa and one virulence factor (VF0160 FeoAB) achieved an overall 97.5% classification accuracy in discriminating CRLM from non-metastatic CRC, indicating the potential of fecal metagenomic biomarkers for future risk stratification. However, prospective validation in larger multicenter cohorts is required before clinical translational utility.

CONCLUSION: Collectively, our findings suggest that gut microbiota dysbiosis and functional reprogramming are strongly associated with CRLM progression, potentially through remodeling the hepatic pre-metastatic niche via the gut-liver axis.},
}

Humans
*Liver Neoplasms/secondary/microbiology
*Colorectal Neoplasms/pathology/microbiology
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome
Male
Female
Feces/microbiology
Middle Aged
Aged
Liver/pathology/microbiology
Case-Control Studies
Metagenomics
Biomarkers, Tumor

@article {pmid42979661,
year = {2026},
author = {Li, G and Dong, S and Liu, C and Yan, H and Yang, J and Rensen, PCN and Shi, B and Wang, Y},
title = {Dietary butyrate alleviates high-fat diet-induced colonic mucosal impairment accompanied by increased gut-derived indole-3-acetic acid and enhanced PPARγ signaling.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1971187},
pmid = {42979661},
issn = {1664-2392},
mesh = {Animals ; Male ; Mice ; *Diet, High-Fat/adverse effects ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Humans ; *Colon/metabolism/drug effects/pathology ; *PPAR gamma/metabolism ; Gastrointestinal Microbiome/drug effects ; *Indoleacetic Acids/metabolism ; Signal Transduction/drug effects ; *Butyric Acid/pharmacology ; Caco-2 Cells ; Intestinal Barrier Function ; *Butyrates/pharmacology ; },
abstract = {INTRODUCTION: High-fat diet (HFD) induces intestinal barrier impairment, associated with gut microbiota dysbiosis, endotoxin translocation and metabolic dysfunction. Dietary butyrate has been reported to improve intestinal homeostasis, but the underlying mechanism remains incompletely understood. This study aimed to investigate the effects of dietary butyrate on HFD-induced colonic mucosal dysfunction and to explore underlying mechanisms with respect to the role of gut microbiota and its metabolites.

METHODS: Male APOE*3-Leiden.CETP mice, a well-established translational model for diet-induced metabolic dysfunction, were fed an HFD with or without 5% sodium butyrate. Metabolic phenotypes, plasma lipopolysaccharide (LPS), colonic histology, inflammatory responses, and tight junction-associated changes were assessed. Fecal microbiota transplantation (FMT) was performed in antibiotic-treated recipient mice to assess the contribution and transferability of butyrate-shaped gut microbiota. Cecal metagenomic sequencing and LC/MS-based colonic indole-3-acetic acid (IAA) measurement were performed. Caco-2 cells were used to assess the direct effects of sodium butyrate and IAA on enterocytes and to determine, through pioglitazone treatment and PPARγ knockdown, whether PPARγ mediates IAA-induced enterocyte responses.

RESULTS: Dietary butyrate induced favorable changes in multiple colonic barrier-associated parameters, including improved colonic architecture, lower circulating LPS levels, decreased Tnf-a and Il-1b expression, and increased CLDN2, Reg-family, and PPARγ expression in the colon. In addition, butyrate reduced body weight gain, fat mass accumulation and improved glucose metabolism. FMT from butyrate-treated donors partially reproduced these beneficial effects in HFD-fed recipients. Metagenomic analysis showed enrichment of Bacteroidota and Bacteroides, particularly B. uniformis and B. thetaiotaomicron, accompanied by increased colonic IAA levels. In Caco-2 cells, IAA increased the expression of PPARγ, Reg4, and CLDN2. While PPARγ agonist pioglitazone mimicked the upregulation of REG4 and CLDN2 expression by IAA, siRNA-induced PPARγ knockdown attenuated IAA-induced REG4 and CLDN2 upregulation.

CONCLUSION: Dietary butyrate improves colonic mucosal homeostasis under HFD feeding, accompanied by gut microbial remodeling and increased colonic IAA levels. Together with the PPARγ-dependent epithelial response to IAA observed in Caco-2 cells, these findings suggest a potential mechanistic framework linking butyrate-associated microbial changes, IAA metabolism, and epithelial PPARγ signaling.},
}

Animals
Male
Mice
*Diet, High-Fat/adverse effects
*Intestinal Mucosa/metabolism/drug effects/pathology
Humans
*Colon/metabolism/drug effects/pathology
*PPAR gamma/metabolism
Gastrointestinal Microbiome/drug effects
*Indoleacetic Acids/metabolism
Signal Transduction/drug effects
*Butyric Acid/pharmacology
Caco-2 Cells
Intestinal Barrier Function
*Butyrates/pharmacology

@article {pmid42981279,
year = {2026},
author = {Chen, J and Cheng, YQ and Fan, LP and Zhou, X and Jiang, JY and Wu, F and Liang, PW and Liu, Y and Zuo, ZL and Zhu, GX},
title = {Environmental enrichment is associated with changes in the gut microbiome and resistome of captive pythons.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0360735},
doi = {10.1371/journal.pone.0360735},
pmid = {42981279},
issn = {1932-6203},
mesh = {Animals ; *Boidae/microbiology ; *Gastrointestinal Microbiome/genetics ; Environment ; Metagenomics ; },
abstract = {Environmental enrichment is widely used to improve the welfare of captive animals, yet its effects on reptilian gut microbiota remain poorly understood. Here, we used shotgun metagenomic sequencing to investigate the gut microbiome and resistome of two captive python species: Burmese python (Python bivittatus) and reticulated python (Malayopython reticulatus), before and after environmental enrichment. We found that environmental enrichment was associated with increased α-diversity in Burmese pythons, as indicated by significantly higher ACE and observed species indices, while NMDS ordination revealed differences in the observed patterns of community composition between the two species. Pseudomonadota and Bacteroidota were dominant phyla in the gut microbiota of both python species, but their relative abundances responded differently to enrichment between hosts. Functional analyses suggested an enhanced metabolic potential in Burmese pythons, particularly in carbohydrate metabolism and environmental information processing, accompanied by increased abundance of carbohydrate-active enzymes. In addition, enrichment may influence the gut resistome, with Pseudomonadota contributing the majority of antibiotic resistance genes. Overall, our results demonstrate that environmental enrichment measures, such as dietary changes and improvements in water and air quality, are associated with changes in the gut microbiome and resistome of captive pythons in a host-dependent manner, highlighting the combined roles of diet and environmental conditions in the observed changes in the gut microbiota. These findings provide exploratory insights into the functional responses and host-microbiome evolution of reptile gut microbiota to captivity and have important implications for the management and welfare of captive animals.},
}

Animals
*Boidae/microbiology
*Gastrointestinal Microbiome/genetics
Environment
Metagenomics

@article {pmid41841608,
year = {2026},
author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K},
title = {Gut Microbiome Composition and Function, Diet, and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.},
journal = {The American journal of gastroenterology},
volume = {121},
number = {11},
pages = {2695-2709},
pmid = {41841608},
issn = {1572-0241},
support = {//Danone/ ; },
mesh = {Humans ; Double-Blind Method ; Cross-Over Studies ; Female ; Fermentation ; Male ; Adult ; *Oligosaccharides/adverse effects/administration & dosage ; Breath Tests ; *Dietary Fiber/adverse effects ; *Fructans/adverse effects/administration & dosage ; *Flatulence ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Fatty Acids, Volatile/metabolism ; Hydrogen/analysis ; *Dietary Carbohydrates/adverse effects ; },
abstract = {INTRODUCTION: Specific foods are associated with abdominal bloating, which can significantly affect quality of life. To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.

METHODS: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics), and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized before each challenge to identify factors predicting response and after the challenge to elucidate mechanisms underpinning food-induced bloating.

RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, 7 (7/39, 17.9%) participants were fructan responders and 8 (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and nonresponders to both challenges, including greater abdominal girth (fructan, P = 0.009; α-GOS, P = 0.030). α-GOS responders had higher breath hydrogen (H 2) prechallenge than α-GOS nonresponders (P = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (prechallenge, adjusted P -value (P adj) = 0.024; postchallenge, P adj = 0.042) and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders (P adj = 0.041).

DISCUSSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H 2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.},
}

Humans
Double-Blind Method
Cross-Over Studies
Female
Fermentation
Male
Adult
*Oligosaccharides/adverse effects/administration & dosage
Breath Tests
*Dietary Fiber/adverse effects
*Fructans/adverse effects/administration & dosage
*Flatulence
*Gastrointestinal Microbiome/physiology
Middle Aged
Fatty Acids, Volatile/metabolism
Hydrogen/analysis
*Dietary Carbohydrates/adverse effects

@article {pmid42431948,
year = {2026},
author = {Neshat, SA and Santillan, E and Wuertz, S},
title = {Uncovering microbial life-history strategies under disturbance: a trait-based computational analysis of anaerobic systems.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42431948},
issn = {2055-5008},
mesh = {Anaerobiosis ; *Bioreactors/microbiology ; Sewage/microbiology ; Metagenomics/methods ; *Bacteria/classification/genetics ; *Microbiota ; },
abstract = {Trait-based approaches are helpful in simplifying ecosystem complexity to explore disturbance-diversity-function relationships. These frameworks classify organisms based on their functional characteristics-traits that influence growth, survival and reproduction-providing a mechanistic basis to understand how communities respond to changes in their environment. The application of these approaches has been successful in ecology, but to date has only been tested in a few microbial ecosystems, namely, soil microbial communities and aerobic bioreactors treating wastewater. Here, we employed Grime's competitor-stress-tolerant-ruderal framework in replicated mesophilic anaerobic bioreactors exposed to a disturbance (biomass removal) with varied frequencies at a constant number of disturbance events for 90 days. Bioreactors were inoculated with sludge from full-scale anaerobic digesters and fed with a mixture of primary and waste activated sludge. A genome-resolved metagenomics approach was utilised to assess the microbial communities in terms of composition and functional potential. We found that communities across the disturbance range were clustered into three groups, suggesting the adoption of a three-way life-history strategy. This study demonstrates, for the first time, the applicability of trait-based life-history strategies in anaerobic microbial systems under disturbance using genome-resolved techniques, providing a new perspective for understanding and managing microbial ecosystems under disturbance conditions.},
}

Anaerobiosis
*Bioreactors/microbiology
Sewage/microbiology
Metagenomics/methods
*Bacteria/classification/genetics
*Microbiota

@article {pmid42436166,
year = {2026},
author = {Chen, Y and Ma, J and Guo, Z and Chen, J and Wang, X and Xiao, J and Hu, D and Yan, J and Deng, W and Nu, Z and He, H and He, W and Luo, J and Zhang, YP and Li, Y},
title = {A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis).},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42436166},
issn = {2055-5008},
support = {CY22624109//Yunnan Provincial Universities Service Key Industry Technology Project - Doctoral Student Industry-Oriented Scientific Research Innovation Training Project/ ; KC-242410789//Graduate Research and Innovation Project of Yunnan University/ ; 2021YFD1200904//National Key Research and Development Program of China/ ; 32470654//National Natural Science Foundation of China/ ; 202407AA110003//Special funds for central guidance of local scientific and technological development/ ; 202601BC070001//Major Program of Yunnan Fundamental Research Projects/ ; XDYC-QNRC-2023-0371//"Xingdian Talent Support Program" Grant of Yunnan Province/ ; },
mesh = {Animals ; Cattle/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Rumen/microbiology ; *Host Microbial Interactions ; Diet/veterinary ; Transcriptome ; *Bacteria/classification/genetics/isolation & purification ; Adaptation, Physiological ; Stomach/microbiology ; Male ; },
abstract = {The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.},
}

Animals
Cattle/microbiology
Feces/microbiology
*Gastrointestinal Microbiome
Metagenome
Rumen/microbiology
*Host Microbial Interactions
Diet/veterinary
Transcriptome
*Bacteria/classification/genetics/isolation & purification
Adaptation, Physiological
Stomach/microbiology
Male

@article {pmid42611158,
year = {2026},
author = {Vock, I and Bargetzi, A and Weisser, M and Mueller, OK and Junker, M and Mehrkens, A and Neidhoefer, C and Hamelin, B and Hosch, S and Mertz, KD and Keller, PM and Kuehl, R},
title = {Hematogenous vertebral osteomyelitis caused by vaginal microbiota: metagenomic resolution of a polymicrobial anaerobic case.},
journal = {Infection},
volume = {54},
number = {5},
pages = {2999-3004},
pmid = {42611158},
issn = {1439-0973},
mesh = {Humans ; Female ; *Osteomyelitis/microbiology/diagnosis/drug therapy ; *Vagina/microbiology ; *Bacteria, Anaerobic/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; *Coinfection/microbiology ; *Microbiota ; Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Gardnerella vaginalis/isolation & purification ; },
abstract = {We describe a rare case of a 35-year-old female patient suffering from polymicrobial hematogenous vertebral osteomyelitis caused by vaginal microbiota following sexual intercourse. Anaerobic blood cultures yielded Fannyhessea vaginae and Gemelliphila asaccharolytica, and intraoperative tissue cultures from decompression surgery identified Gardnerella vaginalis. Beyond Fannyhessea vaginae and Gemelliphila asaccharolytica, 16S rRNA gene Nanopore sequencing of surgical tissue also detected high amounts of Parvimonas parva, Peptostreptococcus anaerobius, Marseillibacter massiliensis, and Gemelliphila palaticanis. Antibiotic treatment with broad anaerobic coverage resulted in complete clinical resolution. Retrospective metagenomic analysis of a cervical swab obtained 9 months earlier revealed Fannyhessea vaginae and G. vaginalis to be already present in the vaginal microbiota. This case highlights the potential for hematogenous dissemination of vaginal anaerobes after sexual intercourse and underscores the diagnostic challenges posed by fastidious anaerobic bacteria. Molecular techniques are helpful tools in uncovering pathogens that may escape conventional culture methods.},
}

Humans
Female
*Osteomyelitis/microbiology/diagnosis/drug therapy
*Vagina/microbiology
*Bacteria, Anaerobic/genetics/isolation & purification
Adult
RNA, Ribosomal, 16S/genetics
*Coinfection/microbiology
*Microbiota
Metagenomics
Anti-Bacterial Agents/therapeutic use
Gardnerella vaginalis/isolation & purification

@article {pmid42623301,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {86},
number = {21},
pages = {5374-5390},
pmid = {42623301},
issn = {1538-7445},
support = {P30 CA125123/CA/NCI NIH HHS/United States ; R01 CA282786/CA/NCI NIH HHS/United States ; R21 CA218732/CA/NCI NIH HHS/United States ; R37 CA237384/CA/NCI NIH HHS/United States ; 1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
mesh = {Animals ; Humans ; *Pancreatic Neoplasms/metabolism/pathology/microbiology/therapy ; Mice ; Tumor Microenvironment ; *Carcinoma, Pancreatic Ductal/metabolism/pathology/microbiology/therapy ; Cancer-Associated Fibroblasts/metabolism/pathology ; Interleukin-6/metabolism ; *Microbiota ; *Exercise/physiology ; Stromal Cells/metabolism/pathology ; Actins/metabolism ; Male ; Female ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer-associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

Animals
Humans
*Pancreatic Neoplasms/metabolism/pathology/microbiology/therapy
Mice
Tumor Microenvironment
*Carcinoma, Pancreatic Ductal/metabolism/pathology/microbiology/therapy
Cancer-Associated Fibroblasts/metabolism/pathology
Interleukin-6/metabolism
*Microbiota
*Exercise/physiology
Stromal Cells/metabolism/pathology
Actins/metabolism
Male
Female

@article {pmid42697801,
year = {2026},
author = {Htut, M and Lee, K and Nathwani, N and Rosenzweig, M and Janakiram, M and Goldsmith, S and Sanchez, JF and Scott, M and Keats, J and Krishnan, A and Rosen, ST and Wang, SS},
title = {Gut Microbiome Composition Is Associated With Response to CD38 Antibody (Daratumumab) Treatment Among Relapsed Multiple Myeloma Patients.},
journal = {Clinical lymphoma, myeloma & leukemia},
volume = {26},
number = {11},
pages = {743-750},
doi = {10.1016/j.clml.2026.08.004},
pmid = {42697801},
issn = {2152-2669},
mesh = {Humans ; Male ; Female ; *Multiple Myeloma/drug therapy/microbiology/pathology ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Aged ; *Antibodies, Monoclonal/therapeutic use/pharmacology ; Adult ; Treatment Outcome ; },
abstract = {INTRODUCTION: Growing data support interactions between host-gut microbes and treatment responses in multiple myeloma (MM), where a higher abundance of Eubacterium hallii in stool samples has been found among MM patients with negative minimal residual disease after induction therapy. Here, we evaluated changes in the gut microbiome associated with daratumumab (dara) based therapy in 40 MM patients, before and after therapy.

PATIENTS AND METHODS: Patients with relapsed MM and prior autologous transplantation who had received 1 to 4 prior lines of therapy were eligible. Two stool samples were collected, one within 1 week prior to dara (predara) and one immediately after 4 doses of dara (postdara). Metagenomics sequencing was conducted. Microbiome taxonomic analyses were performed using MetaPhlAn4, and microbial functional pathway analyses were conducted using HUMAnN3.6. QIIME2 was used for compositional and statistical analyses.

RESULTS: Of 40 participants enrolled, there were 5 nonresponders; 35 patients achieved partial response (PR) or better (responders). Among responders, 10 patients achieved complete remission (CR), and 25 patients achieved either very good partial response (VGPR) or PR. There were no statistically significant differences between overall pre and postdara gut microbiomes. Differential abundance analysis (ANCOM-BC) showed statistically significant (q ≤ 0.05) overgrowth of Alistipes finegoldii and Acidaminococcus intestini species in responders and Ruminococcus torques, Sellimonas intestinalis and Clostridium symbiosum in nonresponders. Compared to non-CR, CR samples showed enrichment of Faecalibacterium prausnitzii; non-CR samples were enriched in Segatella copri and Faecalimonas umbilicata.

