@article {pmid42010118,
year = {2026},
author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV},
title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.},
journal = {Nature medicine},
volume = {32},
number = {6},
pages = {2096-2106},
pmid = {42010118},
issn = {1546-170X},
support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/genetics ; Female ; Male ; *Genetic Predisposition to Disease ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Feces/microbiology ; *Glucosylceramidase/genetics ; Risk Factors ; Case-Control Studies ; *Microbiota/genetics ; Metagenomics ; Disease Progression ; },
abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.},
}

Humans
*Parkinson Disease/microbiology/genetics
Female
Male
*Genetic Predisposition to Disease
*Gastrointestinal Microbiome/genetics
Aged
Middle Aged
Feces/microbiology
*Glucosylceramidase/genetics
Risk Factors
Case-Control Studies
*Microbiota/genetics
Metagenomics
Disease Progression

@article {pmid42032005,
year = {2026},
author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG},
title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42032005},
issn = {2045-2322},
support = {N. 24-45-20005//RSF grant/ ; },
mesh = {Animals ; *Ixodes/virology ; Russia ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; *Virome/genetics ; Genetic Variation ; },
abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.},
}

Animals
*Ixodes/virology
Russia
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
*Genome, Viral
*Virome/genetics
Genetic Variation

@article {pmid42057074,
year = {2026},
author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T},
title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42057074},
issn = {1746-6148},
mesh = {Animals ; *Microbiota ; Swine ; *Mycoplasma hyopneumoniae/immunology ; *Pneumonia of Swine, Mycoplasmal/prevention & control/microbiology ; *Bacterial Vaccines/administration & dosage/immunology ; *Vaccination/veterinary/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Nanotechnology ; Female ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; },
abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.},
}

Animals
*Microbiota
Swine
*Mycoplasma hyopneumoniae/immunology
*Pneumonia of Swine, Mycoplasmal/prevention & control/microbiology
*Bacterial Vaccines/administration & dosage/immunology
*Vaccination/veterinary/methods
Bronchoalveolar Lavage Fluid/microbiology
Nanotechnology
Female
RNA, Ribosomal, 16S/genetics
Administration, Oral

@article {pmid42173516,
year = {2026},
author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A},
title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {331},
number = {1},
pages = {G38-G59},
doi = {10.1152/ajpgi.00056.2026},
pmid = {42173516},
issn = {1522-1547},
support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Tumor Escape/drug effects ; Male ; Mice ; *Bile Acids and Salts ; Dysbiosis/chemically induced ; STAT1 Transcription Factor/metabolism ; Wnt1 Protein/genetics/metabolism ; STAT3 Transcription Factor/metabolism ; Disease Progression ; B7-H1 Antigen/metabolism ; Humans ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Mice, Inbred C57BL ; Interferon-gamma/metabolism ; },
abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes tumorigenesis, we evaluated the effects of HFD + ABS ± ABx treatment on tumor immune evasion in mice. In HFD + ABS + ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1, and programmed cell death-ligand 1 (PD-L1) was observed, along with apoptosis suppression. Protein expressions of interferon-gamma (IFNγ) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD + ABS + ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFNγ stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1, and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD + ABS + ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFNγ-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.NEW & NOTEWORTHY Coadministration of antibiotics with a high-fat diet and acid bile salts exacerbated dysbiosis, insulin resistance, and systemic inflammation, thereby promoting tumor progression via tumor immune evasion at the squamocolumnar junction (SCJ) in K19-Wnt1/C2mE mice. In the tumor, interferon-gamma-induced programmed death-ligand 1 through the activation of signal transducer and activator of transcription 1 (STAT1) and STAT3. Understanding the link between dysbiosis and tumor immunity might aid in the development of new immunotherapies for SCJ tumors.},
}

Animals
*Diet, High-Fat/adverse effects
*Anti-Bacterial Agents/pharmacology/toxicity
*Tumor Escape/drug effects
Male
Mice
*Bile Acids and Salts
Dysbiosis/chemically induced
STAT1 Transcription Factor/metabolism
Wnt1 Protein/genetics/metabolism
STAT3 Transcription Factor/metabolism
Disease Progression
B7-H1 Antigen/metabolism
Humans
Gastrointestinal Microbiome/drug effects
Cell Proliferation/drug effects
Mice, Inbred C57BL
Interferon-gamma/metabolism

@article {pmid42287197,
year = {2026},
author = {De Visscher, J and Tytgat, B and Hodgson, DA and Wilmotte, A and Willems, A and Verleyen, E and Vyverman, W},
title = {Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {7},
pages = {},
doi = {10.1093/femsec/fiag060},
pmid = {42287197},
issn = {1574-6941},
support = {SD/BA/03A//Belgian Science Policy Office/ ; //EU Horizon 2020 InterAct project MiBiPol/ ; SD/CA/01A//Belspo project HOLANT/ ; //Research Foundation Flanders/ ; },
mesh = {*Lakes/microbiology ; Antarctic Regions ; Arctic Regions ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; *Bacteria/genetics/classification ; },
abstract = {Benthic microbial mat communities are key drivers of ecosystem functioning in polar lakes and ponds, forming the base of aquatic food webs and contributing substantially to nutrient cycling. Although Arctic, sub-Antarctic, and Antarctic microbial mats differ in community composition, their functional genetic potential remains poorly understood. We applied shotgun metagenomic sequencing to study 17 microbial mat communities from Arctic and (sub-)Antarctic lakes differing in salinity, catchment vegetation, and climatic conditions. Stress response genes, especially cold stress, and phosphorus cycling and metabolism genes were highly abundant in all lakes. A large proportion of functional genes was shared between regions, with core functions dominated by transport mechanisms and energy production. However, clear differences in particular gene abundances were observed. Several East-Antarctic lakes and inland ponds in the Transantarctic Mountains showed a dominance of oxygenic photosynthesis and Calvin cycle genes for carbon fixation, likely reflecting the dominance of Cyanobacteriota. In Arctic and sub-Antarctic lakes with catchment vegetation and higher arthropod abundances, lignin and chitin degradation genes were more important. Our study shows that, despite distinct biogeographic patterns in community composition, the functional genetic potential of polar lake microbial mats mainly reflects climatic and local environmental conditions, emphasizing specific adaptations to extreme polar environments.},
}

*Lakes/microbiology
Antarctic Regions
Arctic Regions
*Microbiota/genetics
Ecosystem
Metagenomics
*Bacteria/genetics/classification

@article {pmid42287489,
year = {2026},
author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A},
title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42287489},
issn = {1573-0972},
mesh = {*Fungi/classification/genetics/isolation & purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.},
}

*Fungi/classification/genetics/isolation & purification
*DNA Barcoding, Taxonomic
*Biodiversity
*Wetlands
*Mycobiome
Basidiomycota/genetics/classification
Geologic Sediments/microbiology
*Rhizophoraceae/microbiology
Ecosystem
Ascomycota/genetics/classification/isolation & purification
Phylogeny

@article {pmid42287798,
year = {2026},
author = {Winssy, TD and Anandham, R and Maragatham, S and Uma, D and Karthikeyan, S and Balachandar, D},
title = {Long-term nutrient management shapes soil microbial and metabolic signatures in a century-old semi-arid agroecosystem.},
journal = {Journal of environmental management},
volume = {411},
number = {},
pages = {130209},
doi = {10.1016/j.jenvman.2026.130209},
pmid = {42287798},
issn = {1095-8630},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Nitrogen ; Carbon ; Agroecology ; Agriculture ; Fertilizers ; Microbiota ; },
abstract = {Semi-arid tropical soils inherently contain low soil organic carbon (SOC) and limited nutrient reserves, resulting in poor productivity. Intensive cropping with synthetic fertilizers, further deteriorate soil quality and impair ecosystem functioning. In contrast, organic amendments alone or combined with synthetic fertilizers sustain soil biodiversity through microbially mediated processes. However, how long-term nutrient management shapes soil microbiomes and their functional diversity in semi-arid tropical systems remains largely unknown. To address this gap, we investigated a 116-year-old long-term nutrient management experiment using a multi-omic framework. Shotgun metagenomics characterized the total microbiome (bacteria, archaea, and eukaryota) and associated carbon- and nitrogen-cycling genes under four contrasting nutrient management practices: unfertilized control, inorganic fertilizer alone (IC), organic amendment alone (OM), and integrated nutrient management combining organic and inorganic inputs (INM). OM and INM significantly improved soil nutrient stocks, SOC, microbial biomass, and enzyme activities compared with IC and Control. These treatments also enhanced microbial diversity and shifted communities toward copiotrophic and functionally beneficial taxa, whereas IC and Control were dominated by stress-tolerant oligotrophs. Pathway analysis showed that carbon fixation dominated the C-cycling gene pool, with alternative autotrophic pathways prevailing over the Calvin cycle, particularly under OM and INM. These treatments also supported higher abundances of methanogenic and decomposition-associated genes, indicating enhanced carbon turnover. Nitrogen-cycling functions exhibited pathway-specific responses: OM enriched N-fixation and assimilatory nitrate reduction genes, whereas INM enhanced denitrification and dissimilatory nitrate reduction pathways. IC showed increased nitrification potential but the weakest biologically regulated N pathways. Volatomics profiling showed that OM and INM produced more diverse and metabolically active volatile organic compounds that were strongly associated with SOC and key biological attributes. Collectively, our study underscores the importance of carbon-rich organic inputs in rebuilding soil carbon stocks, reinforcing biological processes, and enhancing nutrient cycling for long-term sustainability of agriculture in semi-arid tropical regions.},
}

*Soil Microbiology
*Soil/chemistry
Nitrogen
Carbon
Agroecology
Agriculture
Fertilizers
Microbiota

@article {pmid42287872,
year = {2026},
author = {Wu, J and Wang, B and Li, Y and Zhang, X and Peng, Y and Liu, Q and Zhang, C and Lian, B and Cao, H and Li, K and Wang, H},
title = {Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in the Bohai sea.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108193},
doi = {10.1016/j.marenvres.2026.108193},
pmid = {42287872},
issn = {1879-0291},
abstract = {Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.},
}

