@article {pmid41672081,
year = {2026},
author = {Miller, KJ and Wolff, IM and Montes de Oca Valeriano, LA and Soto-Giron, MJ and Jangi, S and Schott, EM and Charbonneau, MR and Ballok, AE and Toledo, GV},
title = {Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial.},
journal = {Beneficial microbes},
volume = {17},
number = {5},
pages = {477-489},
doi = {10.1163/18762891-bja00109},
pmid = {41672081},
issn = {1876-2891},
mesh = {Humans ; *Synbiotics/administration & dosage/analysis ; Feces/microbiology ; Female ; Middle Aged ; Adult ; Young Adult ; Adolescent ; *Gastrointestinal Microbiome ; Metagenomics ; *Bacteria/isolation & purification/genetics/classification ; Microbial Viability ; },
abstract = {The viability and persistence of orally administered microbes in the human gut are essential to their biological function. We previously described the development of two synbiotic medical foods, SBD111 and SBD121, each comprising four food-derived microbial strains and prebiotic fibres for the dietary management of postmenopausal bone loss and rheumatoid arthritis, respectively. Here, we report a randomised, open-label clinical study examining gut persistence of SBD111 and SBD121 microbes by testing faecal samples from healthy adults following administration for seven days. Thirty-eight participants, aged 18-64 years with a body mass index (BMI) of 18.5-35 kg/m2, were randomised to receive one of the two synbiotic medical foods daily for one week, followed by a four-week monitoring period. Employing quantitative PCR (qPCR), shotgun metagenomics, and culture-based assays, we evaluated the presence and viability of the microbial strains comprising each synbiotic medical food during and after administration. SBD111 and SBD121 were well-tolerated with minimal adverse events reported. Strains were detected in over 80% of participants during the administration period, with strain abundance peaking in the first week. Persistence in the follow-up period varied by strain and detection method. The microbial strains were detected by qPCR and metagenomic sequencing for a median of seven days and three days during the follow-up period, respectively. However, Bacillus amyloliquefaciens was consistently detected for seven days by both methods. Culture-based assays confirmed the presence of viable strains from both synbiotic medical foods in stool samples up to one-week post-consumption. Faecal metagenome diversity and metabolic functional potential remained stable throughout the administration and follow-up periods. Collectively, these results establish that SBD111 and SBD121 deliver viable microbes that transiently persist in the gut, reinforcing their promise for safe and targeted dietary interventions and highlighting the value of multi-platform detection strategies for comprehensive microbial persistence assessment. This trial, funded by Sōlarea biō, is registered at ClinicalTrials.gov (NCT06614166).},
}

Humans
*Synbiotics/administration & dosage/analysis
Feces/microbiology
Female
Middle Aged
Adult
Young Adult
Adolescent
*Gastrointestinal Microbiome
Metagenomics
*Bacteria/isolation & purification/genetics/classification
Microbial Viability

@article {pmid42189388,
year = {2026},
author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G},
title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.},
journal = {Science China. Life sciences},
volume = {69},
number = {9},
pages = {3112-3126},
pmid = {42189388},
issn = {1869-1889},
mesh = {Male ; Animals ; *Testis/drug effects/metabolism ; *Carbon Quantum Dots/toxicity ; Mice ; *Fertility/drug effects ; *Gastrointestinal Microbiome/drug effects ; Blood-Testis Barrier/drug effects ; Testosterone ; *Infertility, Male/chemically induced ; Intestinal Barrier Function ; },
abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.},
}

Male
Animals
*Testis/drug effects/metabolism
*Carbon Quantum Dots/toxicity
Mice
*Fertility/drug effects
*Gastrointestinal Microbiome/drug effects
Blood-Testis Barrier/drug effects
Testosterone
*Infertility, Male/chemically induced
Intestinal Barrier Function