DISCUSSION/CONCLUSION: Our results suggest differences in species between clinical responders and nonresponders, but larger prospective studies are needed to confirm these results.},
}

Humans
Male
Female
*Multiple Myeloma/drug therapy/microbiology/pathology
Middle Aged
*Gastrointestinal Microbiome/drug effects
Aged
*Antibodies, Monoclonal/therapeutic use/pharmacology
Adult
Treatment Outcome

@article {pmid42949890,
year = {2026},
author = {Wang, H and Chang, X and Han, S and Guo, J and Xia, Z and Xiong, W},
title = {Multi-omics integration reveals L-arginine as a key mediator linking dietary protein to weight change in cats: an exploratory study.},
journal = {Journal of animal science},
volume = {104},
number = {},
pages = {},
pmid = {42949890},
issn = {1525-3163},
mesh = {Animals ; *Arginine/metabolism ; Cats/physiology ; *Dietary Proteins/metabolism/administration & dosage/pharmacology ; Diet/veterinary ; Animal Feed/analysis ; Male ; Multiomics ; Female ; Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; },
abstract = {Cats exhibit an insufficient endogenous capacity for arginine synthesis, making dietary protein a core factor in nitrogen homeostasis. In this study, we investigated whether protein level-induced body weight change is mediated by host-microbiome interactions and serum metabolites. A 180-d trial was conducted on 30 cats fed three isocaloric diets with varying crude protein levels (LP: 28%, MP: 36%, HP: 46%). Fecal shotgun metagenomic sequencing, serum short-chain fatty acid analysis, untargeted metabolomics, and targeted amino acid profiling were integrated and then subjected to causal mediation analysis. The HP diet improved protein digestibility (HP: 93.29% vs. LP: 89.36%, P = 0.027) and attenuated body weight loss (HP: -3.43% vs. -14.52%, P = 0.031) without compromising fecal scores (all groups: 2.5-3.0 throughout the trial) or intestinal barrier integrity, as indicated by unchanged serum DAO, D-LA, and LPS levels. The MP group significantly enhanced humoral immunity, as evidenced by higher serum IgA, IgG, and IgM concentrations (P < 0.05 vs. LP and HP), while the HP group boosted antioxidant capacity, with significantly increased SOD and T-AOC activities (P < 0.05 vs. LP and MP). High protein increased the abundance of Phocaeicola and decreased that of Megasphaera. Serum arginine biosynthesis pathways and branched-chain amino acids were significantly enriched in MP and HP groups compared with the LP group (P < 0.05 for both comparisons). Crucially, multi-omics network and causal mediation analysis identified L-arginine as a statistically confirmed key regulatory node in the protein-weight relationship, as evidenced by a significant indirect effect (ACME = 0.208, P = 0.006) and a non-significant direct effect (ADE = 0.31, P = 0.23). These results suggested that L-arginine may serve as a key regulatory node mediating this process linking dietary protein to body weight in cats, providing a novel mechanistic target for precision nutritional interventions in feline weight management.},
}

Animals
*Arginine/metabolism
Cats/physiology
*Dietary Proteins/metabolism/administration & dosage/pharmacology
Diet/veterinary
Animal Feed/analysis
Male
Multiomics
Female
Animal Nutritional Physiological Phenomena
Gastrointestinal Microbiome
Feces/microbiology/chemistry

@article {pmid42970519,
year = {2026},
author = {Naumova, OY and Dobrynin, PV and Litwin, G and Rychkov, SY and Milham, MP and Grigorenko, EL},
title = {Salivary microbiome, socioeconomic status, and cognitive performance: Triangulating the relationship.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0361602},
pmid = {42970519},
issn = {1932-6203},
mesh = {Humans ; *Microbiota ; Child ; *Cognition/physiology ; *Social Class ; Adolescent ; Female ; Male ; *Saliva/microbiology ; Black or African American ; Hispanic or Latino ; Wechsler Scales ; Socioeconomic Disparities in Health ; },
abstract = {Research increasingly demonstrates that endogenous bacterial communities (microbiomes) are associated with both cognitive functioning and socioeconomic status (SES). In this study, we used a metagenomics approach to characterize oral microbiome diversity in Hispanic and African American children aged 6-16 years. We examined how microbiome composition and SES were related to cognitive performance, as assessed by the Wechsler Intelligence Scale for Children (WISC). Our findings indicate that SES and the microbiome contributed complementary, comparably sized influences on cognitive functioning. Together, variability in conventional SES indicators and microbiome composition accounted for approximately 10% of the variability in WISC scores. These results highlight the importance of integrating both social and biological determinants of health when studying cognitive performance and other psychological outcomes.},
}

Humans
*Microbiota
Child
*Cognition/physiology
*Social Class
Adolescent
Female
Male
*Saliva/microbiology
Black or African American
Hispanic or Latino
Wechsler Scales
Socioeconomic Disparities in Health

@article {pmid42971771,
year = {2026},
author = {Murthy, SSN and Chuan, J and Jiang, Y and Chen, W and Beiko, RG and Li, X},
title = {Seasonal and Environmental Influences on Microbial Community Dynamics in the Dunk River Watershed, Prince Edward Island, Canada.},
journal = {Environmental microbiology},
volume = {28},
number = {11},
pages = {},
doi = {10.1111/1462-2920.70469},
pmid = {42971771},
issn = {1462-2920},
support = {//Canadian Food Inspection Agency/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Dalhousie University/ ; },
mesh = {*Rivers/microbiology/chemistry ; Seasons ; *Microbiota ; Prince Edward Island ; *Bacteria/classification/isolation & purification/genetics ; Ecosystem ; Metagenomics ; },
abstract = {Riverine ecosystems are crucial biogeochemical hubs, with their microbial communities playing a key role in nutrient cycling and overall ecosystem health. This study used shotgun metagenomic sequencing to characterize the seasonal and environmental drivers of taxonomic and functional microbial community structure (read depth between 1.91 and 30.44 bp) in four tributaries of the Dunk River watershed in Prince Edward Island (PEI), a landscape shaped by intensive agriculture and groundwater-dominated streamflow, where the seasonal and land-use impacts on the river's microbiome remain understudied. Although taxonomic composition showed no significant spatial variation among sampling sites, functional profiling identified subtle but distinct spatial signatures, primarily driven at the site with the least human impacts. Mass effects driven by above- or below-ground water dispersal pathways may override local selective pressures, resulting in a more uniform community structure across different locations. The study also identified significant correlations between certain rare microbial taxa and nutrient concentrations. This work provides critical baseline data on microbial ecology in PEI river systems, indicating that while temporal factors are the primary identifiable drivers among the measured variables, a substantial majority of the community variance remains unexplained, likely reflecting the inherent stochasticity of open riverine ecosystems.},
}

*Rivers/microbiology/chemistry
Seasons
*Microbiota
Prince Edward Island
*Bacteria/classification/isolation & purification/genetics
Ecosystem
Metagenomics

@article {pmid42972344,
year = {2026},
author = {Rutkowska, N and Wojtynek, J and Śliżewska, W and Nielipiński, M and Sypka, M and Kurek, Z and Łukanowska, O and Prażanowska, W and Modrzejewska, P and Lewocha, B and Horążak, W and Naporowski, I and Bednarek, W and Nielipińska, D and Drożdżyński, P and Marchut-Mikołajczyk, O},
title = {Integrating culture-dependent and culture-independent approaches to explore the diversity of endophytic bacteria associated with Urtica dioica L. in Poland with screening of pigment-producing isolates.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42972344},
issn = {1475-2859},
support = {SKN/SP/571010/2023//Ministerstwo Nauki i Szkolnictwa Wyższego, Poland/ ; SKN/SP/571010/2023//Ministerstwo Nauki i Szkolnictwa Wyższego, Poland/ ; },
mesh = {*Endophytes/isolation & purification/classification/genetics/metabolism ; *Urtica dioica/microbiology ; Poland ; *Bacteria/isolation & purification/classification/metabolism/genetics ; *Pigments, Biological/biosynthesis ; Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Plants can thrive in changing environmental conditions with the help of microorganisms that inhabit their tissues, known as endophytes. However, many endophytes do not grow under standard laboratory conditions, but metagenomic analysis provides insights into microbial diversity and community structure. This study aimed to compare communities of endophytic bacteria from stinging nettle (Urtica dioica L.) isolated throughout different regions of Poland, both culturable and non-culturable, and to identify shared bacterial taxa across all locations, which may represent a putative core microbiome.

RESULTS: From all regions, 66 bacterial isolates were obtained. 32% of them were identified, mostly as Bacillus and Pseudomonas members, which are common endophytes of many plants. Although a substantial proportion of reads remained unclassified, metagenomic data enabled the tentative identification of several genera present across all samples, including Acinetobacter, Bacillus, Citrobacter, Enterococcus, Escherichia, Klebsiella, Paenibacillus, Salmonella, Vibrio, and Xanthomonas. Among the isolates, Exiguobacterium sp. SP2-R3 exhibited the most intense orange pigmentation. The results indicate that the pigment is putatively quinone-like and demonstrates promising scavenging activity.

CONCLUSIONS: The study deepens our understanding of U. dioica L. endophytic communities and highlights the value of combining cultivation-based methods with metagenomic approaches. Also, among the isolates with visible potential to produce pigments, the best producer was selected and identified. It is recognized that those isolates may possess additional valuable properties that warrant deeper investigation.},
}

*Endophytes/isolation & purification/classification/genetics/metabolism
*Urtica dioica/microbiology
Poland
*Bacteria/isolation & purification/classification/metabolism/genetics
*Pigments, Biological/biosynthesis
Phylogeny
Biodiversity
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid42972501,
year = {2026},
author = {Huang, Y and Shi, J and Li, Z and Ma, Y and He, P and Yang, R and Lei, Z},
title = {Effects of castration-associated hormonal changes on rumen microbiota, metabolism, and meat quality in Holstein cattle.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42972501},
issn = {1471-2180},
support = {2026CXZX-781//Gansu Provincial Department of Education: "Innovation Star" Project/ ; 25ZDNA008//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology/metabolism ; *Rumen/microbiology/metabolism ; Male ; *Hormones/blood/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Meat/analysis ; *Orchiectomy/veterinary ; *Gastrointestinal Microbiome ; *Microbiota ; Animal Feed/analysis ; *Red Meat/analysis ; Metabolomics ; },
abstract = {BACKGROUND: It remains unclear whether hormones and microorganisms affect growth performance and meat quality, and whether there is an interaction between them. In this study, nine Holstein bulls and nine Holstein steers were fed for 270 days under the same management conditions. We combined rumen microbiomics, metabolomics, and epithelial transcriptomics with serum and muscle metabolomics as well as serum hormone detection, to explore how rumen microbes and hormones jointly regulate growth performance and beef quality of Holstein cattle.

RESULTS: Compared with bull group, the Lightness (L*), Redness (a*), Yellowness (b*), intramuscular fat and marbling score were significantly increased in steer group (P < 0.05). Serum testosterone, triiodothyronine, thyroxine, growth hormone, leptin, and glucagon levels were significantly lower in steer group, which also reflected that castration inhibited final body weight (FBW), average daily gain (ADG), dry matter intake (DMI), gain feed ratio (G/F) (P < 0.05). Cellulase, pectinase, β-glucosidase, acetate, propionate and butyrate were significantly lower, while α-amylase and lipase were significantly higher in steer group (P < 0.05). The rumen metagenome indicates unclassified_o_Bacteroidales and unclassified_f_Lachnospiraceae were significantly abundant of steer and bull groups, respectively; the functions that determined beef quality were primarily in lipid and fat anabolic pathway; and the hormones and microbes had a strong correlation. Serum and muscle metabolites of steer group were involved in fatty acid metabolism, whereas bull group were primarily involved in amino acid and protein metabolism; and Lysophosphatidylethanolamines (LPE (0:0/20:3) and (20:3/0:0)) significantly influenced marbling score and intramuscular fat. The explanations of comprehensive membership value (CMV) in the rumen microbiome, rumen metabolism, serum metabolism, muscle metabolism, and rumen epithelial genes were 29.90%, 4.50%, 10.50%, 1.60%, and 0.01%.

CONCLUSION: Castration could inhibit growth performance and improve meat quality, by mainly regulating rumen microorganisms (29.90%) and serum metabolism (10.50%); this study also provides a significant theoretical basis for analyzing the regulatory mechanisms of castration on growth performance and meat quality of cattle.},
}

Animals
Cattle/growth & development/microbiology/metabolism
*Rumen/microbiology/metabolism
Male
*Hormones/blood/metabolism
Bacteria/classification/genetics/isolation & purification/metabolism
*Meat/analysis
*Orchiectomy/veterinary
*Gastrointestinal Microbiome
*Microbiota
Animal Feed/analysis
*Red Meat/analysis
Metabolomics

@article {pmid42973669,
year = {2026},
author = {Scaffidi, AD and Scaffidi, SJ and Carling, J and Fajfer, A and Ali, M and Ono, R and Hilyard, A and Buksbaum, RE and Kumar, V and Shukla, R and Mishra, S and Jain, S and Yadav, H and Heckmann, BL},
title = {Rubicon is a critical regulator of immune barrier integrity and limits enteric pathogen infection.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1889997},
pmid = {42973669},
issn = {1664-3224},
mesh = {Animals ; Intestinal Barrier Function ; Mice ; Mice, Knockout ; *Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology ; *Intestinal Mucosa/immunology/metabolism/microbiology ; *Salmonella typhimurium/immunology ; Gastrointestinal Microbiome/immunology ; *Salmonella Infections/immunology ; Mice, Inbred C57BL ; Enterobacteriaceae Infections/immunology ; },
abstract = {INTRODUCTION: Intestinal immune barrier integrity is governed by coordinated epithelial renewal, junctional organization, and vesicular trafficking. Herein, we identify a previously undefined role for the noncanonical autophagy protein Rubicon in the maintence of the intestinal immune barrier. Rubicon-dependent vesicular pathways, including conjugation of ATG8 proteins to single membranes (CASM) function to support vesicle trafficking homeostasis.

METHODS: Mice with global deletion of Rubicon (Rubcn[-]/[-]) were used to evaluate impact on gut permeability using FITC-dextran, overall intestinal anatomy and histopathology, junction protein homeostasis, and pathogen response.

RESULTS AND DISCUSSION: Loss of Rubicon led to impaired intestinal barrier function and increased intestinal permeability, supported by a 10-fold increase in circulating FITC-dextran. Rubicon-deficiency was also associated with multiple anatomical changes including elongation of the small and large intestines, shortened small-intestinal villi, epithelial hyperplasia, and lymphoid expansion, amongst others. Mechanistically, Rubicon-deficiency resulted in aberrant trafficking and mislocalization of key junctional proteins including E-cadherin and occludin. Furthermore, metagenomic analysis of the intestinal microbial community revealed broad restructuring of the intestinal microbiota compared to WT animals. Importantly, Rubicon-deficiency hypersensitized mice to enteric pathogen infection. Rubcn[-]/[-] mice exhibited accelerated and worsened mortality in addition to systemic bacteremia following infection with Salmonella Typhimurium. Bacterial burden was significantly in multiple tissues including mesenteric lymph nodes, spleen, and liver, further supporting failure of the intestinal barrier following loss of Rubicon. Collectively, these findings identify Rubicon as a novel and foundational regulator of IEC vesicular processing, epithelial junctional organization, intestinal barrier function, and host defense beyond established roles in innate immune cells.},
}

Animals
Intestinal Barrier Function
Mice
Mice, Knockout
*Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology
*Intestinal Mucosa/immunology/metabolism/microbiology
*Salmonella typhimurium/immunology
Gastrointestinal Microbiome/immunology
*Salmonella Infections/immunology
Mice, Inbred C57BL
Enterobacteriaceae Infections/immunology

@article {pmid42974438,
year = {2026},
author = {Pruksangkul, S and Termsaithong, T and Mhuantong, W and Limpiyakorn, T and Sonthiphand, P},
title = {Effects of chemical fertilizer application on soil properties, banana (Musa paradisiaca) yields, and soil microbiomes in a long-term cultivation field.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21912},
pmid = {42974438},
issn = {2167-8359},
mesh = {*Musa/growth & development ; *Fertilizers/analysis ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil/chemistry ; Nitrogen/analysis ; Potassium/analysis ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Hydrogen-Ion Concentration ; Agriculture/methods ; },
abstract = {Due to climate change and increasing food demand, conventional agriculture relies heavily on chemical fertilizers. This study investigated the effects of chemical fertilizer application on soil properties, banana (Musa paradisiaca) yields, and soil microbiomes in a long-term cultivation field. Metagenomic analysis of the 16S rRNA gene provided a comprehensive overview of soil microbial diversity and functional potential. Nitrogen, phosphorus, and potassium (NPK) fertilizers at 0, 119, 238, and 476 kg ha[-1] were applied monthly for one year. Fertilizer application significantly altered soil properties and microbial community dynamics but had no significant effect on banana yields. Higher fertilizer rates reduced soil pH and increased available phosphorus and exchangeable potassium, while total nitrogen and organic matter remained relatively unchanged. Elevated NPK inputs increased the abundance of specific microbial taxa, including Bacillus, Streptomyces, uncultured bacterium JG30-KF-AS9, and Nitrospira, while Xanthobacteraceae, bacteriap25, Micromonosporaceae, Nocardioides, Subgroup 6, and Gemmatimonadaceae consistently represented core taxa across all treatments. Pearson's correlation analysis revealed that soil total nitrogen and exchangeable potassium were positively correlated with the abundance of key plant growth-promoting and nitrifying taxa, including Pseudomonas and Nitrospira, whereas soil pH was negatively correlated with Acidothermus, Nitrospira, and Bacillus, but positively correlated with Subgroup 6. Functional gene profiles further indicated enhanced anaerobic processes associated with carbon, nitrogen, and sulfur cycling. The findings suggest that long-term nutrient accumulation resulting from repeated fertilization and crop residue inputs may sustain banana crops throughout the 10-month production period without additional fertilization. Together, these findings highlight the need for fertilizer regimes tailored to long-term soil nutrient status, contributing to both sustainable agriculture and microbiome-informed crop management.},
}