@article {pmid42287875,
year = {2026},
author = {Yang, X and Wu, P and Li, C and Zheng, Q and Shi, X and Su, H and Wang, T and Xiong, X and Liu, Y and Xiao, Y and Xu, S and Zou, J and Liu, Y},
title = {Bacterial communities and antibiotic resistance genes in seawater adjacent to inhabited and uninhabited xisha coral reef islands: Insights from 16S rRNA and metagenomic sequencing.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108197},
doi = {10.1016/j.marenvres.2026.108197},
pmid = {42287875},
issn = {1879-0291},
abstract = {The Xisha coral reefs are highly biodiverse ecosystems in the South China Sea, China. Bacterial communities drive energy flow and biogeochemical cycling in coral-reef ecosystems, and serve as indicators of reef health. Yet the composition and dynamics of both bacterial assemblages and ARGs within the Xisha coral reefs remain poorly resolved. This study used 16S rRNA amplicon and metagenomic sequencing to compare bacterial community structure across surface and bottom waters, and surface-water ARGs profiles, in Beijiao Reef (BJ; an uninhabited reef) and Qilianyu Islands (QLY; an inhabited island) of the Xisha Islands. The results revealed bacterial community composition, bacterial co-occurrence network structure, and ARGs profiles differed markedly between the two reef areas. Dominant genera-Prochlorococcus_MIT9313, Salinimonas, Synechococcus_CC9902, Vibrio, and Alteromonas-were significantly more abundant in BJ (p < 0.05), whereas QLY showed higher abundances of Planococcus, Psychrobacter, Jeotgalibacillus, Salinicoccus, and Marinococcus (p < 0.05). The QLY bacterial co-occurrence network exhibited greater complexity (higher clustering coefficients and modularity), whereas the BJ network was simpler but displayed significantly higher closeness-centrality values (p < 0.001). Surface waters of the Xisha Islands were dominated by tetracycline, aminoglycoside, and macrolide resistance genes, whereas sulfonamide and multidrug resistance genes were less abundant. In addition, ARGs concentrations in BJ were slightly higher than those in QLY, suggesting that human habitation may not be a key environmental factor influencing ARGs concentrations in the seawater of the Xisha Islands. Correlation analysis showed that high-abundance ARGs in BJ (msbA, RanA, tetB(P), tet(T)) were linked to phototrophic Prochlorococcus_MIT9313 and Synechococcus_CC9902, whereas QLY dominant ARGs (baeS, patB, MexW) correlated with Gram-negative Vibrio and Pseudomonas. These ARGs are involved in bacterial efflux mechanisms, reflecting adaptive responses to environmental stress. This study provides valuable insights for assessing water quality and evaluating the impacts of human habitation pressure on coral reef ecosystems in the Xisha Islands.},
}

@article {pmid42291259,
year = {2026},
author = {Feng, S and Liu, Q and Chen, Y and Kang, D and Zou, S},
title = {Different grazing intensities affect soil nitrogen cycling by altering microbial nitrogen metabolism in alpine wetlands.},
journal = {iScience},
volume = {29},
number = {6},
pages = {116009},
pmid = {42291259},
issn = {2589-0042},
abstract = {Grazing significantly affects soil nitrogen cycling in eastern Qinghai-Tibet Plateau alpine wetlands. Grazing did not alter soil microbial α-diversity, but shifted community composition via metagenomic analysis. Moderate and heavy grazing reduced soil total and active nitrogen contents by 53.8%-92.0% vs. light grazing, significantly decreased abundances of nitrification genes (amoA and hao) and ammonium assimilation gene (glnA), while increased dissimilatory nitrite reduction to ammonium gene (nirB) by 142.1%. A nitrification bottleneck from impaired nitrification drove active nitrogen decline, and structural equation modeling identified nitrogen cycle gene abundance as the key driver. This study reveals microbial nitrogen cycling mechanisms and provides a scientific basis for sustainable grazing management in alpine wetlands.},
}

@article {pmid42291297,
year = {2026},
author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X},
title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1809022},
pmid = {42291297},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation & purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; },
abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.

METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).

RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p < 0.01). Candida albicans (p = 0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p = 0.038) and Prevotella pallens (p = 0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p < 0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.

CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Lung Diseases, Interstitial/microbiology/diagnosis
Female
*Metagenomics/methods
*Microbiota/genetics
Retrospective Studies
Male
Bacteria/classification/genetics/isolation & purification
Aged
Phenotype
Middle Aged
Sensitivity and Specificity
Metagenome

@article {pmid42293411,
year = {2025},
author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z},
title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1719445},
pmid = {42293411},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; },
abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Animals
*Homeostasis
*Circadian Rhythm
*Bone and Bones/metabolism/physiology
Bone Remodeling
Metabolomics
Fatty Acids, Volatile/metabolism
Osteogenesis

@article {pmid42293535,
year = {2026},
author = {González-Reguero, D and Robas-Mora, M and García Ordiales, E and Fernández-Pastrana, VM and Penalba-Iglesias, D and Probanza Lobo, A and Jiménez Gómez, PA},
title = {Recovery of organic waste from a wastewater treatment plant, improved with plant growth promoting bacteria: model of Quercus suber L.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1754063},
pmid = {42293535},
issn = {1664-302X},
abstract = {Cork oaks (Quercus suber L.) are key tree species in Mediterranean ecosystems, playing a crucial role in fire mitigation due to their thick, fire‑resistant bark, while also contributing to biodiversity conservation and soil stability. Integrating waste valorization strategies with biofertilizers based on plant growth‑promoting bacteria (PGPB) may enhance reforestation efficiency. This study evaluated different irrigation regimes under controlled phytotron conditions, including water, organic fertilizer derived from a wastewater treatment plant (WWTP), and sterilized WWTP fertilizer, combined with Bacillus pretiosus CECT30673[T] and Pseudomonas agronomica CECT30673[T]. Microbial functional diversity (Shannon index), antibiotic resistance profiles, and rhizosphere community structure were assessed using 16S rRNA‑based metagenomic analyses, including taxonomic composition, beta diversity, and genus‑level relative abundances. Plant performance was evaluated through biomass production, stem length, and nutritional parameters, including protein composition, sugar content, and fatty acid profile. The application of PGPBs together with WWTP‑derived fertilizers resulted in a significant increase in plant biomass and stem length compared to traditional water irrigation. Nutritional quality was also significantly improved, with higher protein, sugar, and fatty acid contents. Additionally, the combined treatments reduced minimum inhibitory concentrations (MICs) within the rhizosphere microbial community while maintaining its functional and structural stability. These results demonstrate that combining PGPBs with WWTP‑derived matrices enhances cork oak growth and nutritional quality without disrupting native soil microbiomes, supporting their potential as sustainable tools for Mediterranean reforestation.},
}

@article {pmid42000726,
year = {2026},
author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T},
title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42000726},
issn = {2041-1723},
mesh = {Humans ; *Bacteriophages/genetics/physiology ; Feces/microbiology/chemistry ; *Fatty Liver/microbiology/metabolism/virology ; *Gastrointestinal Microbiome/genetics/physiology ; Ruminococcus/virology/metabolism/genetics ; Metagenomics ; Faecalibacterium prausnitzii/metabolism/genetics/virology ; Bile Acids and Salts/metabolism ; Dysbiosis/microbiology ; *Bacteria/metabolism/genetics ; Metabolomics ; Female ; Male ; Case-Control Studies ; Eubacteriales ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.},
}

Humans
*Bacteriophages/genetics/physiology
Feces/microbiology/chemistry
*Fatty Liver/microbiology/metabolism/virology
*Gastrointestinal Microbiome/genetics/physiology
Ruminococcus/virology/metabolism/genetics
Metagenomics
Faecalibacterium prausnitzii/metabolism/genetics/virology
Bile Acids and Salts/metabolism
Dysbiosis/microbiology
*Bacteria/metabolism/genetics
Metabolomics
Female
Male
Case-Control Studies
Eubacteriales

@article {pmid42278576,
year = {2026},
author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T},
title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278576},
issn = {1422-0067},
mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; },
abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.},
}

Humans
Female
*Lactobacillus/genetics/physiology
*Vagina/microbiology/virology
*Candida/genetics/physiology
*Cervix Uteri/microbiology/virology
*Papillomavirus Infections/virology/microbiology
*Mycobiome/genetics
Metagenomics/methods
Adult
Microbiota
Shotgun Sequencing
Middle Aged
*Human Papillomavirus Viruses/genetics

@article {pmid42280335,
year = {2026},
author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E},
title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280335},
issn = {2072-6643},
support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; },
mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration & dosage/isolation & purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; },
abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.

METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.

RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.},
}

Humans
Child
Male
Female
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
*Amaranthus/chemistry
Body Mass Index
Blood Glucose/metabolism
*Pediatric Obesity/microbiology/blood
*Plant Proteins/administration & dosage/isolation & purification/pharmacology
*Overweight/microbiology
Cholesterol/blood
Insulin/blood
Triglycerides/blood
Feces/microbiology

@article {pmid42280338,
year = {2026},
author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ},
title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280338},
issn = {2072-6643},
support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.

METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.

RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.

CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.},
}

Humans
*Synbiotics/administration & dosage
*Metagenomics/methods
Child, Preschool
*Autism Spectrum Disorder/microbiology/therapy
Male
Child
Female
Pilot Projects
Feces/microbiology
*Gastrointestinal Microbiome
Treatment Outcome
*Precision Medicine/methods

@article {pmid42281243,
year = {2026},
author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE},
title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685381},
pmid = {42281243},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; },
abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Feces/microbiology
Biomarkers/urine/blood
Female
Adult
Male
*Diet
Australia
*Bacteria/classification/genetics/isolation & purification/metabolism
Cross-Over Studies
Middle Aged
Metabolome
Metabolomics
Blood Pressure

@article {pmid42286862,
year = {2026},
author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M},
title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2679497},
pmid = {42286862},
issn = {1949-0984},
mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; },
abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.},
}

Animals
*Cytokinins/blood/metabolism
Humans
Mice
*Diet
*Gastrointestinal Microbiome
*Mammals/metabolism
Metabolomics
Metagenomics
Feces/chemistry
Swine
Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota

@article {pmid41589071,
year = {2026},
author = {Caserta, MT and Mariani, TJ and Walsh, EE and Gill, SR and Gill, AL and Corbett, A and Harrington, D and Chu, C and Qiu, X},
title = {Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Infants Infected With Respiratory Syncytial Virus.},
journal = {The Journal of infectious diseases},
volume = {233},
number = {6},
pages = {1027-1035},
doi = {10.1093/infdis/jiag049},
pmid = {41589071},
issn = {1537-6613},
support = {58711//Merck Investigator Studies Program/ ; //Merck and Co, Inc/ ; },
mesh = {Humans ; *Respiratory Syncytial Virus Infections/diagnosis/virology ; *Respiratory Sounds/etiology ; Infant ; Male ; Severity of Illness Index ; Female ; *Biomarkers/analysis ; Recurrence ; Microbiota ; Respiratory Syncytial Virus, Human ; Acute Disease ; },
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospitalization in infants, and those with RSV disease appear more likely to develop recurrent wheeze. We examined nasal airway gene expression and microbiome composition during primary RSV infection to test associations with illness severity and identify infants with recurrent wheeze.