@article {pmid42437920,
year = {2026},
author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A},
title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.},
journal = {Cardiovascular diabetology},
volume = {25},
number = {1},
pages = {},
pmid = {42437920},
issn = {1475-2840},
mesh = {Humans ; Male ; Middle Aged ; *Prediabetic State/blood/physiopathology/diagnosis/therapy/microbiology ; Adult ; *Cardiorespiratory Fitness ; Multiomics ; *Proteomics/methods ; *High-Intensity Interval Training ; *Metabolomics/methods ; Obesity/blood/physiopathology ; Adaptation, Physiological ; Biomarkers/blood ; Oxygen Consumption ; Young Adult ; Time Factors ; Gastrointestinal Microbiome ; Treatment Outcome ; Feces/microbiology ; China ; Metagenomics/methods ; },
abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.},
}

Humans
Male
Middle Aged
*Prediabetic State/blood/physiopathology/diagnosis/therapy/microbiology
Adult
*Cardiorespiratory Fitness
Multiomics
*Proteomics/methods
*High-Intensity Interval Training
*Metabolomics/methods
Obesity/blood/physiopathology
Adaptation, Physiological
Biomarkers/blood
Oxygen Consumption
Young Adult
Time Factors
Gastrointestinal Microbiome
Treatment Outcome
Feces/microbiology
China
Metagenomics/methods

@article {pmid42505077,
year = {2026},
author = {Zhang, Q and Li, D and Liu, B and Zhang, Y and Li, M and Guo, R and Ni, Y and Chen, S and Ni, B and Qiu, L and Xing, G and Dong, H and Yan, Q and Li, S and Zou, X and Cao, B},
title = {A Comprehensive Microbial Gene Catalog of the Human Airway Microbiome Across Anatomical Sites and Geographic Regions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {56},
pages = {e76589},
pmid = {42505077},
issn = {2198-3844},
support = {BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; 82341113//National Natural Science Foundation of China/ ; 025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Respiratory System/microbiology ; Virulence Factors/genetics ; Antimicrobial Peptides/genetics ; Metagenomics/methods ; *Bacteria/genetics ; },
abstract = {The respiratory microbiota is a critical determinant of airway health, yet functional characterization remains challenging due to the lack of a high-resolution reference catalog. To address this gap and enable systematic investigation at both species and gene levels, we constructed the integrated Human Airway Microbiome Gene Catalog (iHAMGC) through high-throughput metagenomic analysis of 12,273 airway samples. This catalog comprises 24,185,985 non-redundant microbial genes and provides extensive taxonomic and functional annotations, with a particular focus on clinically relevant elements, including antibiotic resistance genes, virulence factors, and antimicrobial peptides. We further resolved the bacterial hosts of resistance genes and virulence factor genes, as well as taxa contributing to antimicrobial peptide activity. The iHAMGC captures site-specific microbial and functional variations across distinct airway niches and reveals regional differences in functional potential. By offering a comprehensive, publicly accessible reference for airway microbial genes, the iHAMGC serves as a foundational resource for advancing our understanding of the airway microbiota in respiratory health and disease.},
}

Humans
*Microbiota/genetics
*Respiratory System/microbiology
Virulence Factors/genetics
Antimicrobial Peptides/genetics
Metagenomics/methods
*Bacteria/genetics

@article {pmid42685687,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Chang, K and Li, S and Zhang, Y and Yu, H and Wang, C and Yao, X and Chen, S and Nie, X and Zhao, J and Lu, B and Li, Y and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {The human oral and airway viral genome catalog from metagenomes enables virome characterization informing respiratory health.},
journal = {Med (New York, N.Y.)},
volume = {7},
number = {10},
pages = {101269},
doi = {10.1016/j.medj.2026.101269},
pmid = {42685687},
issn = {2666-6340},
mesh = {Humans ; *Virome/genetics ; *Metagenome/genetics ; *Genome, Viral/genetics ; *Mouth/virology ; *Respiratory Tract Infections/virology ; Female ; *Respiratory System/virology ; Prospective Studies ; Male ; Aged ; Metagenomics ; },
abstract = {BACKGROUND: Viral communities of the upper aerodigestive tract represent an important component of the human microbial ecosystem but remain poorly characterized due to the limited availability of habitat-specific reference resources.