*Musa/growth & development
*Fertilizers/analysis
*Soil Microbiology
*Microbiota/drug effects
*Soil/chemistry
Nitrogen/analysis
Potassium/analysis
Phosphorus/analysis
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Hydrogen-Ion Concentration
Agriculture/methods

@article {pmid42975318,
year = {2026},
author = {Bajaj, JS and Davis, BC and Puri, P and Gallagher, ML and Fagan, A and Obolewicz, H and Mousel, T and Boja, SH and Sikaroodi, M and Gillevet, PM},
title = {Rifamycin use and gut microbial antibiotic resistance genes in cirrhosis: Results from a double-blind, placebo-controlled clinical trial.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2757339},
doi = {10.1080/19490976.2026.2757339},
pmid = {42975318},
issn = {1949-0984},
mesh = {Humans ; *Rifamycins/therapeutic use/pharmacology/administration & dosage ; Double-Blind Method ; *Liver Cirrhosis/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Female ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; Middle Aged ; Aged ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance gene (ARG) carriage is associated with poor outcomes in patients with liver cirrhosis, which is worsened by repeated antibiotic exposure and hospitalizations. While the semi-synthetic rifamycin derivative, rifaximin, has recently been linked to ARG expansion preclinically, the effects of rifamycin SV MMX (RiVM) on the gut resistome remain unknown. We evaluated longitudinal resistome changes with RiVM in cirrhosis. The randomized, double-blind, placebo-controlled RIVET trial (15 RiVM, 15 placebo) included compensated cirrhosis patients who underwent shotgun metagenomic sequencing before/after 30 days of therapy. ARGs were annotated using the Comprehensive Antibiotic Resistance Database. The longitudinal resistome was evaluated using univariable and multi-variable methods (LEfSe, paired-Wilcoxon testing, and MaAsLin3), and machine learning (ML) was used to determine ARG changes at subject and group levels. RiVM induced minimal perturbation of the gut resistome, without significant change in ARGs versus after FDR adjustment. Complementary approaches (univariable and multivariable) identified a trend towards lower vancomycin resistance ARGs, including vanW and vanT operon-associated genes, after RiVM exposure. In contrast, several Enterobacteriaceae-associated multidrug efflux regulators (including evgS, emrK, and mdtA) showed nominal increases post-rifamycin that did not withstand FDR. Group-level ML demonstrated limited discrimination between groups; however, within-subject longitudinal models achieved improved classification performance. No increase in infections or treatment-related safety concerns was observed. We conclude that rifamycin MMX was not associated with infections and did not enrich antimicrobial resistance genes compared to placebo in a small randomized 30-day clinical trial in patients with compensated cirrhosis. There was a tendency towards reduced vancomycin resistance and ARG reduction after rifamycin exposure. Registration: NCT04082780 www.clinicaltrials.gov.},
}

Humans
*Rifamycins/therapeutic use/pharmacology/administration & dosage
Double-Blind Method
*Liver Cirrhosis/microbiology/drug therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Female
*Bacteria/genetics/drug effects/isolation & purification/classification
*Gastrointestinal Microbiome/drug effects/genetics
Male
Middle Aged
Aged
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics

@article {pmid42976166,
year = {2026},
author = {López-Gutiérrez, S and Espinosa-Barrera, LA and Soto-Hernández, A and Zuleta-Prada, H and Bustos-Brito, C and Cardona-Félix, CS and Utrilla, J and Velazquez-Cruz, B and Cárdenas-Conejo, Y and Araujo-León, JA and Aguilar-Hernández, V and Osuna-Castro, JA and Esquivel, B and Serrano-Posada, H and Centeno-Leija, S},
title = {A Baltic Sea microbiome-derived Type III polyketide synthase produces host-protective alkylresorcinols in E. coli.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0361965},
doi = {10.1371/journal.pone.0361965},
pmid = {42976166},
issn = {1932-6203},
mesh = {*Escherichia coli/metabolism/genetics ; *Polyketide Synthases/metabolism/genetics/chemistry ; *Resorcinols/metabolism/chemistry ; *Microbiota ; },
abstract = {Marine microorganisms are a prolific source of novel polyketide synthases (PKSs) that generate structurally diverse and functional polyketides. Here, we identify a novel type III PKS, ArsMB, from Pontimonas sp. via metagenomic mining of a Baltic Sea microbiome. Heterologous expression of arsMB synthetic gene in an Escherichia coli host that lacks a native type III PKS, combined with a two-step strategy to boost acyl-CoA precursor availability in a glucose-mineral medium, enabled the in vivo synthesis of two cell-associated alkylresorcinols, identified by GC-MS as 5-pentadecyl-1,3-benzenediol (ars1) and 5-tridecyl-1,3-benzenediol (ars2). The product profile is consistent with a tetraketide alkylresorcinol biosynthetic pathway utilizing C16 and C14 acyl starter units, drawn from the host acyl-CoA pool. In agreement, AlphaFold2-based structural modeling predicts a Cys139/His275/Asn308 catalytic triad and a long hydrophobic substrate tunnel compatible with long-chain acyl starter units. E. coli producing the amphipathic cell-associated alkylresorcinols ars1/ars2 exhibited increased resistance to muralytic digestion by endolysins and to hydrogen peroxide. These findings expand the known repertoire of marine-derived type III PKSs and highlight the biotechnological potential of ArsMB-derived alkylresorcinols.},
}

*Escherichia coli/metabolism/genetics
*Polyketide Synthases/metabolism/genetics/chemistry
*Resorcinols/metabolism/chemistry
*Microbiota

@article {pmid42976318,
year = {2026},
author = {Gray, K and Benis, A and Dueholm Müller, S and Winkel, K and Borda, A},
title = {Informatics for the Planet: Integrating Species, Ecosystems, and Geophysical Data to Manage the Health of Earth Systems.},
journal = {JMIR medical informatics},
volume = {14},
number = {},
pages = {e113778},
doi = {10.2196/113778},
pmid = {42976318},
issn = {2291-9694},
mesh = {*Ecosystem ; *Earth, Planet ; Humans ; *Medical Informatics ; Climate Change ; },
abstract = {Biomedical and health informatics has traditionally focused on human-centric clinical data to support individual patient care and health systems. However, contemporary health challenges driven by climate change, biodiversity loss, and ecological degradation demand an expanded paradigm that addresses interdependencies among human, animal, and environmental health. This editorial introduces a new JMIR Medical Informatics section called "Planetary Health Informatics"-an essential evolution extending informatics praxis beyond human health care and toward Earth's interconnected systems. JMIR Medical Informatics is launching a call for papers for this new section dedicated to advancing planetary health informatics (PHI) theory, methods, and applications for a sustainable future shaped by humans' impact on Earth. We invite authors to submit work that explores how PHI integrates species, ecosystem, and geophysical data to address critical global challenges, including metagenomic disease surveillance, climate-related hazard forecasting, environmental pollution monitoring, and health infrastructure decarbonization. By synthesizing broader ecological frameworks, we present a road map for transforming fragmented data streams into planetary-scale intelligence.},
}

*Ecosystem
*Earth, Planet
Humans
*Medical Informatics
Climate Change

@article {pmid42967701,
year = {2026},
author = {Liu, Y and Niu, Y and Xu, N and Li, M and Dong, M and Zhou, Z and Ma, Y and Wang, C and Li, Y and Si, Z and Fang, H and Chai, H and Sun, Y and Chen, P},
title = {Unraveling multidimensional heterogeneity of the Astragalus microbiome: An integrative multi-omics and machine learning framework for biomarker discovery.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120864},
doi = {10.1016/j.foodres.2026.120864},
pmid = {42967701},
issn = {1873-7145},
mesh = {*Machine Learning ; Multiomics ; *Microbiota/genetics ; Rhizosphere ; Biomarkers/analysis ; Plant Roots/microbiology ; *Astragalus Plant/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; China ; },
abstract = {Astragalus (primarily represented by A. mongholicus and A. membranaceus) is a widely used functional food whose quality is closely associated with geographical origin, a concept known as geoherbalism. However, the relationship between its microbiota and bioactive constituents across different plant species, production regions, cultivation patterns, and chemotypes remains poorly understood. In this study, we characterized the endophytic microbial communities of Astragalus roots from 61 samples collected across six major cultivation regions in four Chinese provinces using high-throughput amplicon sequencing (targeting the 16S rRNA and ITS regions). We further integrated publicly available rhizosphere metagenomic (PRJNA1119562) and root transcriptomic (PRJNA1119057) datasets to explore microbial functional potential and host-microbe interactions. Machine learning models were developed to predict the levels of key bioactive ingredients (Astragaloside IV [AS-IV] and Calycosin-7-O-β-D-glucoside [CG]), and candidate biomarkers were validated by qPCR. The composition and diversity of endophytic microbiota varied significantly with plant species, geographical origin, cultivation pattern (cultivated, imitated-wild, and wild), and chemotype. Specific taxa, including Penicillium, Coprinopsis, and Pseudomonas, were enriched in high-quality samples, and species-specific microbial signatures were also observed. Rhizosphere metagenomic profiling revealed enhanced energy and amino acid metabolism in low-quality samples, suggesting potential competition for key substrates. Transcriptomic analysis identified differentially expressed genes involved in secondary metabolism, some of which correlated with specific rhizosphere microbes. Lactarius and Alistipes were identified as candidate microbial biomarkers through machine learning and further validated by qPCR assays targeting their corresponding ITS and 16S rRNA gene sequences, respectively, achieving accuracies of 85% and 95% in internal and external validation. However, the relatively limited validation cohorts may not fully represent the geographic and cultivation diversity of Astragalus, and larger-scale validation using samples covering broader geographic origins and cultivation conditions is required to further confirm the robustness and generalizability of these microbial biomarkers. Overall, this study provides a comprehensive characterization of the Astragalus microbiome, highlighting its strong associations with plant species, geoherbalism, cultivation practices, and bioactive accumulation. The validated biomarkers offer promising tools for quality assessment and support microbiome-based strategies for improving the functional quality of Astragalus as a food ingredient.},
}

*Machine Learning
Multiomics
*Microbiota/genetics
Rhizosphere
Biomarkers/analysis
Plant Roots/microbiology
*Astragalus Plant/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Metagenomics
China

@article {pmid42967713,
year = {2026},
author = {Chen, S and Chen, R and Tong, S and Liu, W and Ni, L and Lv, X},
title = {Deciphering the microbial regulation of volatile flavor compounds and biogenic amines in Hongqu vinegar fermentation: An integrated metagenomic and metabolomic insight.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120889},
doi = {10.1016/j.foodres.2026.120889},
pmid = {42967713},
issn = {1873-7145},
mesh = {*Fermentation ; *Biogenic Amines/analysis/metabolism ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/analysis/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Taste ; *Food Microbiology ; *Flavoring Agents/analysis ; Gas Chromatography-Mass Spectrometry ; China ; Microbiota ; },
abstract = {Hongqu vinegar (HQV), one of China's four most prestigious traditional vinegars, is celebrated for its unique sensory attributes and potential health benefits, which are closely associated with the complex microbial communities within the fermentation starter, Hongqu. However, the microbial determinants driving the divergence in flavor quality and safety profiles among HQVs produced using distinct regional starters remain poorly defined. This study employed an integrated metabolomic and metagenomic approach to dissect the microbial regulation of volatile flavor compounds (VFCs) and biogenic amines (BAs) throughout the fermentation of HQVs produced with two geographically distinct starters: Gutian Hongqu and Wuyi Hongqu. Key microbial regulatory mechanisms driving flavor formation and BAs accumulation were elucidated through comprehensive functional gene annotation and metabolic pathway reconstruction. Our results reveal significant divergence in BA and VFC profiles between Gutian Hongqu vinegar (GT-HQV) and Wuyi Hongqu vinegar (WY-HQV). Notably, WY-HQV exhibited approximately 2.3-fold higher total BAs, particularly the hazardous amines histamine and tyramine, by the end of the acetic acid fermentation stage, underscoring critical safety considerations for starter selection. GC-MS-based metabolomic profiling revealed that GT-HQV was characterized by significantly higher levels of desirable VFCs (e.g., ethyl acetate, isoamyl lactate, α-terpineol, hexanoic acid, acetoin). Concurrently, GT-HQV showed a 7.5-fold higher lactic acid content, which contributed to its smoother and more balanced sensory profile. Metagenomic analysis linked these phenotypic disparities to distinct microbial community structures and functional potentials, with Weissella, Pediococcus, Klebsiella, Pantoea, Lentilactobacillus, Lactiplantibacillus, Monascus, and Aspergillus identified as key differentiating taxa differentiating GT-HQV and WY-HQV fermentation, suggesting their pivotal roles in shaping the distinct final product attributes. Functional gene annotation confirmed that the divergence in BA profiles and VFC formation is largely attributed to the distinct functional potentials, specifically the genes governing amino acid decarboxylation and fatty acid/ester metabolism. Lactic acid bacteria (LABs), particularly Lentilactobacillus species, were identified as key microbial taxa harboring the primary genetic potential for hazardous BA accumulation in WY-HQV. Collectively, this study elucidates the core functional microbiota and key metabolic genes influencing the biosynthesis of BAs and characteristic VFCs during HQV brewing, providing a scientific foundation for targeted enhancement of flavor quality and safety through starter culture optimization and microbiome engineering.},
}

*Fermentation
*Biogenic Amines/analysis/metabolism
*Acetic Acid/metabolism/analysis
*Volatile Organic Compounds/analysis/metabolism
*Metagenomics/methods
*Metabolomics/methods
Taste
*Food Microbiology
*Flavoring Agents/analysis
Gas Chromatography-Mass Spectrometry
China
Microbiota

@article {pmid42967915,
year = {2026},
author = {Zhang, Y and Gilbert, JA and Nie, L and Zhang, YM and Huang, P and Luo, W and Xu, X and Sun, R and Fan, K and Shi, K and Xu, X and Zhou, NY and Zhang, JB and Chu, H},
title = {Herbicide degradation is driven by communication-mediated division of labor in synthetic communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42967915},
issn = {2041-1723},
support = {42407176)//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M753333//China Postdoctoral Science Foundation/ ; },
mesh = {*Herbicides/metabolism ; Soil Microbiology ; Biodegradation, Environmental ; Quorum Sensing ; Zea mays ; *Soil Pollutants/metabolism ; Bacteria/metabolism/genetics ; *Microbiota ; Soil/chemistry ; Acyl-Butyrolactones/metabolism ; },
abstract = {The persistence of herbicide residues poses a major challenge to agricultural productivity and soil health in the Northeast Black Soil region of China. To address this, we employed a 'top-down' strategy to construct two synthetic microbial communities (SynComs YKB and HKB) which enhanced the co-degradation of multiple herbicides under both laboratory and soil conditions. Multi-omics analyses demonstrated that each SynCom functioned through a metabolic division of labor and utilized quorum sensing (QS) to regulate this metabolism. Specifically, Acyl-homoserine lactones governed the functional dynamics of YKB and autoinducer-2 primarily regulated HKB. QS molecules modulated stable microbial interactions and biodegradation through both direct and indirect regulatory effects. Maize pot experiments combined with metagenomic profiling demonstrated that the SynComs provided additional benefits for the soil ecosystem and confirmed the critical role of QS-mediated interactions between the SynComs and indigenous microorganisms. Overall, we present a bioaugmentation strategy to alleviate herbicide residues in soil ecosystems, offering insights into communication mechanisms, interaction models and design principles of SynComs for environmental bioremediation.},
}

*Herbicides/metabolism
Soil Microbiology
Biodegradation, Environmental
Quorum Sensing
Zea mays
*Soil Pollutants/metabolism
Bacteria/metabolism/genetics
*Microbiota
Soil/chemistry
Acyl-Butyrolactones/metabolism

@article {pmid42805588,
year = {2026},
author = {Metris, A and Guan, R and Ampatzoglou, A and Murphy, B},
title = {Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.},
journal = {Journal of food protection},
volume = {89},
number = {11},
pages = {100933},
doi = {10.1016/j.jfp.2026.100933},
pmid = {42805588},
issn = {1944-9097},
mesh = {Humans ; *Microbiota ; },
abstract = {Advances in sequencing technologies have enabled increasingly detailed characterization of the human microbiome in clinical studies, but interpretation of microbiome modulation that has relevance to health and disease characterization or safety assessments remains methodologically challenging. Taxonomic profiles generated by amplicon or shotgun sequencing are inherently compositional, sparse, and limited by detection, which complicates differential abundance analysis and may lead to unstable or misleading conclusions, especially in low-biomass settings where contamination and under-detection are concerns. Here, we review strategies used to analyze and complement sequencing-derived taxonomic count data, with the aim of obtaining more quantitative information on microbial differential abundance and viability. These include transformations for relative abundance-based analyses and bias corrections between samples based on mathematical assumptions or additional experimental measurements such as spike-ins, broad-range qPCR, and flow cytometry. We find that there is no consensus on which method best addresses compositionality and that detection level and significance of low-level microbes in health and disease are overlooked. We discuss the limitations of sequence-based methods, such as the biases induced by the experimental and analytical process, as well as viability measurements for meaningful differential abundance assessment. We illustrate the need to integrate prevalence as well as abundance and the importance of covariates in models in the case of bacterial vaginosis. Overall, meaningful assessment of microbiome perturbations requires not only statistical correctness of differential abundance analysis but also careful study design, appropriate measurement choices, quantitative context, and explicit recognition of the biological and analytical limits of sequencing-derived data.},
}

Humans
*Microbiota

@article {pmid42965683,
year = {2026},
author = {Li, S and Cheng, R and He, M and Hu, Q and Xu, H and Wu, X and Liu, X and Cai, X and Miao, Z},
title = {Exploring the relationship among nutrition, gut microbiota and musculoskeletal health in children with Duchenne muscular dystrophy: a cross-sectional study.},
journal = {European journal of nutrition},
volume = {65},
number = {8},
pages = {},
pmid = {42965683},
issn = {1436-6215},
support = {S23053//Sichuan Medical Association Foundation/ ; 2024-YF05-00493-SN//Foundation of Chengdu Municipal Science and Technology/ ; 82404268//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Child ; Female ; *Gastrointestinal Microbiome/physiology ; *Nutritional Status ; Bone Density ; *Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications ; Body Composition ; China ; Energy Intake ; Child, Preschool ; Adolescent ; Diet ; },
abstract = {AIMS: This study was aimed to explore the nutritional risk standards and nutritional support strategies in Chinese children with DMD.