METHODS: Previously healthy infants with RSV infection were enrolled (December 2019-December 2023). Clinical and demographic data were collected, as were 2 anterior nasal swabs and a nasal wash for metagenome and transcriptome sequencing. Disease severity was measured by the improved Global Respiratory Severity Score (iGRSS). Participants were followed for approximately 1 year to identify recurrent wheeze. Multivariate regression models were developed to identify correlates and predictors of disease severity and recurrent wheeze, respectively.

RESULTS: One hundred infants (90 hospitalized) were enrolled (mean ± SD age, 3.2 ± 2.3 months; 61% male). An overall 405 genes (false discovery rate, 0.10) were significantly and consistently associated with illness severity (iGRSS), implicating innate immune and interleukin signaling pathways. The abundance of nasal Dolosigranulum was inversely associated with iGRSS, while the abundance of Haemophilus was directly associated with iGRSS. Predictive models based on nasal gene expression during infection had the power to classify recurrent wheeze (in-sample area under the curve, 0.992; cross-validated area under the curve, 0.882), while metagenomic features did not improve predictive performance.

CONCLUSIONS: We prospectively followed infants with primary RSV infection and identified associations among nasal gene expression, microbiome composition/function, and acute disease severity and recurrent wheeze. Host transcriptional profiles during infection were predictive of recurrent wheeze within the following year.},
}

Humans
*Respiratory Syncytial Virus Infections/diagnosis/virology
*Respiratory Sounds/etiology
Infant
Male
Severity of Illness Index
Female
*Biomarkers/analysis
Recurrence
Microbiota
Respiratory Syncytial Virus, Human
Acute Disease

@article {pmid42019469,
year = {2026},
author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH},
title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106914},
pmid = {42019469},
issn = {1525-3171},
mesh = {Animals ; *Chickens/genetics/growth & development/physiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Signal Transduction ; *Taurine/metabolism/analogs & derivatives ; p38 Mitogen-Activated Protein Kinases/metabolism/genetics ; *Avian Proteins/metabolism/genetics ; *Muscle Fibers, Skeletal/physiology ; Pectoralis Muscles/growth & development/physiology ; Male ; *Muscle Development ; },
abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.},
}

Animals
*Chickens/genetics/growth & development/physiology/microbiology
*Gastrointestinal Microbiome/physiology
Signal Transduction
*Taurine/metabolism/analogs & derivatives
p38 Mitogen-Activated Protein Kinases/metabolism/genetics
*Avian Proteins/metabolism/genetics
*Muscle Fibers, Skeletal/physiology
Pectoralis Muscles/growth & development/physiology
Male
*Muscle Development

@article {pmid42020464,
year = {2026},
author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH},
title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42020464},
issn = {2045-2322},
support = {5850.0109317.18.9 and 21167-2//Petróleo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Atlantic Ocean ; *Microbiota/genetics ; *Ecosystem ; Metagenomics/methods ; *Seawater/microbiology ; *Bacteria/genetics/classification ; Metagenome ; Water Microbiology ; },
abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.},
}

Atlantic Ocean
*Microbiota/genetics
*Ecosystem
Metagenomics/methods
*Seawater/microbiology
*Bacteria/genetics/classification
Metagenome
Water Microbiology

@article {pmid42127905,
year = {2026},
author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y},
title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.},
journal = {Cell reports. Medicine},
volume = {7},
number = {6},
pages = {102797},
doi = {10.1016/j.xcrm.2026.102797},
pmid = {42127905},
issn = {2666-3791},
mesh = {Humans ; Aged ; *Cognition/physiology ; *Diet, Plant-Based ; *Gastrointestinal Microbiome/physiology/genetics ; China ; Female ; Aged, 80 and over ; Male ; Multiomics ; Longitudinal Studies ; Rural Population ; Feces/microbiology ; Metagenomics ; East Asian People ; },
abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.},
}

Humans
Aged
*Cognition/physiology
*Diet, Plant-Based
*Gastrointestinal Microbiome/physiology/genetics
China
Female
Aged, 80 and over
Male
Multiomics
Longitudinal Studies
Rural Population
Feces/microbiology
Metagenomics
East Asian People

@article {pmid42143575,
year = {2026},
author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J},
title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42143575},
issn = {1751-7370},
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Plasmids/genetics ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Escherichia coli/genetics/drug effects ; Feces/microbiology/chemistry ; Metabolomics ; Male ; Female ; Mice, Inbred C57BL ; },
abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.},
}

Animals
*Bile Acids and Salts/metabolism
*Plasmids/genetics
*Helicobacter Infections/drug therapy/microbiology
*Helicobacter pylori/drug effects/genetics
*Anti-Bacterial Agents/pharmacology/therapeutic use
Mice
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Bacterial/genetics
Gene Transfer, Horizontal
Humans
Metagenomics
Escherichia coli/genetics/drug effects
Feces/microbiology/chemistry
Metabolomics
Male
Female
Mice, Inbred C57BL

@article {pmid42202790,
year = {2026},
author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R},
title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.},
journal = {Cell reports. Medicine},
volume = {7},
number = {6},
pages = {102835},
doi = {10.1016/j.xcrm.2026.102835},
pmid = {42202790},
issn = {2666-3791},
mesh = {*Diabetes Mellitus, Type 2/microbiology/epidemiology ; Humans ; Female ; Sweden/epidemiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Prospective Studies ; Male ; Incidence ; Eubacteriales ; },
abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.},
}

*Diabetes Mellitus, Type 2/microbiology/epidemiology
Humans
Female
Sweden/epidemiology
*Gastrointestinal Microbiome/genetics
Aged
Prospective Studies
Male
Incidence
Eubacteriales

@article {pmid42237904,
year = {2026},
author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH},
title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.},
journal = {Environmental science & technology},
volume = {60},
number = {23},
pages = {16514-16525},
doi = {10.1021/acs.est.6c01505},
pmid = {42237904},
issn = {1520-5851},
mesh = {*Microbiota ; Halogenation ; Hospitals ; Disinfection ; *Virome ; Drug Resistance, Microbial/genetics ; },
abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.},
}

*Microbiota
Halogenation
Hospitals
Disinfection
*Virome
Drug Resistance, Microbial/genetics

@article {pmid42278252,
year = {2026},
author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B},
title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278252},
issn = {1422-0067},
support = {101079425//Centre of Biotechnologie of Sfax/ ; },
mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; },
abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.},
}

*Metagenomics/methods
Tunisia
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Archaea/genetics/classification
Shotgun Sequencing
Phylogeny
*Bacteria/genetics/classification
Metagenome

@article {pmid42278256,
year = {2026},
author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M},
title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278256},
issn = {1422-0067},
support = {RAC# 2240005//King Faisal Specialist Hospital & Research Centre/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota ; *Homeostasis ; *Breast/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.},
}

Humans
Female
*Breast Neoplasms/microbiology/therapy/pathology
*Microbiota
*Homeostasis
*Breast/microbiology
Metagenomics
RNA, Ribosomal, 16S/genetics

@article {pmid42278324,
year = {2026},
author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y},
title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278324},
issn = {1422-0067},
support = {24-14-00059//Russian Science Foundation/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Chromosome Aberrations/radiation effects/drug effects ; RNA, Ribosomal, 16S/genetics ; *Radiotherapy/adverse effects ; Radiation-Protective Agents/pharmacology ; Male ; Lactobacillus ; *Minerals/pharmacology ; *Dysbiosis/etiology ; },
abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Mice
*Gastrointestinal Microbiome/drug effects/radiation effects
Chromosome Aberrations/radiation effects/drug effects
RNA, Ribosomal, 16S/genetics
*Radiotherapy/adverse effects
Radiation-Protective Agents/pharmacology
Male
Lactobacillus
*Minerals/pharmacology
*Dysbiosis/etiology

@article {pmid42278475,
year = {2026},
author = {Ermakov, VS and Falah, K and Nigam, SK},
title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278475},
issn = {1422-0067},
support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; },
abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.},
}

Animals
*Organic Anion Transport Protein 1/metabolism/genetics
Signal Transduction
Mice
*Kidney/metabolism/microbiology
*Fatty Acids, Volatile/metabolism
Mice, Knockout
*Gastrointestinal Microbiome
Humans

@article {pmid42278495,
year = {2026},
author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E},
title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278495},
issn = {1422-0067},
support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; },
mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; },
abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.},
}

Humans
*gamma-Aminobutyric Acid/metabolism/biosynthesis
*Brain/metabolism/physiology
Animals
*Probiotics
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism
*Brain-Gut Axis

@article {pmid42278559,
year = {2026},
author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH},
title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278559},
issn = {1422-0067},
support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; },
mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; },
abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.},
}

Animals
*Titanium/toxicity/chemistry
*Zebrafish/microbiology
*Dysbiosis/microbiology/chemically induced
*Gills/microbiology/drug effects
*Bacterial Translocation/drug effects
*Gastrointestinal Microbiome/drug effects
*Nanoparticles/toxicity
RNA, Ribosomal, 16S/genetics
*Metal Nanoparticles/toxicity/chemistry

@article {pmid41748019,
year = {2026},
author = {Piccinno, G and Asnicar, F},
title = {Advanced computational analysis in metagenomic studies to support precision medicine.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {32},
number = {7},
pages = {1075-1080},
doi = {10.1016/j.cmi.2026.02.018},
pmid = {41748019},
issn = {1469-0691},
mesh = {Humans ; *Precision Medicine/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Microbiota/genetics ; },
abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a nondiseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.

OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.

SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.

CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multicohort data analysis, integration, and validation methods.

IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.},
}

Humans
*Precision Medicine/methods
*Metagenomics/methods
*Computational Biology/methods
*Microbiota/genetics

@article {pmid41850677,
year = {2026},
author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J},
title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {20},
number = {7},
pages = {101770},
pmid = {41850677},
issn = {2352-345X},
mesh = {Animals ; *Neutrophils/metabolism/immunology/drug effects ; *Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism ; *Propionates/metabolism/pharmacology ; Mice ; Mice, Knockout ; *Gastrointestinal Microbiome/immunology ; Transforming Growth Factor beta1/metabolism ; *Liver/pathology/immunology/metabolism ; Fecal Microbiota Transplantation ; Copper-Transporting ATPases/genetics ; Disease Models, Animal ; Male ; Humans ; Hydroxamic Acids ; },
abstract = {BACKGROUND & AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.

METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-β1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.

RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-β1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-β1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-β1.

CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.},
}

Animals
*Neutrophils/metabolism/immunology/drug effects
*Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism
*Propionates/metabolism/pharmacology
Mice
Mice, Knockout
*Gastrointestinal Microbiome/immunology
Transforming Growth Factor beta1/metabolism
*Liver/pathology/immunology/metabolism
Fecal Microbiota Transplantation
Copper-Transporting ATPases/genetics
Disease Models, Animal
Male
Humans
Hydroxamic Acids

@article {pmid41951175,
year = {2026},
author = {Rana, N and Tiewsoh, K and Ray, P and Angrup, A},
title = {Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease.},
journal = {Indian journal of medical microbiology},
volume = {61},
number = {},
pages = {101110},
doi = {10.1016/j.ijmmb.2026.101110},
pmid = {41951175},
issn = {1998-3646},
mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Workflow ; Phylogeny ; Computational Biology/methods ; Bacteria/classification/genetics ; Software ; },
abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.

METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.

RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.

CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.},
}

Humans
*Renal Insufficiency, Chronic/microbiology
*Metagenomics/methods
*Microbiota/genetics
Workflow
Phylogeny
Computational Biology/methods
Bacteria/classification/genetics
Software

@article {pmid41966472,
year = {2026},
author = {Merkhan, K and Chaudhry, AS},
title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.},
journal = {Anaerobe},
volume = {98},
number = {},
pages = {103046},
doi = {10.1016/j.anaerobe.2026.103046},
pmid = {41966472},
issn = {1095-8274},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Methane/metabolism/biosynthesis ; Fermentation ; *Animal Feed/analysis ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; Archaea/metabolism ; Bacteria/classification/genetics/metabolism ; *Food Additives ; },
abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.

METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72 h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20 g kg[-1] DM) for each PFA.

RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20 g kg[-1] DM, followed by GBL with a 28.5% reduction at 10 g kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.

CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.},
}

Animals
*Rumen/microbiology/metabolism
Cattle
*Methane/metabolism/biosynthesis
Fermentation
*Animal Feed/analysis
*Microbiota/drug effects
Fatty Acids, Volatile/metabolism
Archaea/metabolism
Bacteria/classification/genetics/metabolism
*Food Additives

@article {pmid41974712,
year = {2026},
author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y},
title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41974712},
issn = {2041-1723},
support = {R21 AI180737/AI/NIAID NIH HHS/United States ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; *Lupus Erythematosus, Systemic/microbiology/immunology/therapy ; Multiomics ; Male ; Mice ; *Faecalibacterium prausnitzii/physiology ; Disease Models, Animal ; Th17 Cells/immunology ; *Dysbiosis/microbiology/therapy/immunology ; Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Feces/microbiology ; *Probiotics/administration & dosage ; T-Lymphocytes, Regulatory/immunology ; Mice, Inbred C57BL ; Metagenome ; Metabolomics ; },
abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.},
}

Animals
*Lupus Erythematosus, Systemic/microbiology/immunology/therapy
Multiomics
Male
Mice
*Faecalibacterium prausnitzii/physiology
Disease Models, Animal
Th17 Cells/immunology
*Dysbiosis/microbiology/therapy/immunology
Humans
*Gastrointestinal Microbiome/immunology/genetics
Feces/microbiology
*Probiotics/administration & dosage
T-Lymphocytes, Regulatory/immunology
Mice, Inbred C57BL
Metagenome
Metabolomics

@article {pmid41975031,
year = {2026},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41975031},
issn = {2399-3642},
support = {DairyBio//Dairy Australia/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Methane/metabolism ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Australia ; },
abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.},
}

Animals
*Rumen/microbiology
Cattle/microbiology
*Methane/metabolism
Metagenome
*Gastrointestinal Microbiome
*Microbiota
Australia

@article {pmid41975041,
year = {2026},
author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , },
title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.},
journal = {British journal of cancer},
volume = {135},
number = {1},
pages = {139-151},
pmid = {41975041},
issn = {1532-1827},
support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; },
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy/methods ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).

METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.

RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.

CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.

PROSPERO: CRD42023433704.},
}

Humans
*Rectal Neoplasms/microbiology/therapy
*Neoadjuvant Therapy/methods
*Gastrointestinal Microbiome
*Biomarkers, Tumor
Treatment Outcome

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
mesh = {Animals ; *Ticks/microbiology ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenome ; Sheep/microbiology ; Soil Microbiology ; Marmota/microbiology ; *Livestock/microbiology ; *Animals, Wild/microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Caves/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

Animals
*Ticks/microbiology
Gene Transfer, Horizontal
Metagenomics/methods
*Bacteria/genetics/classification/drug effects/isolation & purification
Metagenome
Sheep/microbiology
Soil Microbiology
Marmota/microbiology
*Livestock/microbiology
*Animals, Wild/microbiology
Microbiota
*Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial
Caves/microbiology
Genes, Bacterial
Anti-Bacterial Agents/pharmacology

@article {pmid41986664,
year = {2026},
author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J},
title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41986664},
issn = {2399-3642},
mesh = {*Soil Microbiology ; *Microbiota/genetics ; Arctic Regions ; *Metagenomics ; *Metagenome ; Russia ; *Bacteria/genetics ; *Genes, Microbial ; },
abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.},
}

*Soil Microbiology
*Microbiota/genetics
Arctic Regions
*Metagenomics
*Metagenome
Russia
*Bacteria/genetics
*Genes, Microbial

@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; China ; Animals ; Fermentation ; Metagenome ; Food Microbiology ; Polymorphism, Single Nucleotide ; Lactobacillus helveticus/genetics ; Phylogeny ; Metagenomics ; Biodiversity ; beta-Galactosidase/metabolism ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}

*Cheese/microbiology
*Microbiota/genetics
China
Animals
Fermentation
Metagenome
Food Microbiology
Polymorphism, Single Nucleotide
Lactobacillus helveticus/genetics
Phylogeny
Metagenomics
Biodiversity
beta-Galactosidase/metabolism

@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {17},
number = {6},
pages = {e0286825},
pmid = {42041249},
issn = {2150-7511},
support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; R01AI153332,R21AI186346//National Institute of Allergy and Infectious Diseases/ ; F32AI186285//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Female ; *Streptococcus agalactiae/genetics/growth & development/physiology ; *Vagina/microbiology ; Humans ; *Streptococcal Infections/microbiology ; Pregnancy ; Epithelial Cells/microbiology ; Animals ; Bacterial Adhesion ; Microbiota ; Akkermansia ; Mice ; },
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}

Female
*Streptococcus agalactiae/genetics/growth & development/physiology
*Vagina/microbiology
Humans
*Streptococcal Infections/microbiology
Pregnancy
Epithelial Cells/microbiology
Animals
Bacterial Adhesion
Microbiota
Akkermansia
Mice

@article {pmid42057198,
year = {2026},
author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J},
title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42057198},
issn = {1756-994X},
support = {2021-01637//Vetenskapsrådet/ ; 967569//Västerbotten Läns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; 09150162410022/ZONMW_/ZonMw/Netherlands ; },
mesh = {Humans ; *COVID-19/epidemiology/microbiology ; *Life Style ; Infant ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; Pandemics ; Feces/microbiology ; Metagenome ; Male ; Female ; Longitudinal Studies ; Hygiene ; },
abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.

METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.

RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.

CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.},
}

Humans
*COVID-19/epidemiology/microbiology
*Life Style
Infant
SARS-CoV-2
*Gastrointestinal Microbiome
Pandemics
Feces/microbiology
Metagenome
Male
Female
Longitudinal Studies
Hygiene

@article {pmid42103932,
year = {2026},
author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B},
title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.},
journal = {EMBO molecular medicine},
volume = {18},
number = {6},
pages = {2404-2435},
pmid = {42103932},
issn = {1757-4684},
support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
mesh = {Animals ; *Oocytes/physiology/drug effects/metabolism/cytology ; Female ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome ; Mice ; Fecal Microbiota Transplantation ; Aging ; Metabolome ; Fertility ; },
abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.},
}

Animals
*Oocytes/physiology/drug effects/metabolism/cytology
Female
*Glutamic Acid/metabolism
*Gastrointestinal Microbiome
Mice
Fecal Microbiota Transplantation
Aging
Metabolome
Fertility

@article {pmid42119030,
year = {2026},
author = {Yu, J and Tang, SN and Lee, PKH},
title = {Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag120},
pmid = {42119030},
issn = {1751-7370},
support = {//TAL Apparel Limited/ ; 9231297//City University of Hong Kong/ ; },
mesh = {*Bacteria/virology/genetics/classification ; *Wastewater/microbiology/virology ; *Virome ; Sewage/virology/microbiology ; Metagenomics ; Bioreactors/virology/microbiology ; Water Purification ; *Microbiota ; *Host Microbial Interactions ; Ecosystem ; },
abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1046 and 1386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.},
}

*Bacteria/virology/genetics/classification
*Wastewater/microbiology/virology
*Virome
Sewage/virology/microbiology
Metagenomics
Bioreactors/virology/microbiology
Water Purification
*Microbiota
*Host Microbial Interactions
Ecosystem

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary niches drive microbial community assembly, network reorganization, and symbiont evolution in freshwater fish gut microbiomes.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42139081},
issn = {1751-7370},
support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; },
mesh = {Animals ; *Symbiosis ; Fresh Water ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; China ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

Animals
*Symbiosis
Fresh Water
*Fishes/microbiology
*Gastrointestinal Microbiome
Metagenomics
China
*Diet
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Sequence Analysis, DNA

@article {pmid42172982,
year = {2026},
author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C},
title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {157},
number = {},
pages = {158288},
doi = {10.1016/j.phymed.2026.158288},
pmid = {42172982},
issn = {1618-095X},
mesh = {Animals ; Homeostasis/drug effects ; Male ; *Zonula Occludens-1 Protein/metabolism ; *Bile Acids and Salts/metabolism ; Liver/drug effects/metabolism ; Rats ; Rats, Sprague-Dawley ; *Quinazolines/pharmacology ; *Cholestasis/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Liver Diseases/drug therapy/metabolism ; },
abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.

OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.

METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and α-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.

RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.

CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.},
}

Animals
Homeostasis/drug effects
Male
*Zonula Occludens-1 Protein/metabolism
*Bile Acids and Salts/metabolism
Liver/drug effects/metabolism
Rats
Rats, Sprague-Dawley
*Quinazolines/pharmacology
*Cholestasis/drug therapy/metabolism
Gastrointestinal Microbiome/drug effects
Intestines/drug effects
Fecal Microbiota Transplantation
Disease Models, Animal
*Liver Diseases/drug therapy/metabolism

@article {pmid42176010,
year = {2026},
author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E},
title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42176010},
issn = {1432-184X},
mesh = {Animals ; *Isopoda/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; *Hepatopancreas/microbiology ; Metagenome ; Metagenomics ; Lignin/metabolism ; Phylogeny ; Italy ; },
abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.},
}

Animals
*Isopoda/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
*Hepatopancreas/microbiology
Metagenome
Metagenomics
Lignin/metabolism
Phylogeny
Italy

@article {pmid42176589,
year = {2026},
author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q},
title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128552},
doi = {10.1016/j.micres.2026.128552},
pmid = {42176589},
issn = {1618-0623},
mesh = {*Phosphorus/metabolism ; Soil Microbiology ; *Trichoderma/physiology/metabolism ; Rhizosphere ; *Pseudomonas/metabolism/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pyrus/microbiology/growth & development/metabolism ; Biomass ; Microbiota ; Metagenome ; Plant Roots/microbiology ; },
abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.},
}

*Phosphorus/metabolism
Soil Microbiology
*Trichoderma/physiology/metabolism
Rhizosphere
*Pseudomonas/metabolism/genetics
*Soil/chemistry
RNA, Ribosomal, 16S/genetics
*Pyrus/microbiology/growth & development/metabolism
Biomass
Microbiota
Metagenome
Plant Roots/microbiology

@article {pmid42217591,
year = {2026},
author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H},
title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.},
journal = {Pharmacological research},
volume = {229},
number = {},
pages = {108273},
doi = {10.1016/j.phrs.2026.108273},
pmid = {42217591},
issn = {1096-1186},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy ; Animals ; Metabolomics ; Precision Medicine ; },
abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.},
}

Humans
*Gastrointestinal Microbiome
*Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy
Animals
Metabolomics
Precision Medicine

@article {pmid42241861,
year = {2026},
author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L},
title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130128},
doi = {10.1016/j.jenvman.2026.130128},
pmid = {42241861},
issn = {1095-8630},
mesh = {Animals ; *Aquaculture ; *Nitrogen/metabolism ; Anti-Bacterial Agents ; *Probiotics ; Metagenomics ; China ; Microbiota ; Penaeidae ; },
abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.},
}

Animals
*Aquaculture
*Nitrogen/metabolism
Anti-Bacterial Agents
*Probiotics
Metagenomics
China
Microbiota
Penaeidae

@article {pmid42242027,
year = {2026},
author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M},
title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128569},
doi = {10.1016/j.micres.2026.128569},
pmid = {42242027},
issn = {1618-0623},
mesh = {Animals ; *Bifidobacterium longum/physiology ; *Metabolome ; Multiomics ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Mice ; Disease Models, Animal ; Liver/metabolism/pathology ; *Fatty Liver/metabolism/microbiology ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Male ; Metagenomics ; Intestinal Barrier Function ; Metabolomics ; *Metabolic Diseases ; },
abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.},
}

Animals
*Bifidobacterium longum/physiology
*Metabolome
Multiomics
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Mice
Disease Models, Animal
Liver/metabolism/pathology
*Fatty Liver/metabolism/microbiology
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
Male
Metagenomics
Intestinal Barrier Function
Metabolomics
*Metabolic Diseases

@article {pmid42250135,
year = {2026},
author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M},
title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42250135},
issn = {1573-0972},
mesh = {*Agriculture/methods ; Soil Microbiology ; Climate Change ; Crops, Agricultural/microbiology/growth & development ; Microbiota ; Stress, Physiological ; Ecosystem ; Biotechnology ; Mycorrhizae ; },
abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.},
}

*Agriculture/methods
Soil Microbiology
Climate Change
Crops, Agricultural/microbiology/growth & development
Microbiota
Stress, Physiological
Ecosystem
Biotechnology
Mycorrhizae

@article {pmid42252802,
year = {2026},
author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M},
title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {3},
pages = {e70324},
pmid = {42252802},
issn = {2190-6009},
support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; },
mesh = {Humans ; *Cachexia/etiology ; *Bacteriophages/genetics ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; *Neoplasms/complications ; Metagenomics/methods ; Metagenome ; Feces/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).},
}

Humans
*Cachexia/etiology
*Bacteriophages/genetics
Male
Female
*Gastrointestinal Microbiome
Aged
*Neoplasms/complications
Metagenomics/methods
Metagenome
Feces/microbiology
Middle Aged

@article {pmid42256221,
year = {2026},
author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V},
title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826972},
pmid = {42256221},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/therapy/microbiology ; *Inflammatory Bowel Diseases/therapy/microbiology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Animals ; Probiotics/therapeutic use ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.},
}

Humans
*Dysbiosis/therapy/microbiology
*Inflammatory Bowel Diseases/therapy/microbiology
*Precision Medicine/methods
*Gastrointestinal Microbiome
Intestinal Barrier Function
Animals
Probiotics/therapeutic use

@article {pmid42267567,
year = {2026},
author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL},
title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.},
journal = {Zoological research},
volume = {47},
number = {3},
pages = {827-842},
doi = {10.24272/j.issn.2095-8137.2025.141},
pmid = {42267567},
issn = {2095-8137},
mesh = {Animals ; *beta-Thalassemia/genetics/complications/veterinary/microbiology ; *Macaca fascicularis ; *Gastrointestinal Microbiome/physiology ; Mutation ; *Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics ; *beta-Globins/genetics/metabolism ; Male ; },
abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.},
}

Animals
*beta-Thalassemia/genetics/complications/veterinary/microbiology
*Macaca fascicularis
*Gastrointestinal Microbiome/physiology
Mutation
*Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics
*beta-Globins/genetics/metabolism
Male

@article {pmid42267859,
year = {2026},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70307},
pmid = {42267859},
issn = {2045-8827},
support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; },
mesh = {*Rhizosphere ; *Metagenomics ; Soil Microbiology ; *Allium/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fertilizers/analysis ; Soil/chemistry ; },
abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.},
}

*Rhizosphere
*Metagenomics
Soil Microbiology
*Allium/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fertilizers/analysis
Soil/chemistry

@article {pmid42268876,
year = {2026},
author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR},
title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351562},
pmid = {42268876},
issn = {1932-6203},
mesh = {Humans ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/immunology ; Aged ; Healthy Volunteers ; Metagenomics ; Case-Control Studies ; Bacteria/genetics/isolation & purification/classification ; COVID-19 ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

METHODS: BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).

RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p < 0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p = 0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q < 0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.

CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.},
}

Humans
*Immunocompromised Host
*Bronchoalveolar Lavage Fluid/microbiology
Male
*Microbiota/genetics
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/immunology
Aged
Healthy Volunteers
Metagenomics
Case-Control Studies
Bacteria/genetics/isolation & purification/classification
COVID-19
SARS-CoV-2

@article {pmid42269618,
year = {2026},
author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M},
title = {Variations in the latitudinal diversity gradients of the ocean microbiome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.016},
pmid = {42269618},
issn = {1934-6069},
abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.},
}

@article {pmid42269619,
year = {2026},
author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y},
title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.009},
pmid = {42269619},
issn = {1934-6069},
abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.},
}

@article {pmid42270094,
year = {2026},
author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B},
title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261460118},
pmid = {42270094},
issn = {1526-2359},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation & purification/genetics ; Aged ; Fungi/isolation & purification ; },
abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology/pathology
*Microbiota
*Lung Neoplasms/microbiology/pathology
Bronchoalveolar Lavage Fluid/microbiology
Female
Case-Control Studies
Male
Sputum/microbiology
Prospective Studies
Middle Aged
*Respiratory System/microbiology
Bacteria/isolation & purification/genetics
Aged
Fungi/isolation & purification

@article {pmid42270219,
year = {2026},
author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y},
title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119489},
doi = {10.1016/j.foodres.2026.119489},
pmid = {42270219},
issn = {1873-7145},
mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; },
abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.},
}

China
Fermentation
*Hot Temperature
*Microbiota
*Taste
*Food Microbiology
Bacteria/metabolism/classification/genetics
Rivers
Flavoring Agents
*Fermented Foods/microbiology

@article {pmid42270261,
year = {2026},
author = {Vandana, and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP},
title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119548},
doi = {10.1016/j.foodres.2026.119548},
pmid = {42270261},
issn = {1873-7145},
mesh = {Animals ; *Polyphenols/pharmacology ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Fruit/chemistry ; *Cognitive Dysfunction/chemically induced/prevention & control/drug therapy ; *Arsenic/toxicity ; Male ; *Rubus/chemistry ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; Disease Models, Animal ; },
abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.},
}

Animals
*Polyphenols/pharmacology
*Plant Extracts/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice
*Fruit/chemistry
*Cognitive Dysfunction/chemically induced/prevention & control/drug therapy
*Arsenic/toxicity
Male
*Rubus/chemistry
Oxidative Stress/drug effects
Antioxidants/pharmacology
Disease Models, Animal

@article {pmid42271572,
year = {2026},
author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E},
title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {6},
pages = {},
pmid = {42271572},
issn = {1574-6941},
support = {//CNRS/ ; ANR-24-CE01-6539-01//French National Research Agency/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Caves/microbiology/chemistry ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; South Africa ; *Geologic Sediments/microbiology ; Metagenome ; Oxidation-Reduction ; },
abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.},
}

*Groundwater/microbiology/chemistry
*Caves/microbiology/chemistry
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
South Africa
*Geologic Sediments/microbiology
Metagenome
Oxidation-Reduction

@article {pmid42272754,
year = {2026},
author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C},
title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779298},
pmid = {42272754},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Metabolomics ; *Constipation/microbiology/immunology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; *Rhinitis, Allergic/microbiology/immunology/metabolism/complications ; Child ; Female ; Feces/microbiology ; Male ; Amino Acids/metabolism ; Multiomics ; Bacteria/classification/genetics ; Metabolome ; },
abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.

METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.

RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P = 0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and γ-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC = 0.946).

CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.},
}

Humans
*Metagenomics/methods
*Metabolomics
*Constipation/microbiology/immunology/metabolism/complications
*Gastrointestinal Microbiome/genetics
*Rhinitis, Allergic/microbiology/immunology/metabolism/complications
Child
Female
Feces/microbiology
Male
Amino Acids/metabolism
Multiomics
Bacteria/classification/genetics
Metabolome

@article {pmid42276515,
year = {2026},
author = {Hassanien, A and Saadaoui, I and Sayadi, S},
title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2026.06.006},
pmid = {42276515},
issn = {1638-6183},
abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.},
}

@article {pmid40903035,
year = {2026},
author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X},
title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.},
journal = {Gut},
volume = {75},
number = {7},
pages = {1322-1337},
doi = {10.1136/gutjnl-2024-334699},
pmid = {40903035},
issn = {1468-3288},
mesh = {Animals ; *Irinotecan/adverse effects/toxicity ; Humans ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology ; *Tryptophan/metabolism ; *Diarrhea/chemically induced/microbiology ; Female ; Indoleacetic Acids/metabolism ; *Bacteroides/metabolism ; Male ; Intestinal Mucosa/drug effects/microbiology ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.

OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.

DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.

RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.

CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.},
}

Animals
*Irinotecan/adverse effects/toxicity
Humans
Mice
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/drug therapy/microbiology
*Tryptophan/metabolism
*Diarrhea/chemically induced/microbiology
Female
Indoleacetic Acids/metabolism
*Bacteroides/metabolism
Male
Intestinal Mucosa/drug effects/microbiology
Mice, Inbred C57BL

@article {pmid41700755,
year = {2026},
author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {23},
pages = {e22628},
pmid = {41700755},
issn = {2198-3844},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Plant Diseases/microbiology/genetics ; Rhizosphere ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; Forecasting ; },
abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.},
}

*Soil Microbiology
*Plant Roots/microbiology
*Plant Diseases/microbiology/genetics
Rhizosphere
Machine Learning
Metagenome/genetics
*Microbiota/genetics
Forecasting

@article {pmid41713061,
year = {2026},
author = {Cokro, A and Albert Ng, TC and Hill, ED and Lee, C and Chandra Segeran, US and Arumugam, K and Williams, RBH and Wuertz, S},
title = {Microbial community biomarkers can forecast methane production in full-scale anaerobic digesters.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128828},
doi = {10.1016/j.jenvman.2026.128828},
pmid = {41713061},
issn = {1095-8630},
mesh = {*Methane/biosynthesis ; *Bioreactors/microbiology ; Anaerobiosis ; Sewage/microbiology ; *Microbiota ; Biomarkers ; Wastewater/microbiology ; Singapore ; Machine Learning ; },
abstract = {Methane production from wastewater sludge via anaerobic digestion is a complex process and a disturbance in any one of the microbial stages can lead to eventual failure. Hence, it is desirable to detect disturbances as soon as possible. Although machine learning has been used to predict methane production from a variety of different substrates, there are no studies using metagenomic or -transcriptomic microbial community data as predictor variables. We used random forest analysis on a combination of physicochemical and microbial predictors to forecast methane production from three full-scale sludge digesters representing replicates of one another in a wastewater treatment plant in Singapore. Digesters were sampled for 25 weeks, and 42 physicochemical variables were measured along with shotgun metagenome and total RNA transcriptome sequencing. Models built using samples from a single digester yielded reactor-specific predictors, largely due to the limited sample size per reactor and the influence of rarer taxa. When data from the three digesters were combined, the best predictors included both substrate-related physicochemical parameters, such as chemical oxygen demand, and microbial taxa. Simulation using learning curves indicated that 150 to 200 samples instead of the 75 used would have yielded the most accurate methane prediction. The selection of many unidentified operational taxonomic units as microbial predictors suggests the existence of important yet unknown microorganisms in anaerobic digestion. The prediction model supports onsite digester surveillance by identifying digester-specific predictors through sufficient sampling, after which only those predictors need to be measured for subsequent monitoring.},
}

*Methane/biosynthesis
*Bioreactors/microbiology
Anaerobiosis
Sewage/microbiology
*Microbiota
Biomarkers
Wastewater/microbiology
Singapore
Machine Learning

@article {pmid41722567,
year = {2026},
author = {Thurimella, K and Wu, E and Li, C and Graham, DB and Owens, RM and Plichta, DR and Sokol, CL and Xavier, RJ and Bacallado, S},
title = {Identifying microbial protease allergens through protein language model-guided homology.},
journal = {Cell systems},
volume = {17},
number = {3},
pages = {101510},
pmid = {41722567},
issn = {2405-4720},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI151163/AI/NIAID NIH HHS/United States ; },
mesh = {*Allergens/immunology ; Humans ; Animals ; *Serine Proteases/immunology/metabolism ; Metagenomics/methods ; Hypersensitivity/immunology ; Microbiota ; },
abstract = {Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic SPs in metagenomic data. First, we develop a model to identify the catalytic serine residue in serine hydrolases, demonstrating how pLMs capture structural information. Next, we create a deep learning framework to detect candidate SP allergens across gene catalogs, using the conserved catalytic triad to identify homologs in gut and oral sites despite low sequence identity. Our model predicts a putative SP allergen resembling V8 protease, a known trigger for protease-activated receptor 1. It also identifies a cysteine protease similar to Der f 1 from dust mites. Immunization with these proteases induced allergic responses, validating their allergenic potential experimentally. This approach uncovers candidate allergens beyond traditional methods, offering new targets for allergy research. A record of this paper's transparent peer review process is included in the supplemental information.},
}

*Allergens/immunology
Humans
Animals
*Serine Proteases/immunology/metabolism
Metagenomics/methods
Hypersensitivity/immunology
Microbiota

@article {pmid41762314,
year = {2026},
author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN},
title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {5},
pages = {},
pmid = {41762314},
issn = {1573-2983},
support = {202760-2-000//RUDN University/ ; },
mesh = {Biodegradation, Environmental ; *Metagenomics ; *Hydrocarbons/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics ; Petroleum/metabolism ; Microbial Consortia ; Aerobiosis ; Polycyclic Aromatic Hydrocarbons/metabolism ; },
abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.},
}

Biodegradation, Environmental
*Metagenomics
*Hydrocarbons/metabolism
Anaerobiosis
*Bacteria/metabolism/genetics
Petroleum/metabolism
Microbial Consortia
Aerobiosis
Polycyclic Aromatic Hydrocarbons/metabolism

@article {pmid41878990,
year = {2026},
author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B},
title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {32},
pages = {e17444},
pmid = {41878990},
issn = {2198-3844},
support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; },
mesh = {Animals ; China/epidemiology ; *Herbivory ; Humans ; *Animals, Domestic/virology ; *Virome/genetics ; *Viruses/genetics/classification ; },
abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.},
}

Animals
China/epidemiology
*Herbivory
Humans
*Animals, Domestic/virology
*Virome/genetics
*Viruses/genetics/classification

@article {pmid42139982,
year = {2026},
author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R},
title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128553},
doi = {10.1016/j.micres.2026.128553},
pmid = {42139982},
issn = {1618-0623},
mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; *Water Microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; Eutrophication ; China ; Biodiversity ; },
abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.},
}

*Lakes/microbiology
*Metagenomics/methods
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Ecosystem
Metagenome
Phylogeny
*Water Microbiology
Carbon/metabolism
Nitrogen/metabolism
Eutrophication
China
Biodiversity

@article {pmid42161089,
year = {2026},
author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S},
title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.},
journal = {Placenta},
volume = {181},
number = {},
pages = {168-174},
doi = {10.1016/j.placenta.2026.05.010},
pmid = {42161089},
issn = {1532-3102},
mesh = {Female ; Humans ; Pregnancy ; *Placenta/virology ; *DNA, Viral/analysis ; *RNA, Viral/analysis ; Pre-Eclampsia/virology ; Adult ; *Virome ; Cesarean Section ; },
abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.},
}

Female
Humans
Pregnancy
*Placenta/virology
*DNA, Viral/analysis
*RNA, Viral/analysis
Pre-Eclampsia/virology
Adult
*Virome
Cesarean Section

@article {pmid42161263,
year = {2026},
author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {Cell host & microbe},
volume = {34},
number = {6},
pages = {1033-1049.e8},
pmid = {42161263},
issn = {1934-6069},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological/genetics ; DNA Methylation ; Fecal Microbiota Transplantation ; Infant ; *Bacteria/genetics/drug effects ; Metagenomics ; Probiotics ; Feces/microbiology ; Akkermansia ; },
abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.},
}

Humans
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Adaptation, Physiological/genetics
DNA Methylation
Fecal Microbiota Transplantation
Infant
*Bacteria/genetics/drug effects
Metagenomics
Probiotics
Feces/microbiology
Akkermansia