METHODS: We integrated 19,997 public and 2,673 newly sequenced oral and airway metagenomes to establish the Oral and Airway Viral Genome Catalogue (OAVGC). Viral genomes were reconstructed and characterized through taxonomic assignment, prokaryotic host prediction, functional annotation, and assessment of putative antibacterial activity. Our prospective longitudinal aging cohort, alongside 5 in-house datasets and publicly cohorts, were analyzed to investigate associations between airway virome profiles and respiratory health.

FINDINGS: The OAVGC comprised 141,459 high-quality viral genomes (completeness ≥90%) clustered into 68,708 viral operational taxonomic units (vOTUs). Approximately half of these viruses and families are previously undescribed, with independent cross-cohort detection and PCR assays providing additional support for their occurrence. Across multiple respiratory infection cohorts, the virome exhibited convergent diversity reductions and compositional signatures. In the prospective cohort, the baseline airway virome was correlated with host lung function and geriatric health scores. Virome-based machine learning classifiers demonstrated potential for predicting the future occurrence of upper respiratory tract infections up to 12 months in advance, outperforming bacteriome-based models in our prediction analyses.

CONCLUSIONS: The OAVGC provides an unprecedented genomic and functional resource for investigating the ecological and clinical associations of the oral-airway virome, revealing its potential impact on respiratory health and capacity to predict future infections.

FUNDING: National Natural Science Foundation of China (82341113) and National Key R&D Program of China (2022YFA1304303).},
}

Humans
*Virome/genetics
*Metagenome/genetics
*Genome, Viral/genetics
*Mouth/virology
*Respiratory Tract Infections/virology
Female
*Respiratory System/virology
Prospective Studies
Male
Aged
Metagenomics

@article {pmid42848247,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Tumor microenvironment and gut microbiome in immunotherapy resistance in gastric cancer: clinical questions, biological mechanisms, and evidence-based therapeutic perspectives.},
journal = {Medical oncology (Northwood, London, England)},
volume = {43},
number = {11},
pages = {},
pmid = {42848247},
issn = {1559-131X},
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology ; *Tumor Microenvironment/immunology ; *Drug Resistance, Neoplasm/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Immunotherapy/methods ; },
abstract = {Immune checkpoint inhibitors (ICIs) have improved systemic therapy for advanced gastric and gastroesophageal junction cancer, yet primary and acquired resistance remain common and are incompletely explained by established tumor biomarkers. This narrative review evaluates the connected roles of the tumor microenvironment (TME), host immunity, and the gut microbiome in shaping ICI resistance in gastric cancer. We performed a structured PubMed search through 28 August 2026 and prioritized gastric cancer-specific clinical and translational evidence, supplemented by systematic reviews, meta-analyses, and mechanistically relevant studies from other tumor types when necessary. Within the gastric cancer TME, cancer-associated fibroblasts, myeloid cells, regulatory T cells, extracellular matrix remodeling, hypoxia, angiogenesis, and T-cell exhaustion can promote immune exclusion or dysfunction. Microbial diversity, microbial metabolites, antibiotics, proton pump inhibitors, defined live biotherapeutics, fecal microbiota transplantation, and diet may influence systemic antitumor immunity, but most human evidence is retrospective, cross-sectional, or derived from non-gastric cancers. Clinically, antibiotic stewardship, reassessment of unnecessary acid suppression, and nutritional optimization are reasonable supportive measures, whereas routine probiotic supplementation, Clostridium butyricum MIYAIRI 588 for ICI sensitization, and fecal microbiota transplantation remain investigational in gastric cancer. Future studies should integrate longitudinal exposures, serial TME profiling, stool metagenomics, medication use, nutritional status, and clinical outcomes. The TME-gut microbiome axis is therefore a biologically plausible framework for biomarker-guided research, but current evidence does not justify empiric microbiome-directed anticancer therapy in gastric cancer.},
}

Humans
*Stomach Neoplasms/immunology/microbiology/drug therapy/therapy/pathology
*Tumor Microenvironment/immunology
*Drug Resistance, Neoplasm/immunology
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Immunotherapy/methods