METHODS: This cross-sectional study included 217 children with DMD. Nutritional status was determined by measuring body composition and clinical testing indicators. Three-day 24-h diet recalls were used to assess nutrient intake. Metagenomic sequencing was performed to detect gut microbiota.

RESULTS: Children with obesity or high body fat percentage (BF%) had higher levels of caloric intake and lower levels of bone mineral density (BMD) and osteocalcin. Age increased the risk of low muscle mass (95% confidence interval [CI] 1.053‒2.152). Overweight (95% CI 0.078‒0.658), obesity (95% CI 0.003‒0.139), low BF% (95% CI 0.015‒0.524) and high levels of calories from protein (95% CI 0.001‒0.001) were protective factors for low muscle mass. The GC exposure (95% CI 1.03‒1.53) increased the risk of low BMD, whereas low body fat percentage (95% CI 0.11‒0.71) decreased the risk of low BMD. Gut microbiota was closely associated with the BMD Z-score, body fat percentage (P < 0.01), age, GC exposure, and P1NP (P < 0.05). DMD children with low BMD had a higher abundance of Bacteroides vulgatus and a lower abundance of Prevotella copri (P < 0.05).

CONCLUSION: BF% rather than obesity was the risk factor for low muscle mass in DMD. SMI may be a more accurate index for muscle mass assessment than SMM. High level of calories from protein may be benefit to SMI. Treatments targeting gut microbiota may alleviate glucocorticoid-induced low BMD in DMD.},
}

Humans
Cross-Sectional Studies
Male
Child
Female
*Gastrointestinal Microbiome/physiology
*Nutritional Status
Bone Density
*Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications
Body Composition
China
Energy Intake
Child, Preschool
Adolescent
Diet

@article {pmid42965706,
year = {2026},
author = {Haferkamp, S and Schilling, B and Baumgart, L and Gesierich, A and Glutsch, V and Drexler, K and Wein, L and Morak, M and Erdmann, M and Berking, C and Piccinno, G and Derosa, L and Zitvogel, L and Wang, Y and Heinzerling, L},
title = {Microbiome-derived TOPOSCORE is associated with response to immune checkpoint inhibitor re-induction after chemotherapy in primary resistant metastatic melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {11},
pages = {},
pmid = {42965706},
issn = {1432-0851},
support = {70113416//German Cancer Aid / Stiftung Deutsche Krebshilfe/ ; },
mesh = {Humans ; *Melanoma/drug therapy/microbiology/pathology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Male ; *Drug Resistance, Neoplasm ; Female ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Prospective Studies ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: Primary resistance to immune checkpoint inhibitors (ICIs) remains a major challenge in metastatic melanoma. The prospective multicenter PROMIT trial showed that intermittent chemotherapy could restore sensitivity to ICI re-induction in a subset of patients. We investigated whether gut microbiome ecosystem states characterized by TOPOSCORE were associated with tumor response in this setting.

METHODS: In the phase II PROMIT trial (NCT04225390), 24 patients with longitudinal stool samples were included in this exploratory microbiome analysis. ICI-resistant patients received two cycles of dacarbazine followed by ICI re-induction. Stool samples underwent shotgun metagenomic sequencing. Microbiome ecosystem states were classified into SIG1- or SIG2-associated ecosystem states using the TOPOSCORE framework, which is based on species-interacting groups (SIGs) defined by ecological co-abundance patterns.

RESULTS: Baseline TOPOSCORE distributions and s-scores were not associated with clinical outcome. In the nine patients with complete BL-CTX-ICI sampling, six retained the same TOPOSCORE category throughout treatment and three changed category. Of the two patients with PR, one remained SIG2 throughout, whereas the other changed from SIG2+ to SIG1+ after chemotherapy and returned to SIG2+ during ICI re-induction. Analyses using all available samples at each phase likewise did not show significant differences in s-score among PR, SD, and PD groups.

CONCLUSIONS: Baseline TOPOSCORE classification was insufficient to predict treatment outcome in this cohort. Longitudinal TOPOSCORE patterns were heterogeneous, and the small number of complete longitudinal profiles precludes conclusions that chemotherapy induced a favorable microbiome transition. These exploratory findings support further evaluation of microbiome ecosystem dynamics in larger prospective cohorts.},
}

Humans
*Melanoma/drug therapy/microbiology/pathology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Male
*Drug Resistance, Neoplasm
Female
*Gastrointestinal Microbiome/drug effects
Middle Aged
Prospective Studies
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid42967695,
year = {2026},
author = {Feng, T and Guan, XY and Shang, Q and Jiang, Y and Li, ZY and Qi, J and Yu, MM},
title = {Dynamics of biogenic amine formation in fermented mandarin fish: Insights from precursor utilization and microbial succession.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120858},
doi = {10.1016/j.foodres.2026.120858},
pmid = {42967695},
issn = {1873-7145},
mesh = {Animals ; *Biogenic Amines/analysis/metabolism ; *Fermentation ; Amino Acids/analysis/metabolism ; Bacteria/metabolism/classification/genetics ; *Fishes/metabolism ; *Food Microbiology ; Putrescine/analysis ; Microbiota ; *Fermented Foods/microbiology ; Histamine/analysis ; Metagenomics ; Cadaverine/analysis ; },
abstract = {The high protein content of mandarin fish (Siniperca chuatsi) provides abundant substrates for biogenic amines (BAs) formation during fermentation, but the temporal dynamics and microbial drivers of BAs accumulation remain unclear. This study systematically investigated the succession of free amino acids (FAAs), BAs, and bacterial communities during fermentation. Results showed that the total FAAs peaked on day 5, whereas total BAs reached a maximum on day 10 (767.58 mg/kg). The BAs surge initiated at day 7.5, approximately 2.5 days after the FAAs peak. Putrescine, cadaverine, histamine, and tyramine were the predominant BAs, accounting for >98% of total BAs. Correlation analysis revealed strong negative correlations between BAs and their precursor FAAs (|R| = 0.588-0.842), suggesting the decarboxylation-driven conversion. Microbial succession identified candidate genera positively associated with BAs accumulation, including Vibrio and Morganella, while the late-stage decline of Vibrio and the increase of Vagococcus coincided with BAs reduction. Metagenomic analysis revealed that amino acid decarboxylase gene abundance peaked at day 10, while BA-degrading gene abundance peaked at day 15, consistent with the BAs dynamics. Days 5 to 10 are identified as a period that may warrant enhanced monitoring in industrial practice. A sequential temporal pattern linking substrate availability, microbial shifts, and BAs dynamics is described. These findings provide insights into the sequential dynamics of BAs formation in fermented mandarin fish and provide a scientific foundation for quality management in traditional fermented fish products.},
}

Animals
*Biogenic Amines/analysis/metabolism
*Fermentation
Amino Acids/analysis/metabolism
Bacteria/metabolism/classification/genetics
*Fishes/metabolism
*Food Microbiology
Putrescine/analysis
Microbiota
*Fermented Foods/microbiology
Histamine/analysis
Metagenomics
Cadaverine/analysis

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: evidence from the national cohort study in the United States.},
journal = {The International journal of neuroscience},
volume = {136},
number = {11},
pages = {1507-1518},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
mesh = {Humans ; Female ; *Microbiota ; Male ; *Stroke/epidemiology/microbiology ; United States/epidemiology ; Cross-Sectional Studies ; Middle Aged ; Cohort Studies ; *Mouth/microbiology ; Adult ; Aged ; Risk Factors ; Nutrition Surveys ; },
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional NHANES 2009-2012 data from 4,438 adults. Survey-weighted logistic regression estimated associations of stroke with oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon and Simpson), and periodontal measures (probing depth, attachment loss, tooth count), adjusting for demographic, socioeconomic, behavioral, and cardiometabolic covariates.

RESULTS: In crude models, each 1-mm increase in probing depth (odds ratio [OR] 1.89, 95% CI 1.39-2.56) and attachment loss (OR 1.50, 95% CI 1.32-1.71) raised stroke odds; each additional tooth lowered them (OR 0.91, 95% CI 0.88-0.94). After stepwise adjustment, attachment loss (OR 1.23, 95% CI 1.04-1.46; P=0.017) and tooth count (OR 0.96, 95% CI 0.92-0.99; P=0.024) remained significant, whereas probing depth did not (OR 1.30, 95% CI 0.90-1.88; P=0.156), with a threshold near 1.46 mm. β-Diversity clusters did not differ after adjustment (global P=0.61), and neither α-diversity index was significant (Shannon fully adjusted OR 1.29, 95% CI 0.97-1.72; P=0.081). Periodontal associations were consistent across sex and age strata; null findings in younger participants reflected limited power.

CONCLUSION: Attachment loss and tooth count were associated with stroke prevalence independently of traditional risk factors, whereas microbiome diversity indices were not. These measures may help refine risk assessment. The cross-sectional design precludes causal inference, and prospective cohorts with adjudicated outcomes and metagenomic profiling are needed.},
}

Humans
Female
*Microbiota
Male
*Stroke/epidemiology/microbiology
United States/epidemiology
Cross-Sectional Studies
Middle Aged
Cohort Studies
*Mouth/microbiology
Adult
Aged
Risk Factors
Nutrition Surveys

@article {pmid42833075,
year = {2026},
author = {Wang, X and Wang, J and Rehman, A and Ming, H},
title = {Response mechanisms of marine microbial communities during sulfamethoxazole co-metabolic degradation.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108421},
doi = {10.1016/j.marenvres.2026.108421},
pmid = {42833075},
issn = {1879-0291},
mesh = {*Sulfamethoxazole/metabolism ; *Microbiota/drug effects ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism ; Seawater/microbiology ; },
abstract = {Antibiotics, as typical emerging contaminants posing significant ecological risks, are frequently detected in global coastal environments. Their biotransformation in marine environments depends on the stress responses of functional microbial communities, while the underlying response mechanisms remain unclear. Through integrated metagenomic and metabolomic approaches, this study systematically investigated the structural and functional responses of marine microbial communities during the co-metabolic degradation of sulfamethoxazole (SMX), a representative antibiotic. A marine microbial consortium was employed for SMX co-metabolism with alginate, prototypical marine natural organic matter, as the co-substrate. Results revealed that under SMX stress, the microbial community underwent a marked shift in OTU composition, alongside significant increases in richness and diversity. The dominant functional taxon Vibrionaceae exhibited a significant decrease in relative abundance from 97.0% to 82.7%, while Paracoccaceae with SMX degradation potential and other low-abundance (<0.01%) functional taxa were significantly enriched, collectively sustaining stable alginate metabolism and facilitating SMX co-metabolism. Co-occurrence network analysis revealed enhanced interspecies associations. Moreover, the functional profile of the microbial community was profoundly reshaped. Specifically, the microbial community activated adaptive responses, enhancing TCS activation, EPS and endospore production, flagellar motility and chemotaxis, antioxidant capacity and DNA repair, and antibiotic resistance, to mitigate the toxicity of SMX and its intermediates. Concurrently, metabolic strategies were altered via regulation of key pathways (e.g., carbohydrate metabolism and amino acid metabolism), which increased by 7.8% and 17.5% in relative abundance compared to the control, boosting energy supply and SMX-degrading enzyme synthesis to enable SMX co-metabolism. This study provides new insights into the response mechanisms of marine microbial communities to SMX stress and the ecological risk assessment of antibiotics in coastal waters.},
}

*Sulfamethoxazole/metabolism
*Microbiota/drug effects
*Water Pollutants, Chemical/metabolism
Bacteria/metabolism
Biodegradation, Environmental
*Anti-Bacterial Agents/metabolism
Seawater/microbiology

@article {pmid42961364,
year = {2026},
author = {Alghafri, M and Edwards, L and Moyes, D and Nibali, L},
title = {Antimicrobial Resistance in Periodontal Disease: Rethinking Adjunctive Therapy in the Metagenomics Era, the Pressing Need for Precision Treatment and Periodontal Resistome Mapping.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {21},
pages = {},
pmid = {42961364},
issn = {1582-4934},
mesh = {Humans ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbiota/drug effects ; *Periodontal Diseases/microbiology/drug therapy ; *Precision Medicine ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; },
abstract = {Systemic antibiotics are effective when used as adjunctive therapy in the treatment of periodontitis; however, their use must be balanced against antimicrobial resistance, which is a major threat to global public health. This review provides an expert synthesis of the literature and a field-level overview of antimicrobial resistance in periodontal therapy, highlighting current knowledge and emerging directions, while examining how adjunctive antibiotic protocols may contribute to resistance within the periodontal microbiome through emerging metagenomic insights. To provide this synthesis, the PubMed database was searched for English-language publications using combinations of the terms periodontitis, systemic antibiotics, antimicrobials, resistance, resistome, therapeutic adjuncts, resistance genes, susceptibility, antibacterial and drug resistance, and the findings are presented as a narrative review. The evidence indicates that a substantial proportion of patients with periodontitis harbour subgingival microbiota that are non-susceptible to at least one antibiotic used in periodontal therapy. Across the included studies, antimicrobial resistance was most frequently reported in Prevotella and Porphyromonas species, while some studies also identified virulence-associated factors in Staphylococcus aureus, a non-classical periodontal organism detected within the subgingival microbiota. Overall, current evidence indicates a high prevalence of antibiotic resistance genes in the subgingival microbiota of patients with periodontitis and highlights the ecological consequences of adjunctive antibiotic use. These findings reinforce the need to optimize antibiotic prescribing protocols within an antibiotic stewardship framework and support further metagenomic investigations to refine understanding of resistance patterns, gene-transfer mechanisms and microbiome disruption, with the aim of advancing precision-based periodontal care.},
}

Humans
*Metagenomics/methods
*Anti-Bacterial Agents/therapeutic use/pharmacology
Microbiota/drug effects
*Periodontal Diseases/microbiology/drug therapy
*Precision Medicine
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial

@article {pmid42961615,
year = {2026},
author = {Dolker, S and Ghosh, A and Singh, VK and Joshi, BD and Sharma, LK and Thakur, M},
title = {Exploring sex- and captivity-associated gut microbial diversity in Bengal Tigers (Panthera tigris tigris).},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42961615},
issn = {1573-4978},
mesh = {Animals ; *Tigers/microbiology/genetics ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Feces/microbiology ; Bacteria/genetics/classification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Endangered Species ; },
abstract = {BACKGRO UND: The gut microbiome plays a critical role in host nutrition, immune regulation, metabolic stability, and overall physiological health in wildlife. However, gut microbiome data from large carnivores remain limited, particularly for endangered tiger populations. This study conducted a comparative analysis of fecal microbiomes from captive and wild Bengal tigers, integrated with publicly avai lable datasets from Amur, Malayan, and South China tigers, to understand how captivity and host factors influence microbial assembly. ME THOD S AND RESULTS: Across all tiger subspecies, Firmicutes and Proteobacteria dominated as core bacterial phyla, with Actinobacteriota, Bacteroidota, and Fusob acteriota forming a conserved microbial backbone. Wild Bengal tigers exhibited higher microbial richness and diversity than captive tigers . Beta diversity analyses demonstrated clear clustering by habitat (captive versus wild), but substantial overlap between male and female captive Bengal tigers, indicating that captivity-associated conditions exert influences on gut microbiome structure than sex. Comparative analyses among tiger subspecies revealed broad overlap in microbial community composition, suggesting limited phylogenetic influence. South China and Amur tigers displayed the lowest richness compared to Bengal and Malayan tigers. Furthermore, analysis identified an enrichment of protein fermentation-associated taxa in captive tigers, whereas wild tigers showed a greater abundance of environmentally associated taxa. CONCLUSIONS: The study provides evidences that captivity promotes reduction in gut microbial diversity in Bengal tigers, and highlights the potential utility of microbiome-informed captive management. Integrating gut microbiome monitoring into conservation breeding, zoo exchange and reintroduction programmes may improve adaptive fitness in endangered tiger populations.},
}

Animals
*Tigers/microbiology/genetics
Female
Male
*Gastrointestinal Microbiome/genetics
Phylogeny
Feces/microbiology
Bacteria/genetics/classification
Biodiversity
RNA, Ribosomal, 16S/genetics
Sex Factors
Endangered Species

@article {pmid42963371,
year = {2026},
author = {Li, S and Huang, J and Lin, D and Luo, D and Fu, W and Liu, J},
title = {Electroacupuncture alleviates chronic pain and comorbid depression through Gut-Metabolite-Brain axis remodeling to restore mPFC Glu/GABA balance.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42963371},
issn = {2158-3188},
mesh = {Animals ; *Electroacupuncture ; *gamma-Aminobutyric Acid/metabolism ; Rats ; *Chronic Pain/therapy/metabolism ; Male ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome/physiology ; *Depression/therapy/metabolism ; *Prefrontal Cortex/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Comorbidity ; },
abstract = {The comorbidity of chronic pain and depression is increasingly recognized as a systemic disorder involving dysregulated microbiota-gut-brain communication. Although electroacupuncture (EA) has demonstrated therapeutic efficacy for both pain and depression, the mechanisms linking peripheral microbial-metabolic remodeling to central neurotransmitter regulation remain incompletely understood. Here, we employed an integrated multi-omics approach in a spared nerve injury (SNI) rat model to investigate the gut-metabolite-brain mechanisms underlying EA's efficacy. EA significantly alleviated mechanical hypersensitivity and depressive-like behaviors while restoring mPFC Glu/GABA balance, accompanied by normalization of the glutamate transporter EAAT2 and the GABA-synthesizing enzyme GAD67. Metagenomic analysis showed that EA remodeled the gut microbial ecosystem by increasing microbial diversity, suppressing opportunistic pathobionts, including Bacillus cereus, Alistipes onderdonkii, while enriching SCFA-associated genera, including Butyricimonas and Romboutsia. These alterations were accompanied by coordinated remodeling of amino acid and butanoate metabolism. Correlation network analysis identified Pipecolic acid as a central metabolic node linking gut microbial alterations with mPFC GABAergic neurotransmission and behavioral recovery. Although individual bacterial genera did not significantly mediate its restoration, causal mediation analysis demonstrated that the Pipecolic acid-GABA axis significantly mediated improvements in both mechanical allodynia and anhedonia, supporting Pipecolic acid as a functional metabolic hub linking peripheral metabolic remodeling to central GABAergic regulation. Collectively, these findings identify peripheral metabolic remodeling as a key mechanistic interface through which EA coordinates gut microbial ecology and central neurochemical homeostasis, providing a systems-level framework for understanding the therapeutic mechanisms of acupuncture in pain-depression comorbidity.},
}