@article {pmid42176766,
year = {2026},
author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM},
title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.},
journal = {Neuroscience and biobehavioral reviews},
volume = {187},
number = {},
pages = {106775},
doi = {10.1016/j.neubiorev.2026.106775},
pmid = {42176766},
issn = {1873-7528},
mesh = {Humans ; *Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology ; *Oxidative Stress/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/immunology/metabolism ; *Neuroinflammatory Diseases/immunology/metabolism ; Probiotics ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.},
}

Humans
*Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology
*Oxidative Stress/physiology
Animals
*Gastrointestinal Microbiome/physiology
*Inflammation/immunology/metabolism
*Neuroinflammatory Diseases/immunology/metabolism
Probiotics

@article {pmid42184159,
year = {2026},
author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C},
title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {6},
pages = {},
pmid = {42184159},
issn = {1574-6941},
support = {//Scientific Committee on Antarctic Research/ ; 542264307//German Research Foundation/ ; 569718716//German Research Foundation/ ; },
mesh = {Antarctic Regions ; *Phytoplankton/metabolism/genetics/classification ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Diatoms ; Seawater/microbiology ; Polysaccharides/metabolism ; *Microbiota ; },
abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.},
}

Antarctic Regions
*Phytoplankton/metabolism/genetics/classification
Seasons
*Bacteria/metabolism/genetics/classification/isolation & purification
Diatoms
Seawater/microbiology
Polysaccharides/metabolism
*Microbiota

@article {pmid42202778,
year = {2026},
author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M},
title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.},
journal = {Cell host & microbe},
volume = {34},
number = {6},
pages = {1135-1150.e6},
doi = {10.1016/j.chom.2026.05.001},
pmid = {42202778},
issn = {1934-6069},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/surgery/metabolism ; Female ; *Feces/microbiology/chemistry ; *Adenoma/microbiology/surgery ; *Metabolome ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Aged ; Metagenomics ; Metagenome ; },
abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.},
}

Humans
*Colorectal Neoplasms/microbiology/surgery/metabolism
Female
*Feces/microbiology/chemistry
*Adenoma/microbiology/surgery
*Metabolome
*Gastrointestinal Microbiome
Case-Control Studies
Middle Aged
Aged
Metagenomics
Metagenome

@article {pmid42219044,
year = {2026},
author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A},
title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.},
journal = {Journal of microbiological methods},
volume = {246},
number = {},
pages = {107565},
doi = {10.1016/j.mimet.2026.107565},
pmid = {42219044},
issn = {1872-8359},
mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Pasteurellaceae/genetics/isolation & purification/classification ; Chickens/microbiology ; DNA Primers/genetics ; Cecum/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Poultry Diseases/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Pasteurellaceae Infections/veterinary/microbiology/diagnosis ; },
abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.},
}

Animals
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Pasteurellaceae/genetics/isolation & purification/classification
Chickens/microbiology
DNA Primers/genetics
Cecum/microbiology
DNA, Bacterial/genetics
Sequence Analysis, DNA
*Poultry Diseases/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Phylogeny
*Pasteurellaceae Infections/veterinary/microbiology/diagnosis

@article {pmid42249511,
year = {2026},
author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H},
title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42249511},
issn = {2049-2618},
support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Aging/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Adaptive Immunity ; *Vitamin B 6/blood/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology/microbiology ; Immunity, Mucosal ; Ileum/immunology/microbiology ; },
abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.

RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.

CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.},
}

Animals
*Aging/immunology
Mice
*Gastrointestinal Microbiome/immunology
*Adaptive Immunity
*Vitamin B 6/blood/metabolism
Mice, Inbred C57BL
Intestinal Mucosa/immunology/microbiology
Immunity, Mucosal
Ileum/immunology/microbiology

@article {pmid42249721,
year = {2026},
author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W},
title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {11},
pages = {e70422},
doi = {10.1111/mec.70422},
pmid = {42249721},
issn = {1365-294X},
support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; Temperature ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota/genetics ; Seasons ; *Ecosystem ; Metagenomics ; },
abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.},
}

*Soil Microbiology
Temperature
*Bacteria/genetics/classification
*Archaea/genetics/classification
*Microbiota/genetics
Seasons
*Ecosystem
Metagenomics

@article {pmid40762941,
year = {2026},
author = {Wei, R and Long, J and Xia, H and Sun, Y and Zhang, L and Li, X and Zhang, H and Wang, R and Gao, S and Chen, Y and Gu, Y and Wang, X and Wang, J},
title = {Galacto-oligosaccharides enrich galactosidase-encoded rather than all Lachnospiraceae bacteria to redress abnormal gut microbiota and lipid metabolism in pregnancy.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1858-1870},
pmid = {40762941},
issn = {1869-1889},
mesh = {Female ; Animals ; Pregnancy ; *Lipid Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology ; *Diabetes, Gestational/microbiology/metabolism ; Mice ; Liver/metabolism/drug effects ; Dietary Supplements ; Blood Glucose/metabolism ; Dysbiosis/microbiology ; },
abstract = {Among the various pregnancy complications, gestational diabetes mellitus (GDM) is one of the most prevalent and damaging adverse conditions. GDM is characterised by dysregulated gut microbiota and dysglycaemia. There is a keen search for active ingredients that can modify gut dysbiosis and glycaemic imbalances. In this study, the effects of dietary supplementation with high fibre and galacto-oligosaccharides (GOS) on GDM were evaluated. We found that GOS effectively alleviated blood glucose, hepatic inflammatory response, and lipid metabolism in high-fat-induced GDM mice. Furthermore, GOS redressed GDM-associated gut dysbiosis and altered glycerolipid metabolic pathways. GOS supplementation significantly downregulated the levels of fat synthesis genes and inflammatory factors in the liver and upregulated the expression of lipolytic catabolic genes (Cyp4a10). In dietary GOS supplementation, Lachnospiraceae bacteria strongly co-occurred with saturated lysophosphatidylcholine in the glycerolipid metabolic pathway. Metagenomic analyses illustrated that Lachnospiraceae bacteria-hosted α-galactosidase genes enriched upon GOS intake. GOS supplementation reduces lipopolysaccharide (LPS) entry into the systemic circulation by repairing intestinal mucosal damage, inhibits inflammatory cell production by reducing hepatic and intestinal Toll-like receptor-4 (TLR-4) expression and potentially ameliorates blood glucose dysregulation in GDM by modulating glycerophospholipid metabolism. These results revealed that dietary supplementation of GOS during pregnancy may be a promising intervention against GDM.},
}

Female
Animals
Pregnancy
*Lipid Metabolism/drug effects
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology
*Diabetes, Gestational/microbiology/metabolism
Mice
Liver/metabolism/drug effects
Dietary Supplements
Blood Glucose/metabolism
Dysbiosis/microbiology

@article {pmid41275986,
year = {2026},
author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , },
title = {Prebiotic Administration to Chronic Kidney Disease Patients Modifies Their Fecal Microbiome and Host Metabolism.},
journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation},
volume = {36},
number = {3},
pages = {419-429},
doi = {10.1053/j.jrn.2025.10.015},
pmid = {41275986},
issn = {1532-8503},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Feces/microbiology ; *Renal Insufficiency, Chronic/microbiology/metabolism/therapy ; Female ; Male ; Inulin/administration & dosage ; Pilot Projects ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Aged ; Oligosaccharides/administration & dosage ; Dysbiosis ; Amino Acids ; },
abstract = {OBJECTIVE(S): Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.

METHODS: We conducted a nonrandomized, open-label, three-phase pilot trial to investigate the effect of daily oral prebiotic, oligofructose-enriched inulin (p-inulin), on stool functional metagenome and changes in plasma, urine, and stool metabolites in 13 CKD patients. The study comprised a pretreatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).

RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In plasma, metabolic biosynthetic pathways for valine, leucine, and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and nonpolar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine, and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.

CONCLUSION(S): P-inulin administration to CKD patients resulted in a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.},
}

Humans
*Prebiotics/administration & dosage
*Feces/microbiology
*Renal Insufficiency, Chronic/microbiology/metabolism/therapy
Female
Male
Inulin/administration & dosage
Pilot Projects
Middle Aged
*Gastrointestinal Microbiome/drug effects
Aged
Oligosaccharides/administration & dosage
Dysbiosis
Amino Acids

@article {pmid41652998,
year = {2026},
author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I},
title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.},
journal = {Biological research for nursing},
volume = {28},
number = {3},
pages = {406-417},
doi = {10.1177/10998004261423546},
pmid = {41652998},
issn = {1552-4175},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Infant ; *Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use ; Pregnancy ; *Antidepressive Agents/adverse effects/therapeutic use ; Adult ; Infant, Newborn ; Feces/microbiology ; },
abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.},
}

Humans
Female
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Infant
*Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use
Pregnancy
*Antidepressive Agents/adverse effects/therapeutic use
Adult
Infant, Newborn
Feces/microbiology

@article {pmid41680419,
year = {2026},
author = {Pedrazzini, C and Funari, R and Cucini, C and Nardi, F and Grabenweger, G and Widmer, F and Enkerli, J},
title = {Population genomics identifies Italian and North American origins of Popillia japonica in Switzerland.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41680419},
issn = {2045-2322},
support = {No. 861852//European Union's Horizon 2020/ ; },
mesh = {Animals ; Switzerland ; *Coleoptera/genetics/classification ; Phylogeny ; North America ; Introduced Species ; Italy ; Genetics, Population ; *Metagenomics/methods ; Genomics ; },
abstract = {The Japanese beetle (Popillia japonica), native to Japan, is a major invasive species in North America and Europe. Its colonization of Europe began on the Azores (1970s), followed by Italy (2014) and southern Switzerland (2017). In 2023, the presence of the pest was reported in three areas of Switzerland: Kloten (Canton of Zürich, north-eastern Switzerland), Basel (Canton of Basel-Landschaft, northern Switzerland), and in eastern Canton of Valais (South Switzerland) near the Italian border. In 2024, P. japonica individuals were discovered in several other Swiss Cantons. To trace P. japonica spread and origins in Switzerland, we investigated 42 individuals from infested areas, comprising scattered findings across Switzerland. Phylogenetic and population structure analyses using whole-genome resequencing, including data of previously sequenced samples from Japan, North America, the Azores, Italy, and Southern Switzerland, revealed distinct P. japonica migration patterns. Populations in Basel, Valais, and central Switzerland likely originated from Ticino/Northern Italy via road or rail transport. Conversely, the population near Zürich Airport was identified as an independent introduction from North America, likely through unintentional air transport. These findings offer insights into P. japonica spread across Switzerland, highlighting the need for enhanced monitoring and identification of invasion pathways.},
}

Animals
Switzerland
*Coleoptera/genetics/classification
Phylogeny
North America
Introduced Species
Italy
Genetics, Population
*Metagenomics/methods
Genomics

@article {pmid41692940,
year = {2026},
author = {Le, B and Jia, L and Pang, T and Han, S and Duan, Y and Zhao, XM},
title = {A review of computational approaches for metagenomics by long-read sequencing.},
journal = {Science China. Life sciences},
volume = {69},
number = {6},
pages = {1825-1839},
pmid = {41692940},
issn = {1869-1889},
mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Humans ; },
abstract = {The metagenomic next-generation sequencing (mNGS), also known as short-read sequencing (SRS), is widely used to explore microbial composition and function. However, short reads, due to their difficulty in crossing repetitive regions, can lead to fragmented assemblies, hampering the comprehensive characterization of microbial genomes. In contrast, long-read sequencing (LRS) technologies, such as those from Pacific Biosciences (PacBio) and Oxford Nanopore, can span these complex repetitive regions and reconstruct continuous genomes, which enables high-resolution taxonomic classification and the precise recovery of essential genetic elements. This review provides a systematic overview of the computational approaches for long-read metagenomics, highlighting the progress in taxonomic profiling strategies, assembly and binning methods, and the detection of genetic elements. Furthermore, the review discusses the application of LRS in detecting structural variations (SVs), identifying methylation patterns, and characterizing strains. By combining advanced technologies and computational improvements, this review indicates the transformative potential of LRS in enhancing our understanding of microbial diversity, functions, and interactions within microbial communities.},
}

*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Computational Biology/methods
Microbiota/genetics
Sequence Analysis, DNA/methods
Humans

@article {pmid41698031,
year = {2026},
author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C},
title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {7},
pages = {5989-6001},
doi = {10.1021/acs.jafc.5c11900},
pmid = {41698031},
issn = {1520-5118},
mesh = {Drought Resistance ; *Triticum/microbiology/physiology/growth & development/drug effects/metabolism ; *Silicon/chemistry/pharmacology ; *Quantum Dots/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism ; Rhizosphere ; Seeds/growth & development/microbiology/physiology/drug effects ; Droughts ; Plant Roots/microbiology/growth & development/metabolism ; Water/metabolism ; Microbiota ; Germination ; },
abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.},
}

Drought Resistance
*Triticum/microbiology/physiology/growth & development/drug effects/metabolism
*Silicon/chemistry/pharmacology
*Quantum Dots/chemistry
Bacteria/classification/genetics/isolation & purification/metabolism
Rhizosphere
Seeds/growth & development/microbiology/physiology/drug effects
Droughts
Plant Roots/microbiology/growth & development/metabolism
Water/metabolism
Microbiota
Germination

@article {pmid41785649,
year = {2026},
author = {Dong, W and Ye, T and Zhang, Z and An, L and Peng, Y and Chen, Y and Zhang, Y and Ke, L and Chen, S and Zhao, S and Hu, Y},
title = {Quorum sensing-associated acid adaptation in bacterial communities during pit fermentation of sauce-flavor Baijiu.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111715},
doi = {10.1016/j.ijfoodmicro.2026.111715},
pmid = {41785649},
issn = {1879-3460},
mesh = {*Quorum Sensing ; Fermentation ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Adaptation, Physiological ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Lactic Acid/metabolism ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Sauce-flavor Baijiu is produced by multi-round solid-state fermentation under progressively increasing acidity, yet how bacterial communities adapt to this extreme acid stress and whether quorum sensing (QS)-associated features are involved remain unclear. Here, fermented grains from eight pit-fermentation rounds under both traditional and mechanized processes were analyzed by metagenomic sequencing and physicochemical profiling. The traditional process showed higher moisture, stronger and faster acidification, greater lactic acid accumulation, and more rapid depletion of reducing sugars and starch than the mechanized process. These conditions coincided with a sharper decline in bacterial α-diversity and convergence toward a community overwhelmingly dominated by Acetilactobacillus jinshanensis (>90%) in the traditional process, whereas the mechanized process maintained higher diversity and a multi-species core dominated by A. jinshanensis, Lactobacillus acetotolerans, Bacillus, and actinomycetes. Canonical correspondence analysis identified acidity (lactic acid) as a major environmental factor associated with these divergent trajectories. QS gene profiling revealed process-specific signatures, with the LuxS/AI-2-associated module being the most abundant QS-related feature and significantly enriched in the traditional process. Functional annotation uncovered coordinated enrichment of acid-adaptation genes (ATPF1A, clpP, ATPF1B, dnaK, and groEL) during mid-to-late stages under high acidity. Network analysis further highlighted tighter co-associations among A. jinshanensis, QS modules, and acid-adaptation genes, supporting a community-level QS-associated functional framework for ecological convergence. Collectively, this study links LuxS/AI-2-associated features to acid-adaptation capacity and A. jinshanensis dominance in high-acidity environment. These findings provide ecological insight into microbial resilience in high-acidity solid-state fermentations and offer QS-informed perspectives for future targeted validation in Baijiu production.},
}

*Quorum Sensing
Fermentation
*Bacteria/genetics/classification/metabolism/isolation & purification
Adaptation, Physiological
Food Microbiology
*Fermented Foods/microbiology/analysis
Lactic Acid/metabolism
Microbiota
Hydrogen-Ion Concentration

@article {pmid41951635,
year = {2026},
author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S},
title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41951635},
issn = {2052-4463},
mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Sus scrofa/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Archaea/genetics/classification ; Bacteria/genetics/classification ; },
abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.},
}

Animals
*Feces/microbiology
*Metagenome
*Sus scrofa/microbiology
*Gastrointestinal Microbiome/genetics
Swine/microbiology
Archaea/genetics/classification
Bacteria/genetics/classification

@article {pmid42032279,
year = {2026},
author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G},
title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1739-1753},
pmid = {42032279},
issn = {2058-5276},
support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics/classification ; *Metagenomics/methods ; Colorectal Neoplasms/microbiology ; Substrate Specificity ; Carbohydrate Metabolism ; Mucins/metabolism ; },
abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .},
}

Humans
Metagenome
*Gastrointestinal Microbiome/genetics
*Bacteria/enzymology/genetics/classification
*Metagenomics/methods
Colorectal Neoplasms/microbiology
Substrate Specificity
Carbohydrate Metabolism
Mucins/metabolism

@article {pmid42032281,
year = {2026},
author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J},
title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1626-1638},
pmid = {42032281},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; *Metagenomics/methods ; Algorithms ; Polymorphism, Single Nucleotide ; Streptococcus pneumoniae/genetics ; Plasmodium falciparum/genetics ; Feces/microbiology ; COVID-19/transmission ; Malaria, Falciparum/transmission ; Gastrointestinal Microbiome/genetics ; Metagenome ; Infant ; High-Throughput Nucleotide Sequencing ; },
abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.},
}

Humans
*Metagenomics/methods
Algorithms
Polymorphism, Single Nucleotide
Streptococcus pneumoniae/genetics
Plasmodium falciparum/genetics
Feces/microbiology
COVID-19/transmission
Malaria, Falciparum/transmission
Gastrointestinal Microbiome/genetics
Metagenome
Infant
High-Throughput Nucleotide Sequencing

@article {pmid42059625,
year = {2026},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {14},
number = {6},
pages = {e0362625},
pmid = {42059625},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; R01 DE03013, R01 DE022586, 2R01 DE016937/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Capnocytophaga/genetics/classification/isolation & purification/physiology ; *Mouth/microbiology ; Microbiota ; Phylogeny ; Dental Plaque/microbiology ; Genome, Bacterial ; Metagenomics ; Metagenome ; },
abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.

IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.},
}

Humans
*Capnocytophaga/genetics/classification/isolation & purification/physiology
*Mouth/microbiology
Microbiota
Phylogeny
Dental Plaque/microbiology
Genome, Bacterial
Metagenomics
Metagenome

@article {pmid42067625,
year = {2026},
author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K},
title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.},
journal = {Nature microbiology},
volume = {11},
number = {6},
pages = {1495-1510},
pmid = {42067625},
issn = {2058-5276},
support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Sepsis/microbiology/drug therapy/metabolism ; Humans ; Mice ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Child ; Enterococcus/metabolism ; *Deoxycholic Acid/metabolism/analogs & derivatives ; Intestinal Barrier Function ; Male ; Child, Preschool ; Female ; Metabolomics ; },
abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.},
}

Animals
*Sepsis/microbiology/drug therapy/metabolism
Humans
Mice
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
Disease Models, Animal
Child
Enterococcus/metabolism
*Deoxycholic Acid/metabolism/analogs & derivatives
Intestinal Barrier Function
Male
Child, Preschool
Female
Metabolomics

@article {pmid42093272,
year = {2026},
author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q},
title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.},
journal = {Cancer biology & medicine},
volume = {23},
number = {5},
pages = {737-754},
pmid = {42093272},
issn = {2095-3941},
support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; },
mesh = {Animals ; *CD8-Positive T-Lymphocytes/immunology/metabolism/drug effects ; Mice ; YAP-Signaling Proteins ; Humans ; *Bifidobacterium animalis/immunology ; *Melanoma, Experimental/immunology/pathology ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Cell Proliferation ; Disease Progression ; Cell Line, Tumor ; Gastrointestinal Microbiome ; *Transcription Factors/metabolism ; },
abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.

METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.

RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.

CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.},
}

Animals
*CD8-Positive T-Lymphocytes/immunology/metabolism/drug effects
Mice
YAP-Signaling Proteins
Humans
*Bifidobacterium animalis/immunology
*Melanoma, Experimental/immunology/pathology
*Probiotics/pharmacology
Mice, Inbred C57BL
Cell Proliferation
Disease Progression
Cell Line, Tumor
Gastrointestinal Microbiome
*Transcription Factors/metabolism