Animals
*Electroacupuncture
*gamma-Aminobutyric Acid/metabolism
Rats
*Chronic Pain/therapy/metabolism
Male
*Glutamic Acid/metabolism
*Gastrointestinal Microbiome/physiology
*Depression/therapy/metabolism
*Prefrontal Cortex/metabolism
Rats, Sprague-Dawley
Disease Models, Animal
Comorbidity

@article {pmid42264215,
year = {2026},
author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and , and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH},
title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.},
journal = {The Journal of investigative dermatology},
volume = {146},
number = {11},
pages = {3142-3154.e6},
pmid = {42264215},
issn = {1523-1747},
support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Skin Microbiome/immunology ; *Warts/microbiology/immunology/virology/drug therapy ; *Immunologic Deficiency Syndromes/immunology/microbiology/virology/drug therapy ; Female ; Male ; *Skin/microbiology/immunology/virology ; Receptors, CXCR4/antagonists & inhibitors/genetics ; *Human Papillomavirus Viruses/isolation & purification/immunology ; Adult ; *Papillomavirus Infections/immunology/virology/microbiology ; Primary Immunodeficiency Diseases/immunology ; Adolescent ; Young Adult ; Child ; Metagenomics ; *Genetic Diseases, X-Linked/immunology/microbiology ; Microbiota/immunology ; Papillomaviridae/isolation & purification ; },
abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis syndrome is a rare inborn error of immunity caused by hyperfunctional pathogenic variants in CXCR4, predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and a potential reduction in bacterial infection frequency. Here, we investigated the skin microbiomes of 14 patients with warts, hypogammaglobulinemia, infections, and myelokathexis syndrome using shotgun metagenomics, compared with those of healthy controls. Warts, hypogammaglobulinemia, infections, and myelokathexis skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and an expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in warts, hypogammaglobulinemia, infections, and myelokathexis syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.},
}

Humans
*Skin Microbiome/immunology
*Warts/microbiology/immunology/virology/drug therapy
*Immunologic Deficiency Syndromes/immunology/microbiology/virology/drug therapy
Female
Male
*Skin/microbiology/immunology/virology
Receptors, CXCR4/antagonists & inhibitors/genetics
*Human Papillomavirus Viruses/isolation & purification/immunology
Adult
*Papillomavirus Infections/immunology/virology/microbiology
Primary Immunodeficiency Diseases/immunology
Adolescent
Young Adult
Child
Metagenomics
*Genetic Diseases, X-Linked/immunology/microbiology
Microbiota/immunology
Papillomaviridae/isolation & purification

@article {pmid42271211,
year = {2026},
author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q},
title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42271211},
issn = {1471-2180},
support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Marmota/virology ; Phylogeny ; *Metagenomics/methods ; *Virome/genetics ; *Liver/virology ; Genome, Viral ; China ; *Viruses/genetics/classification/isolation & purification ; Rivers ; Tibet ; Sequence Analysis, DNA ; Metagenome ; },
abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.},
}

Animals
*Marmota/virology
Phylogeny
*Metagenomics/methods
*Virome/genetics
*Liver/virology
Genome, Viral
China
*Viruses/genetics/classification/isolation & purification
Rivers
Tibet
Sequence Analysis, DNA
Metagenome

@article {pmid42953986,
year = {2026},
author = {Shum-Tim, C and Islam, P and Boyajian, JL and Abosalha, A and Kassab, A and Santos, M and Khan, KA and Stern, K and Emad, A and Prakash, S},
title = {Artificial Intelligence-Driven Graph Methods for Microbiome Research: A Systematic Review.},
journal = {WIREs mechanisms of disease},
volume = {18},
number = {6},
pages = {},
pmid = {42953986},
issn = {2692-9368},
support = {252743//Canadian Institute of Health Research/ ; 335999//Fonds de Recherche du Québec-Santé/ ; 351337//Fonds de Recherche du Québec-Santé/ ; 2020-245622//Islamic Development Bank Scholarship/ ; //Ministry of Higher Education of the Arab Republic of Egypt/ ; 504933//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Microbiota/genetics ; *Artificial Intelligence ; Humans ; Animals ; },
abstract = {The complexity of high-throughput sequencing data in microbiome research necessitates advanced analytical methods to decipher microbial community structures and interactions. Graph-based methods, which model taxa as nodes and their relationships as edges, have emerged as a powerful framework for this purpose. However, the rapid evolution of these techniques, from classical network analysis to modern graph representation learning, has created a fragmented and complex methodological landscape. This systematic review provides a comprehensive synthesis and structured overview of the field. We systematically review the literature and propose a three-part classification to categorize the primary contribution of each study: (1) novel methods for microbial network representation, (2) applications of classical graph analysis, and (3) the emerging use of graph representation learning for predictive modeling. We summarize the most frequent applications within each class, including keystone species identification, community clustering, and graph-based disease classification. Furthermore, we identify critical cross-cutting challenges, such as the lack of standardized tools and the need for improved model interpretability. By structuring the current landscape of graph-based methods, this review serves as a crucial guide for researchers to select appropriate models and highlights key gaps to direct future research.},
}

*Microbiota/genetics
*Artificial Intelligence
Humans
Animals

@article {pmid42955203,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Gut Microbiome Signatures and Immune Checkpoint Inhibitor Response in Gastrointestinal Cancers: Reproducibility and Translational Readiness.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42955203},
issn = {1534-6269},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Reproducibility of Results ; Translational Research, Biomedical ; },
abstract = {PURPOSE OF REVIEW: Gut microbial features have been associated with immune checkpoint inhibitor (ICI) outcomes, but whether these signatures are robust across gastrointestinal (GI) tumor types, treatment regimens, and populations remains uncertain. This critical narrative review assesses human evidence, experimental mechanisms, longitudinal sampling, and the criteria needed for clinical implementation.

RECENT FINDINGS: A gastric cancer cohort showed different response-associated microbial features for immunotherapy alone, chemotherapy alone, and combined treatment. Cross-cancer strain-resolved analyses found that signature transportability was strongly conditional on matching ICI regimens. A large primary liver cancer cohort analyzed 315 patients and 777 serial samples and explored a baseline score derived from on-treatment species selection; later samples were available only in a selected subgroup, complicating interpretation. Experimental studies link selected microbes and metabolites with antitumor immunity, but these mechanistic findings do not establish therapeutic efficacy in humans. Fecal microbiota transplantation (FMT) studies in melanoma demonstrate feasibility yet do not establish benefit in GI malignancies. Stool profiles may not represent mucosal or tumor-adjacent communities in upper GI cancer. No stool microbiome signature is currently validated to select ICI therapy in GI oncology. Meaningful translation requires standardized assays, non-ICI comparators to establish treatment-effect prediction, strict separation of discovery and external validation, prospectively handled missingness, and randomized clinical-utility studies.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Neoplasms/drug therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
Reproducibility of Results
Translational Research, Biomedical

@article {pmid42957705,
year = {2026},
author = {Anani, H and Destras, G and Semanas, Q and Martin, FP and Petrier, M and Oddoux, E and Burfin, G and Bulteau, S and Poulain, C and Sinha, D and Motos, A and Gourain, V and Cremet, L and Montassier, E and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Identification of functional bacterial-viral pneumotypes associated with airway inflammation and all-cause mortality in critically ill patients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957705},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness/mortality ; Female ; Male ; Klebsiella pneumoniae/genetics/virology ; *Lung/microbiology/virology ; Middle Aged ; Bacteriophages/genetics/isolation & purification/pathogenicity ; Aged ; Microbiota/genetics ; Cross Infection/microbiology/mortality/virology ; Metagenomics ; Dysbiosis/microbiology ; Streptococcus/genetics ; },
abstract = {Alterations in lung virome and bacteriome compositions have been associated with hospital-acquired pneumonia in critically ill patients, but data on lung microbiome functions underlying progression to severe complications remain unclear. Here, we analyse 184 endotracheal aspirates (ETAs) collected in 94 intubated critically ill patients enrolled in a clinical trial (NCT04793568). Combining viral-metagenomics with metatranscriptomics analyses, we identify a high-risk functional pneumotype observed before the onset of hospital-acquired pneumonia and associated with lung inflammation and mortality. This unfavourable pneumotype is characterised by enrichment in virulent Streptococcus-bacteriophages and temperate Klebsiella-bacteriophages, decreased transcriptional activity of commensal taxa such as Streptococcus and Alloprevotella, and increased transcriptional activity of Klebsiella pneumoniae. Machine-learning models define two-viral- and four-bacterial-factor signatures predicting unfavourable pneumotype (AUC 0.8 and 0.7, respectively). Validation in an independent cohort (NCT02003196) of 117 ICU patients (239 ETAs) demonstrates the robustness of the association of these signatures with the risk of mortality. Causal inference identifies virulent bacteriophages associated with Streptococcus and host genes including IL18R1, ADM and PTX3, as key regulators of severe lung dysbiosis linked to mortality in critically ill patients.},
}

Humans
*Critical Illness/mortality
Female
Male
Klebsiella pneumoniae/genetics/virology
*Lung/microbiology/virology
Middle Aged
Bacteriophages/genetics/isolation & purification/pathogenicity
Aged
Microbiota/genetics
Cross Infection/microbiology/mortality/virology
Metagenomics
Dysbiosis/microbiology
Streptococcus/genetics

@article {pmid42957707,
year = {2026},
author = {Pulliam, C and Xu, M and Holandez-Lopez, K and Xue, D and Shang, Z and Gupta, G and Dioli, OE and Xiao, H and Gou, L and Wu, C and Brodbelt, JS and Wu, E and Peng, X and Chen, H and Li, J},
title = {Genome mining of the tumor microbiome reveals biosynthetic diversity and potential pathology-modulating metabolites.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957707},
issn = {2041-1723},
support = {1R35GM150565//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM139658//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F-1155//Welch Foundation/ ; },
mesh = {Humans ; *Neoplasms/microbiology/metabolism/pathology ; *Microbiota/genetics ; Multigene Family ; Fusobacterium/genetics/metabolism ; Metagenome ; Biosynthetic Pathways/genetics ; Genome, Bacterial ; },
abstract = {Human tumor-associated microbes - the tumor microbiome - have demonstrated an increasingly important role in human health due to their relevance to cancer progression and treatment response. While the metabolism at the host-microbiota interface, such as in the human gut, has been extensively investigated in recent years, the specialized metabolites from the tumor microbiome remain uncharted territory. To address this knowledge gap, we report a survey of the biosynthetic potential of the human tumor microbiome. Utilizing high-quality microbial metagenome-assembled genomes from 3,526 human tumor tissue samples, we identify 528 biosynthetic gene clusters with the potential to encode specialized metabolites relevant to tumor pathology. We reveal that the tumor microbiome encodes known and unknown metabolites spanning multiple biosynthetic classes. From this diverse biosynthetic landscape, we express a conserved family of biosynthetic genes from the genus Fusobacterium, which has a well-established role in cancer, and discover distinct families of long-chain fatty acyl amides. We subsequently find that one of these fatty acyl amides, oleoyl γ-aminobutyric acid, has immunomodulatory and G-protein-coupled receptor partial agonist activities, potentially supporting the influence of Fusobacterium in tumor pathology. The findings of our investigation lay a foundation for further research into the roles of tumor microbe-derived metabolites in cancer.},
}

Humans
*Neoplasms/microbiology/metabolism/pathology
*Microbiota/genetics
Multigene Family
Fusobacterium/genetics/metabolism
Metagenome
Biosynthetic Pathways/genetics
Genome, Bacterial

@article {pmid42957759,
year = {2026},
author = {Nasr, EMT and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, KT and Ferrari, E and Griffin, TJ and Grüning, BA and Hiltemann, S and Hyde, CJ and Jagtap, PD and Kumar, A and Malla, MA and Mehta, S and Métris, KL and Momin, S and Nelson, T and Oba, AJ and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, AP and van Heusden, P and Vohra, M and Zierep, PF and Batut, B},
title = {Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42957759},
issn = {2399-3642},
support = {ANR-11-INBS-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-MPGA-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U24AI183870//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; INV-046492//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV-079648//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 228162/Z/23/Z//Wellcome Trust (Wellcome)/ ; LIBIS/de.NBI Freiburg,//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg)/ ; HORIZON-INFRA-2021-EOSC-01-04//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; },
mesh = {Reproducibility of Results ; *Microbiology ; *Computational Biology/methods ; Microbiota ; Proteomics ; *Software ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org , .eu , .org.au , . fr).},
}

Reproducibility of Results
*Microbiology
*Computational Biology/methods
Microbiota
Proteomics
*Software

@article {pmid42958435,
year = {2026},
author = {Rao, B and Liu, S and Cui, G and Jiang, J and Li, N and Hu, J and Sun, R and Li, A and Zhang, R and Lu, H and Wen, P and Xue, J and Aji, T and Wang, H and Chen, X and Zheng, S and Yu, Z and Ren, Z},
title = {Multikingdom and functional gut microbiota markers for cholangiocarcinoma.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42958435},
issn = {1756-994X},
support = {82570691//National Natural Science Foundation of China/ ; 81672422//National Natural Science Foundation of China/ ; 82470654//National Natural Science Foundation of China/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2025ZD01906305//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; HNCMS202423//Henan Province "Three 100" Program, Special Project for Clinical Medical Scientist Cultivation/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/diagnosis ; Female ; Metagenomics/methods ; Male ; Middle Aged ; Feces/microbiology ; Liver Neoplasms/microbiology/diagnosis ; Biomarkers, Tumor ; Metagenome ; Carcinoma, Hepatocellular/microbiology ; Aged ; },
abstract = {BACKGROUND: While the association between gut microbiota and cholangiocarcinoma (CCA) has been explored, existing research has been limited to bacterial components. The alterations in non-bacterial members (fungi, archaea, and viruses) and their functional characteristics in CCA remain unclear. This study aimed to comprehensively characterize the multi-kingdom gut microbiota and functional profiles in CCA patients and develop a non-invasive diagnostic model.

METHODS: We performed metagenomic sequencing on 700 fecal samples collected from three distinct regions in China, comprising 289 CCA patients, 312 healthy controls, and 99 hepatocellular carcinoma (HCC) patients. Multi-kingdom microbial composition and functional profiles were analyzed. We integrated multiple machine learning algorithms to generate 117 distinct modeling schemes for constructing and screening the optimal CCA diagnostic model. The model was validated across three independent cohorts and tested for specificity against HCC. We also benchmarked the model against established diagnostic approaches by reviewing 15 CCA clinical practice guidelines/consensus statements and their cited evidence and by evaluating model detection in CA19-9-positive and CA19-9-negative patients.

RESULTS: Extensive alterations were identified in CCA patients across multi-kingdom and functional layers, including 198 archaeal, 154 bacterial, 78 fungal, and 120 viral species, as well as 278 genes, 99 pathways, and 151 carbohydrate-active enzymes (CAZymes). A panel of 21 multi-kingdom and functional markers demonstrated superior diagnostic accuracy with an average AUC of 91% across three validation cohorts, outperforming any single-kingdom model. The model exhibited high specificity in distinguishing CCA from HCC, achieving an AUC of 99.74% with a false positive rate of 11.11%. Benchmarking supported a complementary role as a noninvasive screening aid, the model showed pooled sensitivity and specificity of 96.2%, and 78.5%, respectively, and detected 97.6% of CA19-9-negative CCA cases.

CONCLUSIONS: This study represents the first comprehensive characterization of multi-kingdom gut microbiome and functional markers in cholangiocarcinoma. Gut multi-kingdom and functional microbial signatures represent a promising noninvasive tool that may aid the screening and early identification of cholangiocarcinoma in high-risk populations, complementing existing diagnostic approaches.},
}

Humans
*Cholangiocarcinoma/microbiology/diagnosis
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/diagnosis
Female
Metagenomics/methods
Male
Middle Aged
Feces/microbiology
Liver Neoplasms/microbiology/diagnosis
Biomarkers, Tumor
Metagenome
Carcinoma, Hepatocellular/microbiology
Aged

@article {pmid42959031,
year = {2026},
author = {Songel-Sanchis, B and Cosín-Roger, J},
title = {Gut mycobiome dysbiosis in inflammatory bowel disease: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1960101},
pmid = {42959031},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Mycobiome/immunology ; *Fungi/classification/genetics ; },
abstract = {BACKGROUND: The intestinal mycobiome is increasingly recognized as an important component of host-microbiota interactions in inflammatory bowel disease (IBD), yet its contribution to intestinal immune dysregulation remains incompletely characterized. We aimed to characterize alterations in the intestinal mycobiome in patients with inflammatory bowel disease, including Crohn's disease and ulcerative colitis, compared with individuals without IBD, focusing on fungal diversity, taxonomic composition, and relative abundance, as well as their potential associations with disease phenotype and inflammatory activity.

METHODS: A systematic review and meta-analysis was conducted according to PRISMA 2020 guidelines. PubMed/MEDLINE, Embase, and Cochrane Central Register of Controlled Trials were systematically searched from inception to March 2026, with no language or publication-date restrictions. The review was not prospectively registered. Human studies assessing gut fungal communities by internal transcribed spacer (ITS)-based sequencing or shotgun metagenomics were eligible. Alpha and beta diversity, taxonomic composition, and clinically relevant fungal alterations were extracted. Study quality was assessed independently by two reviewers using the Newcastle-Ottawa Scale (NOS), and quantitative analyses were performed using standardized effect estimates and pooled prevalence.

RESULTS: Twenty-eight studies were included in the qualitative and quantitative synthesis. CD was consistently associated with reduced fungal alpha diversity compared with healthy controls, with a pooled weighted mean difference in Shannon diversity of -0.84 (p<0.001), whereas the reduction in UC was more modest (-0.31, p=0.04). Fungal beta diversity consistently differed between IBD and healthy controls. Expansion of Candida spp. was the most reproducible taxonomic alteration, occurring in 82.1% of analyzed cohorts, while depletion of Saccharomyces cerevisiae was reported in 71.4%. Malassezia enrichment was also associated with mucosal inflammation and CARD9-related immune responses. Cross-kingdom interactions involving Candida, Escherichia coli, and Serratia marcescens further highlighted potential fungal-bacterial mechanisms underlying persistent inflammation. Persistent fungal dysbiosis despite clinical remission supported the concept of a "mycobiotic scar."

CONCLUSION: IBD is characterized by substantial disruption of the intestinal mycobiome, particularly in CD, with reduced fungal diversity, expansion of potentially pathogenic Candida spp., and depletion of protective fungal taxa. These alterations may contribute to immune dysregulation and therapeutic refractoriness and support the mycobiome as a potential source of biomarkers and therapeutic targets in IBD.},
}

Humans
*Dysbiosis/microbiology/immunology
*Inflammatory Bowel Diseases/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Mycobiome/immunology
*Fungi/classification/genetics

@article {pmid42585927,
year = {2026},
author = {Ma, J and Qin, K and Qiao, Z and Ren, Z and Yang, X and Liu, Y},
title = {Integrative multi-omics reveals comprehensive gut-liver-adipose metabolic changes in peak laying hens with high or low egg production.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107493},
pmid = {42585927},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/metabolism/genetics/microbiology ; Female ; *Liver/metabolism ; Multiomics ; *Adipose Tissue/metabolism ; *Gastrointestinal Microbiome ; *Metabolome ; *Reproduction ; },
abstract = {Eggs serve as an indispensable global nutritional resource, sustaining the economic foundation of the commercial poultry industry. To meet this continuous demand, egg formation involves an exceptionally energy-intensive biological process requiring continuous yolk precursor synthesis, which imposes a massive metabolic burden on laying hens. However, the comprehensive metabolic differences across the gut-liver-adipose axis between peak laying hens with high or low egg production remain incompletely characterized. A total of 180 healthy Hy-Line Brown laying hens (45-week-old) were continuously fed and monitored for production performance over a 6-week period. Following the exclusion of individuals with extremely low egg production (≤10 eggs during the 6-week monitoring period; n = 5) and candidate hens that repeatedly produced unqualified eggs over multiple weeks (n = 20), the remaining hens were ranked by 6-week average laying rate and allocated into FH (high-production hens at 50 weeks of age, n = 15) and FL (low-production hens at 50 weeks of age, n = 14) groups. Initial body weight did not differ significantly between groups (FH: 1936 ± 29.0 g; FL: 1894 ± 48.2 g; P-value = 0.446). We integrated transcriptomic, untargeted metabolomic, targeted bile acid metabolomics, and microbiome (16S rRNA and metagenomic) profiles to characterize comprehensive metabolic changes across the gut-liver-adipose axis associated with divergent egg-production phenotypes. The results showed that: (1) FH hens exhibited higher serum APOB and lower conjugated bile acids (TCDCA, TCA, and THDCA), with hepatic upregulation of FASN, PPARA, CPT1A, and VTG1 along with downregulation of CYP7A1, CYP7B1, CYP8B1, and CYP27A1; (2) intersecting module hub genes (MHGs) with differentially expressed genes (DEGs) identified 354 upregulated and 299 downregulated core genes, with EEF2 identified as the primary hepatic downregulated hub gene; (3) in abdominal fat, GSEA revealed significant enrichment in fatty acid transport (NES = 1.54), long-chain fatty acid metabolic process (NES = 1.39), and steroid hormone biosynthesis (NES = 1.85), accompanied by significant downregulation of ANGPTL4 and upregulation of HSD3B1, VTG1, VTG2, and VTG3; (4) ileal mucosal transcriptomics identified 619 DEGs (502 upregulated), with GSEA highlighting enrichment in cell junction organization (NES = 1.52) and tube morphogenesis (NES = 1.39), which were further categorized into functional modules including enteric synaptic signaling, epithelial adhesion, mucosal vascularization, and tissue renewal; (5) the functional profile of the ileal microbiota in FH hens showed enrichment of functions related to complex carbohydrate degradation and carbohydrate-binding modules, with keystone taxa including Blautia and Bifidobacterium associated with production and lipid markers. Collectively, these findings suggest that high egg production during the peak laying period is associated with coordinated metabolic differences across the liver, abdominal fat tissue, and intestine. The observed profiles included reduced hepatic translation-related and primary bile acid synthesis-related signatures, adipose endocrine-related changes and microbial functional potential related to carbohydrate utilization and antioxidant-related functional potential. These findings provide candidate multi-omics features for precision nutritional strategies and genetic improvement in commercial poultry.},
}

Animals
*Chickens/physiology/metabolism/genetics/microbiology
Female
*Liver/metabolism
Multiomics
*Adipose Tissue/metabolism
*Gastrointestinal Microbiome
*Metabolome
*Reproduction

@article {pmid42603397,
year = {2026},
author = {Geng, D and Ding, Y and Jiang, Y and Wang, Z and Chen, G and Chang, G and Bai, H},
title = {Multi-omics analysis of cecal microbiota-hypothalamus axis interactions in small-sized meat ducks with divergent residual feed intake.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107310},
pmid = {42603397},
issn = {1525-3171},
mesh = {Animals ; *Ducks/physiology/microbiology/genetics ; *Hypothalamus/physiology/metabolism ; Multiomics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; *Eating ; Male ; Diet/veterinary ; },
abstract = {Residual feed intake (RFI) is an indicator of feed efficiency that reflects variation in nutrient utilization independent of growth. This study characterized physiological traits and multi-omics profiles associated with divergent RFI in small-sized meat ducks. From an initial population of 500 1-day-old ducks, a total of 420 healthy ducks were individually housed from 21 to 42 d to record feed intake, and ducks with low RFI (LRFI) and high RFI (HRFI) were identified for further analyses. During the experiment, 30 ducks per group for growth performance, 15 ducks per group for plasma biochemical and 5 per group for multi-omics. Compared with HRFI ducks, LRFI ducks showed lower feed intake, lower feed conversion ratio (FCR), and lower plasma triglyceride concentrations, whereas body weight gain did not differ between groups. Shotgun metagenomic analysis showed that LRFI ducks were enriched in Bacteroides-related lineages and had higher predicted capacities for complex carbohydrate degradation, lipid and energy metabolism, and cofactor synthesis, whereas HRFI ducks were enriched in taxa including Subdoligranulum variabile and Clostridioides difficile. Untargeted cecal metabolomics revealed distinct lipid- and bile acid-related metabolic profiles between the 2 groups, including differences in long-chain lipid species and bile acid-associated metabolites. Hypothalamic transcriptomic analysis identified differentially expressed genes related to neuropeptide signaling, serotonin biosynthesis, intracellular signaling, and inflammatory regulation, including NMUR2, TPH1, and PTK2B. Correlation analysis integrating microbial taxa, metabolites, and hypothalamic transcripts further revealed coordinated associations among these features in small-sized meat ducks with divergent RFI. Overall, variation in feed efficiency in ducks was associated with differences in cecal microbiota, metabolite profiles, and hypothalamic gene expression, and these results highlight candidate microbial taxa, metabolites, and genes for further validation.},
}

Animals
*Ducks/physiology/microbiology/genetics
*Hypothalamus/physiology/metabolism
Multiomics
*Cecum/microbiology
*Gastrointestinal Microbiome
*Eating
Male
Diet/veterinary

@article {pmid42617270,
year = {2026},
author = {Li, Y and Li, Q and Zhang, X and Wang, Y and Gao, G and Chen, D and Qin, S and Cui, Z and Liu, L and Liu, A and Wang, H and Wang, Q and Tang, B},
title = {Microbiota contributes to regulates the external genitalia development through gut-testis axis in male geese.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107476},
pmid = {42617270},
issn = {1525-3171},
mesh = {Animals ; Male ; *Geese/growth & development/microbiology ; *Testis/growth & development ; *Gastrointestinal Microbiome ; *Genitalia, Male/growth & development ; },
abstract = {Geese is one of the few poultry species with complete external genitalia, and the external genitalia abnormal development has become an important factor limiting the reproductive efficiency of the goose industry. Recent studies have shown that the gut microbiota plays an important role in regulating male reproductive processes, but its regulatory mechanisms in male geese's external genitalia development remain unclear. In this study, male geese with normal development (ND) and abnormal development (AD) external genitalia were selected as the research object, and multi-omics were used to investigate the regulatory of the microbe-mediated gut-testis axis on external genitalia development. At the transcriptomic level, we identified key DEGs (KNG1, P2RY4, SSTR5, and HRH3) in the testis and external genitalia between ND and AD groups, which were significantly enriched in the neuroactive ligand-receptor interaction pathway. Metabolomics analysis revealed that DMs in the ND and AD groups were significantly enriched in pathways related to aromatic amino acid metabolism and neural signal transduction. Furthermore, metagenomic results showed that the ND group was identified key bacterial genera g_Blautia and g_Faecousia affecting external genitalia development, which were associated with SCFAs synthesis and neuroendocrine signaling regulation. Integrated with multi-omics data, it was revealed that gut-derived neuroactive metabolic signals may participate in the molecular regulation of external genitalia development in male goose by modulating GPCRs signaling. Our findings not only provide new insights into the gut-testis axis regulates the development of external genitalia in male geese, but also contribute to improving the reproductive performance of male geese.},
}

Animals
Male
*Geese/growth & development/microbiology
*Testis/growth & development
*Gastrointestinal Microbiome
*Genitalia, Male/growth & development

@article {pmid42623770,
year = {2026},
author = {Li, X and Wang, Y and Wang, Z and Deng, M and Zheng, J and Geng, H and Zhao, G and Wang, Q},
title = {Gut Faecalibacterium regulates host immunity and metabolic profiles to confer resistance against Salmonella infection in chicks.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107550},
pmid = {42623770},
issn = {1525-3171},
mesh = {Animals ; *Chickens/immunology ; *Poultry Diseases/immunology/microbiology ; *Salmonella Infections, Animal/immunology/microbiology ; *Gastrointestinal Microbiome ; Salmonella enteritidis/physiology ; *Immunity, Innate ; *Metabolome ; *Disease Resistance ; Cecum/microbiology ; },
abstract = {To explore the pathogenic mechanism of Salmonella Enteritidis (SE) infection in chicks and the regulatory role of Faecalibacterium, we established a chick SE infection model, systematically analyzing intestinal damage, systemic inflammation, and cecal microbial community changes. Focusing on the differentially abundant Faecalibacterium, we elucidated its regulatory mechanism via metagenomics, transcriptomics, and serum metabolomics. Results showed that SE successfully colonized the chick cecum, causing significant reductions in the thickness of the intestinal mucosal and muscular layers, a decrease in gland depth, and a loss of goblet cells. Concurrently, serum levels of IgA and IL-6 were markedly elevated, indicating the induction of systemic inflammatory responses and severe intestinal damage. Microbiome analysis revealed SE significantly altered cecal microbiota β-diversity, increased Actinobacteria abundance, and decreased the abundance of beneficial bacterial families (Lachnospiraceae and Oscillospiraceae) and the key beneficial genus Faecalibacterium. Functional prediction indicated microbial function remodeling towards enhanced pathogen colonization and pro-inflammation. β-diversity analysis of Faecalibacterium gene set showed clear separation between the Ctrl and SE groups in two-dimensional space: the control group was enriched in immune-related pathways such as Th17 cell differentiation and IL-17 signaling pathway, while the infected group was enriched in pathways related to Salmonella infection and pathogenic Escherichia coli infection. Validation in uninfected chicks showed High_ Faecalibacterium abundance was associated with lower serum IL-6, IL-8, IFN-γ and distinct gene expression profiles. Differentially expressed genes (DEGs) were enriched in immune regulation pathways such as cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and intestinal immune network for IgA. LASSO regression screening identified 16 key associated genes including TM4SF4 and FABP4. Serum metabolomics showed distinct metabolic profiles between High_ and Low_ Faecalibacterium abundance groups, with 26 differential metabolites; N-(2,4-dinitrophenyl) ethylenediamine and Val-Gly-Phe (AUC > 0.8) were potential biomarkers. In conclusion, SE induces pathogenesis by damaging intestinal barrier, triggering inflammation, and disrupting cecal microbiota. Faecalibacterium enhances chick resistance to SE via regulating immune and metabolic homeostasis, providing a basis for avian salmonellosis microecological control.},
}

Animals
*Chickens/immunology
*Poultry Diseases/immunology/microbiology
*Salmonella Infections, Animal/immunology/microbiology
*Gastrointestinal Microbiome
Salmonella enteritidis/physiology
*Immunity, Innate
*Metabolome
*Disease Resistance
Cecum/microbiology

@article {pmid42680886,
year = {2026},
author = {Liu, CC and Dong, SS and Guo, J and Xu, Z and Wang, C and Li, YX and Meng, LL and Yang, XC and Li, M and Fu, K and Guo, Y and Yang, TL},
title = {MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.},
journal = {Nature microbiology},
volume = {11},
number = {10},
pages = {2853-2866},
pmid = {42680886},
issn = {2058-5276},
support = {2023M732810//China Postdoctoral Science Foundation/ ; 2024M762573//China Postdoctoral Science Foundation/ ; 82372458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401762//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370653//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Polymorphism, Single Nucleotide ; Colorectal Neoplasms/microbiology/genetics ; *Genome, Microbial/genetics ; Humans ; *Metagenome ; *Host Microbial Interactions/genetics ; Cluster Analysis ; Clustering Algorithms ; Microbiota/genetics ; *Computational Biology/methods ; },
abstract = {Recovering high-quality microbial genomes from metagenomic sequencing data is essential for accurate profiling and understanding microbial variation. However, existing clustering methods often suffer from limited accuracy and scalability. Here we present MetaCAT (Metagenome Clustering and Association Tool), a framework that combines recovery of microbial genomes from metagenomic data and analysis of their associations with host traits. MetaCAT incorporates a Sparse Weighted Dirichlet Process Gaussian Mixture Model (SWDPGMM) to accurately and efficiently decompose complex datasets and combines k-mer frequency with read coverage to improve genome reconstruction. It also provides a dedicated workflow for microbial single-nucleotide polymorphism identification and metagenome-wide association studies with the host. MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets. Using metagenomic data from colorectal cancer cohorts, it revealed previously unrecognized marker species and microbial single-nucleotide polymorphisms associated with colorectal cancer. MetaCAT provides a scalable framework for microbial community profiling and advances our understanding of host-microbe interactions.},
}

*Metagenomics/methods
Polymorphism, Single Nucleotide
Colorectal Neoplasms/microbiology/genetics
*Genome, Microbial/genetics
Humans
*Metagenome
*Host Microbial Interactions/genetics
Cluster Analysis
Clustering Algorithms
Microbiota/genetics
*Computational Biology/methods

@article {pmid42705201,
year = {2026},
author = {Zhao, X and Meng, T and Zhang, Z and Hu, L and Xiang, X},
title = {Vegetable trimming pellets in laying hen diets drive cecal remodeling and dose-dependent plasma-egg metabolomic dissociation.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107637},
pmid = {42705201},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/blood/microbiology ; Female ; Diet/veterinary ; *Cecum/physiology/microbiology ; Animal Feed/analysis ; *Ovum/physiology/metabolism/chemistry ; *Metabolome ; Animal Nutritional Physiological Phenomena ; *Vegetables/chemistry ; *Gastrointestinal Microbiome/drug effects ; Dose-Response Relationship, Drug ; },
abstract = {Vegetable trimming pellets (TVP) provide a potential route for recovering plant biomass as poultry feed, but their dose-dependent effects across production and biological compartments remain unclear. We evaluated diets containing 0% (A), 3% (B), 6% (C), or 9% (D) TVP (80% lettuce and 20% cabbage trimmings) in 240 17-wk-old Hy-Line Grey hens (6 pens of 10 hens per diet) for 12 wk. Diets had similar calculated crude protein, while calculated metabolizable energy decreased from 2.854 to 2.659 Mcal/kg. We assessed production, egg quality, serum, intestine, cecal microbiota and metagenome, and plasma and egg metabolomes. Full-period feed conversion ratio increased from 2.74 in A to 2.88 in D (P = 0.026), and average daily feed intake differed (P = 0.001), while egg production, egg weight, and egg mass remained similar (P > 0.05). At wk 12, shell breaking strength was lower in D than in A to C (3.55 vs. 3.92 to 4.02 kgf/cm[2]; P = 0.030), and yolk color differed among diets (P = 0.007). Serum hormones, several biochemical indices, catalase, and malondialdehyde differed at wk 12 (P < 0.05; marker-specific n = 3 to 6). Cecal community composition differed (permutational multivariate analysis of variance: R[2] = 0.571, P = 0.0006; dispersion P = 0.229), while Shannon diversity remained similar (P = 0.582). Five A-vs.-D metagenomic pathways met a false discovery rate (FDR) < 0.05. In D vs. A, exploratory screening identified 254 annotated plasma and 338 annotated egg candidates, of which 62 and 80, respectively, also met FDR < 0.05; exact annotation matching identified one shared candidate. Graded TVP inclusion maintained major egg-output traits while producing dose-related shifts in feed use, cecal microbial features, and compartment-specific molecular profiles. At the higher inclusion levels, less favorable feed conversion and the lower late-period shell strength at 9% were the principal practical responses.},
}

Animals
*Chickens/physiology/blood/microbiology
Female
Diet/veterinary
*Cecum/physiology/microbiology
Animal Feed/analysis
*Ovum/physiology/metabolism/chemistry
*Metabolome
Animal Nutritional Physiological Phenomena
*Vegetables/chemistry
*Gastrointestinal Microbiome/drug effects
Dose-Response Relationship, Drug

@article {pmid42722277,
year = {2026},
author = {Xue, X and Ge, Y and Meng, T and Chen, Y and Zhou, L and Xu, D},
title = {Anthropogenic disturbance enhances bacteria-mediated resistome transmission across the sediment-benthos-demersal fish trophic continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129137},
doi = {10.1016/j.envpol.2026.129137},
pmid = {42722277},
issn = {1873-6424},
mesh = {Animals ; *Food Chain ; *Fishes/microbiology ; *Bacteria/genetics ; *Geologic Sediments/microbiology ; *Anthropogenic Effects ; China ; Lakes/microbiology ; Ecosystem ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota ; },
abstract = {Aquatic ecosystems are important environmental reservoirs of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), yet how anthropogenic disturbance influences their distribution and cross-niche transmission through benthic food webs remains poorly understood. Here, we systematically characterized resistome and virulome profiles across trophic niches, including sediments, benthic invertebrates and demersal fishes, along a gradient of anthropogenic disturbance in Gehu Lake, China. Metagenomic analysis identified 1645 ARG and 1939 VFG subtypes, with both gene pools exhibiting pronounced niche differentiation. Sediments harbored the highest abundance and diversity of both gene pools, whereas animal-associated niches exhibited substantial but host-dependent attenuation. Notably, anthropogenic disturbance significantly altered ARG and VFG profiles across all ecological niches, with stronger effects in sediments and benthic organisms than in fish guts, and was generally associated with higher ARG and VFG abundance and diversity. Integrative source-tracking and bacteria-gene association network analyses further demonstrated that bacterial transmission was the primary vector mediating the cross-trophic dissemination of both gene pools. Anthropogenic disturbance reshaped bacterial community structure across niches and enhanced bacterial migration along the food chain, as reflected by the increased contribution of bacteria derived from upstream trophic compartments. KEGG functional profiling suggested that these transmitted bacterial assemblages processed enhanced metabolic and adaptive capacities functions such as xenobiotic degradation. Among the enriched bacterial lineages, Pseudomonadota, Actinomycetota and Bacillota were dominant and showed a higher propensity to harbor ARGs and VFGs, thereby facilitating their persistence, amplification and trophic transfer. Collectively, our findings reveal a disturbance-driven, microbiome-mediated mechanism underlying the co-dissemination of ARGs and VFGs across aquatic food webs, highlighting the critical role of host-associated microbial selection in amplifying environmental health risk.},
}

Animals
*Food Chain
*Fishes/microbiology
*Bacteria/genetics
*Geologic Sediments/microbiology
*Anthropogenic Effects
China
Lakes/microbiology
Ecosystem
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Microbiota

@article {pmid42727575,
year = {2026},
author = {Deng, ZL and Safaei, N and McHardy, AC},
title = {Metax enables accurate cross-domain taxonomic profiling of metagenomes.},
journal = {Cell},
volume = {189},
number = {22},
pages = {7196-7211.e7},
doi = {10.1016/j.cell.2026.08.024},
pmid = {42727575},
issn = {1097-4172},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Humans ; Bacteria/genetics/classification ; },
abstract = {Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomic profiler that integrates coverage-based probabilistic modeling with an expectation-maximization framework to distinguish true microbial signals from artifacts. Across >600 samples from host-associated, environmental, wastewater, and low-biomass clinical settings, including benchmarks with limited reference representation, Metax improved profiling accuracy, achieving on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods. Moreover, this broad evaluation demonstrated that Metax resolved bacterial and viral signatures of peri-implantitis in oral microbiomes and revealed signals suggestive of reagent-borne contaminants and reference misassemblies in plasma-cell-free DNA. By leveraging genome-wide coverage evidence, Metax enables robust cross-domain profiling across diverse sample types and sequencing depths, including settings where reference databases are highly incomplete.},
}

*Metagenome/genetics
*Microbiota/genetics
*Metagenomics/methods
Humans
Bacteria/genetics/classification

@article {pmid42731219,
year = {2026},
author = {Xie, B and Hua, X and Geng, L and Li, K and Liu, G and Fang, Y and Zhao, T and Lu, C and Zhang, C and Han, Z and Yu, B and Li, X},
title = {Cecal microbiota regulates meat quality of Yanshan red jade broilers: insights from metagenomics and targeted metabolomics.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107619},
pmid = {42731219},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology/growth & development ; Female ; *Meat/analysis ; *Cecum/microbiology ; Metagenomics ; *Gastrointestinal Microbiome ; Metabolomics ; *Metabolome ; Fatty Acids ; },
abstract = {This study aimed to elucidate the molecular mechanism of cecal microbiota regulating muscle flavor in Yanshan red jade broilers with natural body weight variation. Eighteen-week-old hens were selected for this study. Targeted metabolomics was applied to determine the fatty acid and amino acid composition of muscle. Metagenomic sequencing was used to analyze the structure and function of cecal microbial communities. A regulatory network between gut microbiota and meat flavor was constructed via correlation analysis. The results showed that the high-weight female (HF) group had significantly better slaughter performance and leg muscle intramuscular fat (IMF) than the low-weight female (LF) group. Metabolomic analysis identified a total of 38 fatty acids and 25 amino acids. The HF group was enriched in umami amino acids such as arginine and serine, while the LF group had higher content of long-chain polyunsaturated fatty acids (PUFAs) and 1-methyl-l-histidine. Metagenomic analysis showed that Eubacterium and Anaerostipes were the characteristic bacteria in the HF group, while Odoribacter was dominant in the LF group. Functional annotation identified a total of 12 differential metabolic pathways, including core pathways such as lipid metabolism and amino acid synthesis. The association network showed that Eubacterium sp. An11 enhanced growth performance and umami quality by promoting muscle protein deposition, Odoribacter_splanchnicus affected muscle nutritional characteristics by regulating fatty acid metabolism, and Pseudoflavonifractor_capillosus was involved in both growth and flavor regulation. This study provides theoretical support and functional strain targets for flavor improvement of high-quality broilers and precise nutritional regulation of gut microbiota.},
}

Animals
*Chickens/microbiology/physiology/growth & development
Female
*Meat/analysis
*Cecum/microbiology
Metagenomics
*Gastrointestinal Microbiome
Metabolomics
*Metabolome
Fatty Acids

@article {pmid42731224,
year = {2026},
author = {Kerek, Á and Hetyésy, M and Tornyos, GÁ and Kaszab, E and Fehér, E and Jerzsele, Á and Tóth, T and Zsédely, E and Fébel, H},
title = {Timing of an antioxidant-acidifier feed additive modulates growth performance and cecal microbiota in broiler chickens during enrofloxacin exposure.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107639},
pmid = {42731224},
issn = {1525-3171},
mesh = {Animals ; *Enrofloxacin/administration & dosage ; *Chickens/growth & development/microbiology/physiology ; Male ; Animal Feed/analysis ; Diet/veterinary ; Cecum/microbiology ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Dietary Supplements/analysis ; *Antioxidants/administration & dosage/metabolism ; *Gastrointestinal Microbiome/drug effects ; Random Allocation ; Fluoroquinolones ; },
abstract = {Nutritional interventions targeting oxidative stress and gut ecology may help sustain broiler performance during antimicrobial perturbation. This study evaluated the timing-dependent effects of an antioxidant-acidifier feed additive, alone or combined with enrofloxacin, on growth performance and cecal microbiota in broilers. A total of 1,200 Ross 308 male broilers were assigned to six treatments (4 pens/treatment; 50 birds/pen) and reared to 42 d: control, enrofloxacin (d15-19), additive for 4 weeks (A4; d15-42), A4+enrofloxacin, additive for 6 weeks (A6; d1-42), and A6+enrofloxacin. The additive was included at 4% of the diet, providing fumaric acid, heat-stable vitamin C, and all-rac-α-tocopheryl acetate. Performance traits were recorded by phase and overall. Cecal contents were collected from 2 birds/pen on d14, d20, and d42 and analyzed by shotgun metagenomic sequencing; microbiota analyses were conducted on pen-level aggregated profiles. Growth performance showed modest, timing-dependent numerical differences: A4 had numerically higher finisher and overall average daily gain, whereas A4+enrofloxacin was associated with lower overall gain than enrofloxacin alone. Cecal community structure was driven primarily by sampling time point. No detectable enrofloxacin-associated separation was observed at d20, whereas a trend toward separation was evident at d42. By d42, only limited genus-level differences were detected, with the strongest signal observed for Phocaeicola in the targeted differential abundance analysis. Overall, additive timing influenced growth responses and cecal microbiota trajectories during enrofloxacin exposure, supporting the importance of supplementation timing when nutritional strategies are used to improve robustness under antibiotic perturbation.},
}

Animals
*Enrofloxacin/administration & dosage
*Chickens/growth & development/microbiology/physiology
Male
Animal Feed/analysis
Diet/veterinary
Cecum/microbiology
*Anti-Bacterial Agents/administration & dosage/pharmacology
Dietary Supplements/analysis
*Antioxidants/administration & dosage/metabolism
*Gastrointestinal Microbiome/drug effects
Random Allocation
Fluoroquinolones

@article {pmid42731658,
year = {2026},
author = {Cui, J and Yan, S and Wang, S and Xia, H and Chen, L and Liu, H and Ma, J and Fu, Y},
title = {Cerium dioxide nanoparticle exposure attenuates mobility-linked antibiotic resistome signatures across the soil-lettuce continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129133},
doi = {10.1016/j.envpol.2026.129133},
pmid = {42731658},
issn = {1873-6424},
mesh = {*Cerium/toxicity ; *Soil Microbiology ; *Nanoparticles ; *Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; *Soil Pollutants ; },
abstract = {Antibiotic resistance genes (ARGs) are contaminants of emerging concern in agricultural microbiomes. Their association with mobile genetic elements (MGEs) can enhance dissemination across soil-plant interfaces, creating potential environmental and food-chain exposure risks. However, how engineered nanoparticles modulate relative ARG abundance and mobility-linked resistome features in plant-associated microbiomes remains poorly understood. Here, we examined the effects of graded, experimentally elevated cerium dioxide nanoparticle (CeO2 NP) loadings in a soil-lettuce system by integrating compartment-resolved metagenomics, ARG-MGE co-occurrence analysis, putative host-reservoir profiling, transcriptomics, and functional assays. Metagenomic profiling identified 16 ARG types and 125 subtypes and revealed niche-dependent microbiome restructuring under CeO2 NP exposure. Rhizosphere relative ARG abundance showed a negative dose-associated trend, although overall inter-group differences were not significant, whereas leaf endophytes showed a weaker response. Relative MGE abundance decreased significantly in both compartments, and lower assembly-level ARG-MGE co-occurrence reflected fewer ARGs detected in MGE-associated genomic contexts, whereas fewer multi-ARG contigs suggested reduced ARG clustering and potential co-selection. Putative host-reservoir analysis associated key efflux determinants with bacterial families whose relative representation declined following CeO2 NP exposure. Transcriptomic profiling of representative putative ARG hosts revealed host-specific responses, including downregulation of genes involved in central metabolism and Sec-dependent trafficking. Complementary host assays showed reduced apparent envelope permeability and lower recovery of tetracycline-resistant recipient-identity colonies in the plasmid-associated host system. Together, under the tested elevated-loading conditions, CeO2 NP exposure was associated with lower relative ARG signals and weaker mobility-linked resistome features across the soil-lettuce continuum, providing mechanistic insight into nanoparticle-resistome interactions in soil-plant systems.},
}

*Cerium/toxicity
*Soil Microbiology
*Nanoparticles
*Drug Resistance, Microbial/genetics
Microbiota/drug effects
Anti-Bacterial Agents/pharmacology
Soil/chemistry
*Soil Pollutants

@article {pmid42759909,
year = {2026},
author = {Hou, J and Li, Q and Li, Y and Liu, M and Xue, M and An, Y and Yao, Y and Xu, H},
title = {Intraspecific rice intercropping reduces the rhizosphere resistome in association with organic acid and low-ARG-burden microbiota enrichment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129180},
doi = {10.1016/j.envpol.2026.129180},
pmid = {42759909},
issn = {1873-6424},
mesh = {*Rhizosphere ; *Oryza/growth & development ; *Soil Microbiology ; *Agriculture/methods ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Genes, Bacterial ; },
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils are an emerging environmental concern. However, sustainable strategies for reducing ARG in crop rhizospheres remain limited. Here, we investigated associations among rhizosphere metabolites, microbial communities, and ARG profiles in an intraspecific rice intercropping system. Compared with monoculture, intraspecific intercropping reduced the relative abundances of total ARGs and ARGs assigned to the Ranks I and II. Intercropping also altered rhizosphere metabolite profiles, with increased organic acid abundance, and was associated with convergent changes in microbial community composition. Nitrospirales, particularly Candidatus Sulfobium, was enriched under intercropping. Metagenome-assembled genomes (MAGs) assigned to this lineage contained relatively few annotated ARGs, which were predominantly classified as ARGs assigned to the Rank IV. Exogenous supplementation reproduced this field-associated pattern: citric acid treatment reduced total ARG and ARGs assigned to the Ranks I and II abundance and concurrently increased the relative abundance of Candidatus Sulfobium. These results support an association among rhizosphere organic acids, low-ARG-burden taxa, and reduced ARG abundance. Collectively, these findings highlight intraspecific rice intercropping as a low-input, source-control approach for cleaner rice production and ARG-risk mitigation.},
}

*Rhizosphere
*Oryza/growth & development
*Soil Microbiology
*Agriculture/methods
*Microbiota
*Drug Resistance, Microbial/genetics
Soil/chemistry
Genes, Bacterial

@article {pmid42778012,
year = {2026},
author = {Fu, X and He, H and Li, C and Huang, Q and Bu, Y and Zhang, D and Hashim, JH and Hashim, Z and Wispriyono, B and Sary, L and Pratama, S and Wieslander, G and Norback, D and Sun, Y},
title = {Classroom dust microbiome-metabolome signatures and ocular health in students: Cross-sectional associations with putative pollutant-transformation and microbial functional profiles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129217},
doi = {10.1016/j.envpol.2026.129217},
pmid = {42778012},
issn = {1873-6424},
mesh = {*Microbiota ; *Dust/analysis ; Humans ; *Metabolome ; Schools ; Cross-Sectional Studies ; *Air Pollution, Indoor/analysis ; },
abstract = {Ocular irritation and tear-film instability are common among school-aged children, yet the microbial and chemical features of classroom dust associated with these outcomes remain poorly characterized. We conducted a cross-sectional multi-omics study in 32 classrooms from eight Indonesian junior high schools, integrating shotgun metagenomics and untargeted LC-MS metabolomics of settled dust with ocular symptoms and tear film break-up time (TFBUT) from 380 students. Classrooms with a low prevalence of ocular irritation were enriched in Actinobacteriota such as Allosaccharopolyspora coralli, Saccharopolyspora dendranthemae, and Brevibacterium epidermidis (LDA > 2, P < 0.05, LEfSe), and in microbial pathways annotated for the degradation of aromatic pollutants and xenobiotics, including xylene, benzoate, toluene and polycyclic aromatic hydrocarbons (LDA > 2, P < 0.05). Consistent with this, classrooms with more stable tear film showed higher signals of metabolites consistent with aromatic-compound and xenobiotic transformation, including 4-hydroxyphenylpyruvic acid, the phthalate-degradation intermediate 4-hydroxyphthalate, 3-hydroxybenzoic acid and 4-hydroxycinnamic acid (q < 0.05), indicating potential microbial degradation of aromatic pollutants in these classrooms. Statistical interactions linked specific genera to these features (e.g. Brevibacterium with trans-cinnamate and p-hydroxyphenylacetic acid, and Sphingomonas with 3-hydroxyphenylacetic acid) in relation to TFBUT, and taxa such as Janibacter and Nocardioides co-occurred with multiple degradation intermediates. These signatures point to microbial pollutant-transformation potential as a candidate modifier of the indoor exposome, warranting longitudinal and mechanistic follow-up.},
}

*Microbiota
*Dust/analysis
Humans
*Metabolome
Schools
Cross-Sectional Studies
*Air Pollution, Indoor/analysis

@article {pmid42805174,
year = {2026},
author = {Perl, M and Guetter, S and Shah, D and Holzinger, S and Becker, L and Tariq, M and Menauer, P and Delahais, S and Lutzny-Geier, G and Scherer, JN and Göttert, S and Herfeld, K and Heinrich, P and Kreitmeier, KG and Gebhard, C and Herr, W and Trefny, MP and Doerr, J and Sameri, S and Harrer, DC and Ziegler-Martin, K and Staudt, S and Hansmann, L and Edinger, M and Wolff, D and Weber, D and Meedt, E and Denk, A and Gessner, A and Holler, E and Wertheimer, T and Neuhaus, K and Zheng, T and Cordas Dos Santos, DM and Theurich, S and Schirmer, M and Kleigrewe, K and Schluter, J and van den Brink, M and Schmitt, M and Feuerer, M and Heuser-Loy, C and Baldwin, J and Gattinoni, L and Rehli, M and Hudecek, M and Bigenwald, C and Zitvogel, L and Subklewe, M and Blumenberg, V and Schubert, ML and Stein-Thoeringer, C and Luu, M and Kobold, S and Fante, MA and Thiele Orberg, E and Poeck, H},
title = {Opposing functions of gut immunomodulatory metabolites on CAR-T therapy.},
journal = {Cell},
volume = {189},
number = {22},
pages = {6968-6987.e14},
doi = {10.1016/j.cell.2026.09.004},
pmid = {42805174},
issn = {1097-4172},
support = {DP2 AI164318/AI/NIAID NIH HHS/United States ; R01 CA269617/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; Mice ; *Immunotherapy, Adoptive/methods ; Pentanoic Acids/metabolism ; Indoles/metabolism ; *Receptors, Chimeric Antigen/metabolism/immunology ; Fatty Acids, Volatile/metabolism ; Female ; },
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has transformed hematological cancer treatment, yet nearly half of patients still relapse or progress. Increasing evidence implicates the gut microbiome and antibiotic exposure as key modulators of clinical outcomes. In a cohort of 129 patients across three German centers, shotgun metagenomics and targeted mass spectrometry revealed that reduced short-chain fatty acids, particularly valeric acid, prior to CAR-T cell therapy correlated with increased risk of disease progression. Conversely, high levels of indole metabolites, including indole-3-carboxaldehyde and indole-3-acetic acid as well as the branched-chain fatty acid isovaleric acid, were linked to adverse outcomes. Functional validation in human and murine CAR-T cell models demonstrated that valeric acid supplementation enhanced, while indole-3-carboxaldehyde and isovaleric acid impaired, CAR-T cell efficacy. These findings reveal the opposing roles of immunomodulatory metabolites on CAR-T cell therapy, carrying significant implications for the design of metabolite-guided, microbiome-based therapeutics.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology
Mice
*Immunotherapy, Adoptive/methods
Pentanoic Acids/metabolism
Indoles/metabolism
*Receptors, Chimeric Antigen/metabolism/immunology
Fatty Acids, Volatile/metabolism
Female

@article {pmid42838722,
year = {2026},
author = {Ware, K and Ollberding, N and Duan, Q and Haslam, D and Phipatanakul, W and Glazman, M and Bernstein, JA},
title = {Ultraviolet irradiation and the home microbiome in childhood asthma: An exploratory environmental analysis.},
journal = {Allergy and asthma proceedings},
volume = {47},
number = {6},
pages = {394-398},
doi = {10.2500/aap.2026.47.260079},
pmid = {42838722},
issn = {1539-6304},
support = {K24 AI106822/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Asthma/etiology/microbiology/epidemiology/diagnosis ; *Microbiota/radiation effects ; *Ultraviolet Rays ; Female ; Male ; Child ; Dust/analysis ; *Air Pollution, Indoor/adverse effects ; Housing ; Environmental Exposure ; Child, Preschool ; },
abstract = {Background: Ultraviolet (UV) filtration units installed into central heating, ventilation, and air conditioning systems have been shown to modify indoor environmental microbiomes (EM), but it remains unclear whether central UV air filtration systems as a targeted intervention alters the EM sufficiently to modify asthma outcomes. Objective: The objective was to investigate changes in the microbiome from dust samples collected before and after installation of a central UV filtration system in homes of children with mild-moderate persistent asthma. Methods: Enrolled pediatric subjects with asthma were randomized to receive UV filtration or sham devices in their heating, ventilation, and air conditioning units. Dust samples were collected from the furnace filters and each child's bedroom inflow air ducts from the first 20 homes randomized at the two largest recruiting sites at the time of device placement and at study completion (12 months), along with periodic measurements of asthma outcomes markers by using the Composite Asthma Severity Index. Microbial DNA from each paired dust sample underwent shotgun metagenomic sequencing, and taxonomic profiles were generated with MetaPhlAn 4. Associations between changes in bacterial species abundance and changes in asthma severity were assessed with Microbiome Multivariable Associations with Linear Models in R. Results: A total of 14 paired dust samples (7 from the UV homes and 7 from the sham homes) from inflow air ducts with sufficient quantity of dust were included for EM analysis. Within the UV filtration homes, false discovery rate adjusted q-values < 0.05 identified associations between worsening asthma severity and reduced relative abundance of common gastrointestinal commensals, such as Bacteroides and Bifidobacterium, previously linked to a reduced risk of allergic disease and asthma; no associations at this threshold were observed in the sham homes. Conclusion: An exploratory study of UV air filtration units installed in homes of children with asthma identified hypothesis-generating associations between bacterial species changes and asthma severity; because the study was underpowered for between-arm comparisons, these findings do not establish that UV air filtration caused the microbiome changes and should not be interpreted as confirmatory of a UV-specific effect.Clinical trial NCT02715375, www.clinicaltrials.gov.},
}

Humans
*Asthma/etiology/microbiology/epidemiology/diagnosis
*Microbiota/radiation effects
*Ultraviolet Rays
Female
Male
Child
Dust/analysis
*Air Pollution, Indoor/adverse effects
Housing
Environmental Exposure
Child, Preschool

@article {pmid42849293,
year = {2026},
author = {Zhou, X and Cui, G and Dong, H and Wen, S and Li, Y and Han, M and Wang, G},
title = {Genotype-dependent phosphorus acquisition responses of two soybean genotypes under combined low phosphorus and salt stress: evidence from root traits, exudates and rhizosphere microbiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111810},
doi = {10.1016/j.plaphy.2026.111810},
pmid = {42849293},
issn = {1873-2690},
mesh = {*Phosphorus/metabolism ; *Rhizosphere ; *Glycine max/genetics/metabolism/microbiology ; *Plant Roots/metabolism/microbiology/genetics ; Genotype ; *Microbiota ; *Salt Stress ; Plant Exudates/metabolism ; },
abstract = {Soil salinization and phosphorus (P) deficiency often co-occur in coastal saline-alkali soils, severely limiting crop productivity. Although root exudates are known to mediate rhizosphere microbiome assembly, the coordinated associations among root exudates, rhizosphere microbes, and P acquisition under combined salinity stress and phosphate deficiency remain unclear. In this study, we used two salt-tolerant soybean genotypes differing in P efficiency (A74, P-efficient; A6, P-inefficient) as materials. In a controlled pot experiment, four treatments were established: control (CK), low P (LP), salt (S), and combined stress (LPS). By integrating root phenotypes, P acquisition traits, root exudate metabolomics, and rhizosphere metagenomics, the genotype-dependent rhizosphere responses were investigated. Results showed that, compared to A6, A74 maintained a more extensive root-soil interface and superior P nutritional status under LP and LPS, exhibiting more robust P acquisition responses. Metabolomics and metagenomics identified 16 candidate metabolites and 12 candidate microbial taxa, respectively. Effect-size and correlation analyses prioritized naringenin and Sinorhizobium as candidate components associated with genotype-dependent P acquisition responses. KO annotation identified Sinorhizobium-associated genes with potential roles in phosphonate and phosphinate metabolism and benzoate degradation (e.g., phnJ, pcaC, and mhpD). In summary, these results support a genotype-dependent rhizosphere response pattern involving naringenin and Sinorhizobium, in which coordinated changes in root traits, exudate profiles, and microbial functional potential were associated with the stronger P acquisition response of A74 under combined stress. These findings identify candidate relationships for future functional validation under saline conditions.},
}

*Phosphorus/metabolism
*Rhizosphere
*Glycine max/genetics/metabolism/microbiology
*Plant Roots/metabolism/microbiology/genetics
Genotype
*Microbiota
*Salt Stress
Plant Exudates/metabolism

@article {pmid42949970,
year = {2026},
author = {Pigani, E and Simoens, K and Bernardi, D and Campese, L and Iudicone, D and Azaele, S and Suweis, S},
title = {Scaling laws link conserved gene-abundance distributions to adaptive expression in diatom communities worldwide.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2615743123},
doi = {10.1073/pnas.2615743123},
pmid = {42949970},
issn = {1091-6490},
support = {862923//AtlantECO/ ; 101059915//Biocean5D/ ; C53D23003420001//NRRP/ ; C93C22002810006//NRRP/ ; 101082021//MARCO-BOLO/ ; },
mesh = {*Diatoms/genetics ; Ecosystem ; Oceans and Seas ; Transcriptome ; Metagenomics ; },
abstract = {Marine microbes sustain Earth's major biogeochemical cycles, yet how they maintain stable ecosystem functions across diverse environments remains unclear. We analyzed metagenomic and metatranscriptomic data from diatom communities sampled during the Tara Oceans global expedition. While gene abundance distributions remain statistically similar across sample, gene expression varies systematically across geographical locations, a global pattern we show reflects predictable scaling laws. Global distributions, scaling relationships, and variability among sampling stations are captured by a stochastic model linking gene abundance dynamics to gene expression. While colder waters are associated with higher transcriptional activity and warmer regions show more selective gene usage, we find that transcript abundance increases nonlinearly with transcript richness. This general scaling is captured by our model and suggests that diatom communities balance high expression of core genes with specific functional diversity. These scaling relationships hold consistently across ocean basins, with temperature, used as an effective large-scale environmental descriptor whose signature cannot be fully disentangled from spatial structure, sufficing to predict transcriptional patterns from genetic composition. Our findings reveal how the stability of gene-abundance structure in diatom ecosystems coexists with transcriptional variability, enabling flexible functional responses.},
}

*Diatoms/genetics
Ecosystem
Oceans and Seas
Transcriptome
Metagenomics

@article {pmid42950786,
year = {2026},
author = {Li, MM and Liu, MC and Lv, AP and Ortúzar, M and OuYang, YT and Chen, LB and Chen, Y and Bian, BR and Yuan, Y and Gao, L and Liu, L and Jiao, JY and Li, WJ},
title = {Metagenome-assembled genomes reveal Labilithrix thermalis sp. nov., an uncultured microorganism in hot springs.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126780},
doi = {10.1016/j.syapm.2026.126780},
pmid = {42950786},
issn = {1618-0984},
abstract = {Geothermal environments harbor diverse microbial communities, including numerous phylogenetically novel lineages that remain largely unexplored. This study characterized two high quality metagenome assembled genomes (MAGs) from hot spring sediments in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences indicated that the two MAGs (JZ-3_bin_45[TS] and QQ_bin_234) should be assigned to the genus Labilithrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two MAGs and other genomes of the genus Labilithrix were below the recommended species thresholds (95% and 70%, respectively), indicating that the two MAGs represent a novel species within the genus Labilithrix. Genome annotation suggested an aerobic, chemoheterotrophic, and motile lifestyle, with the genetic potential for oxidative phosphorylation, tricarboxylic acid (TCA) cycle, starch degradation, assimilatory sulfate reduction, arsenic detoxification, geothermal adaptation, and diverse biosynthetic gene clusters (BGCs). Based on genomic and phylogenetic analysis, these MAGs should be classified as a novel species within this genus, for which the name Labilithrix thermalis sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This study expands the known diversity of the genus Labilithrix and highlights the value of metagenomics for uncovering previously uncultivated microbial taxa and function.},
}

@article {pmid42945300,
year = {2026},
author = {Andrade, B and Ramírez, M and Reyes, G},
title = {Microbial community structure of Penaeus vannamei post-larvae naturally infected with multiple viruses in hatchery tanks.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361576},
pmid = {42945300},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/virology/microbiology ; Larva/virology/microbiology ; Aquaculture ; *Microbiota ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This study offers an observational evaluation of how viral and bacterial infections co-occur with alterations in the microbiome and survival of Penaeus vannamei post-larvae, one of the most economically important species in global aquaculture.

METHODS: Eleven commercial larval production tanks were classified into three distinct infection scenarios using histology and PCR: Baculovirus penaei (BP) monoinfection, mixed infections (BP, white spot syndrome virus [WSSV], and acute hepatopancreatic necrosis disease [AHPND]-causing bacteria), and non-infected controls. High-molecular-weight DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform, followed by evaluation of microbial diversity, community structure, and infection-associated microbial signatures.

RESULTS: Although BP was the most abundant viral genus across infected groups, severe mortality was observed only under mixed-infection conditions, which were closely associated with AHPND-causing bacteria presence and microbiome disruption rather than with BP alone. Deep metagenomic sequencing revealed reduced, distinct microbiome structures in shrimp infected with BP and in those with mixed infections, compared to non-infected individuals. Non-infected post-larvae maintained complex and well-balanced bacterial communities, predominantly composed of Donghicola and Muricauda. Nudiviridae and Oscillospiraceae showed comparable relative abundances in BP-only and mixed-infection groups. In contrast, mixed infections were characterized by a relative increase in Vibrio, together with the PCR-detection of PirAB toxin genes, whereas WSSV remained detectable in the metagenomic dataset despite its comparatively low relative abundance, while the infection remained thermally suppressed and asymptomatic in the larvae. Functionally, infected larval microbiomes were enriched for transposases, retrotransposons, and virulence-factor genes. The near-complete BP-GR25 genome (119,245 bp) was assembled and annotated from larval metagenomes.

CONCLUSION: These results highlight the value of high-throughput sequencing in the early detection of pathogens in aquaculture, where subtle microbial shifts during postlarval stages can be valuable indicators of health status for production.},
}

Animals
*Penaeidae/virology/microbiology
Larva/virology/microbiology
Aquaculture
*Microbiota
Metagenomics
Metagenome

@article {pmid42945345,
year = {2026},
author = {Zang, C and Tang, L and Deek, RA},
title = {Supervised and covariate-adjusted dimension reduction for prediction and visualization using microbiome data.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42945345},
issn = {1477-4054},
support = {R56LM014522/LM/NLM NIH HHS/United States ; S10OD028483/OD/NIH HHS/United States ; //University of Pittsburgh's CTSI Trans-disciplinary Collaboration Pilot Award/ ; RRID:SCR_022735//University of Pittsburgh Center for Research Computing and Data/ ; },
mesh = {Humans ; Principal Component Analysis ; Algorithms ; *Microbiota ; Dimensionality Reduction ; *Gastrointestinal Microbiome ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {Given that the gut microbiome has been shown to play a critical role in human health, discerning the relationship between microbial taxa and disease outcomes or phenotypes is of interest. Often, this involves association testing, predictive modeling, and visualizing trends in the data. Principal coordinates analysis (PCoA) is a commonly used dimension reduction technique in microbiome studies. PCoA relies on pairwise distances between samples and serves as a nonlinear alternative to the classic principal component analysis when non-Euclidean distances are used. Its low-dimensional embeddings provide intuitive visualizations but do not incorporate outcome-related information. Therefore, the low-dimensional principal coordinates may have poor performance in visualizing outcome differences, as well as in downstream disease prediction tasks. Additionally, covariates, such as demographics, lifestyle factors, and technical artifacts, can obscure true biological signals, leading to masked or spurious associations and limited generalizability. To address these limitations, we propose a supervised and covariate adjusted PCoA algorithm. By utilizing outcome information, while simultaneously minimizing the influence of nuisance variables, our method produces low-dimensional embeddings that better separate disease outcomes in visualizations and result in improved accuracy in downstream regression and classification tasks. We demonstrate the effectiveness of the proposed method and highlight its ability to extract important associations between the microbiome and disease outcomes while mitigating nuisance variation through simulations and application to real microbiome profiling studies.},
}

Humans
Principal Component Analysis
Algorithms
*Microbiota
Dimensionality Reduction
*Gastrointestinal Microbiome
*Computational Biology/methods
Prediction Algorithms

@article {pmid42946708,
year = {2026},
author = {Wang, Y and Kim, H and Malmuthuge, N and Zhou, M and Chen, Y and Alexander, TW and Timsit, E and Yao, J and Liang, G and Guan, LL},
title = {Early-life bovine respiratory virome analysis reveals phage-driven adaptation and cross-host evolutionary signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946708},
issn = {2041-1723},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Bacteriophages/genetics/physiology ; Phylogeny ; Humans ; Genome, Viral ; *Respiratory System/virology ; Metagenomics ; Respiratory Tract Infections/virology/veterinary ; Evolution, Molecular ; },
abstract = {Past outbreaks of zoonotic viral infections highlight the importance of understanding respiratory virome ecology. As major food-producing animals with frequent human contact, cattle represent a critical host at the human-animal interface; however, the early-life establishment of their respiratory virome and its evolutionary connections to viruses from other hosts remain underexplored. Here, we longitudinally profile the upper respiratory tract (URT) virome of beef calves from birth to weaning using an optimized viral enrichment procedure and metagenomic workflow. Viral communities exhibited increased richness and turnover, reflecting ecological structuring during early life. Temperate phages dominate the URT phage community and share virulence- and mobility-associated genes with bacterial hosts, likely contributing to host adaptation and colonization persistence. Vertebrate-associated viruses emerge after the first week of life. Targeted reassembly from bovine URT viromes recovers near-complete betacoronavirus-like (CoV-D180) and adenovirus-like (AdV-D56) genomes positioned phylogenetically between bovine and human viral lineages. Competitive mapping of bovine-derived CoV-D180 and AdV-D56 to human respiratory metatranscriptomic datasets reveals genome-specific, regionally structured coverage patterns distinct from reference viruses, supporting shared sequence features in conserved genomic regions across host-associated viral lineages. Collectively, these findings reveal early-life assembly dynamics of the bovine respiratory virome and highlight cross-host signatures in a One Health framework.},
}

Animals
Cattle
*Virome/genetics
*Bacteriophages/genetics/physiology
Phylogeny
Humans
Genome, Viral
*Respiratory System/virology
Metagenomics
Respiratory Tract Infections/virology/veterinary
Evolution, Molecular

@article {pmid42399252,
year = {2026},
author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J},
title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42399252},
issn = {2055-5008},
support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Egg Shell/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Aging ; Metagenomics ; *Host Microbial Interactions ; *Bacteria/classification/genetics/isolation & purification ; Oviposition ; },
abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.},
}

Animals
*Chickens/microbiology
*Egg Shell/chemistry/microbiology
Female
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Aging
Metagenomics
*Host Microbial Interactions
*Bacteria/classification/genetics/isolation & purification
Oviposition

@article {pmid42399687,
year = {2026},
author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y},
title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42399687},
issn = {2399-3642},
mesh = {*Spheniscidae ; Antarctic Regions ; Animals ; *Soil Microbiology ; Oxidation-Reduction ; *Clostridium/metabolism/genetics ; *Iron/metabolism ; Fermentation ; *Microbial Consortia ; },
abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.},
}

*Spheniscidae
Antarctic Regions
Animals
*Soil Microbiology
Oxidation-Reduction
*Clostridium/metabolism/genetics
*Iron/metabolism
Fermentation
*Microbial Consortia