@article {pmid42849679,
year = {2026},
author = {De Lise, F and Sacco, O and Shaikh-Ibrahim, A and Di Fenza, M and Strazzulli, A and Moracci, M and Terrapon, N and Curci, N and Cobucci-Ponzano, B},
title = {Seeding subfamilies in glycoside hydrolase family 116: New insights into the function and inhibitor sensitivity of subfamily 2.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {154792},
doi = {10.1016/j.ijbiomac.2026.154792},
pmid = {42849679},
issn = {1879-0003},
abstract = {Among glycoside hydrolase (GH) families and characterized enzymes reported in CAZy, GHs from Archaea remain largely underrepresented. Recent 'omics' studies have uncovered numerous uncharacterized GH sequences from extremophilic Archaea, providing unprecedented opportunities to study their diversity, structure, function, and properties. The GH family 116 (GH116) was originally built around a characterized archaeal member, revealing homologous sequences in Eukaryota and Bacteria. Although previous studies proposed or attempted GH116 subdivision into distinct subfamilies associated with different substrate specificity and inhibitor sensitivity, such a classification has never been formally established, mainly because few GH116 enzymes have been biochemically characterized. As a result, its functional landscape remains poorly understood. Here, we formally establish GH116 subfamilies, starting from the discovery of nine novel archaeal GH116 sequences identified from metagenomics samples collected from two mud/water pools in the extreme environment of Pisciarelli solfatara. These sequences were assigned to subfamilies 2 and 3, mainly hyperthermophilic archaeal enzymes. By combining phylogenetic analyses, structural modeling, and biochemical studies, we identified subfamily-specific structural domains that may serve as structural markers and suggest that these subfamilies represent functionally specialized groups. Focusing on subfamily 2, previously with only one characterized member, we biochemically characterized two novel enzymes. Our results expand GH116 functional diversity, reporting for the first time β-galactosidase activity within this family and showing β-xylosidase activity in subfamily 2, previously observed only in subfamily 3. We also examined active-site inhibition profiles and, through active-site mapping and mutational analysis, elucidated the molecular basis of inhibitor sensitivity in one enzyme of this subgroup.},
}

@article {pmid42850249,
year = {2026},
author = {Chen, S and Bahadur, A and Zhu, J and Liu, E and Gu, Y and Liang, H and Zhang, W and Li, S and Li, A and Wei, P and Liu, Q and Wu, T and Yang, P and Zou, Y and Han, M and Malard, LA},
title = {Hydrothermal regimes regulate microbiome patterns across vertical profile and their responses to alpine permafrost degradation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42850249},
issn = {2041-1723},
support = {U23A2062//National Natural Science Foundation of China (National Science Foundation of China)/ ; U24A20586//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Permafrost/microbiology ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification ; Soil Microbiology ; Tibet ; Metagenome ; Nitrogen/metabolism ; },
abstract = {Deciphering microbiomes across vertical profiles is critical for understanding biogeochemical cycling and potential biosafety hazards associated with permafrost degradation under climate warming. However, knowledge about microbiome patterns over key profile layers in response to degradation remains limited in the Qinghai-Tibet Plateau. Using metagenomic data obtained from 150 samples of six 15 m-depth alpine permafrost cores along a degradation gradient, we analyzed microbial community structure and functional potential across different main-layers, including the active, frozen fringe, and frozen layers. We found the recovered microbial and functional diversity decreased with profile depth, and declined only in the active layer as permafrost degraded. Interestingly, Pithoviridae, Caulimoviridae, and virulence factors related to adhesion, biofilm formation, and immune regulation were enriched in the frozen fringe layer, along with increasing relative abundance of Lavidaviridae under the degradation. Along the degradation gradient, carbohydrate-active enzymes diversity decreased in the active layer, while the ratio of nitrite reductase genes to nitrous oxide reductase genes increased in the active and the frozen fringe layers. Hydrothermal regimes emerged as the primary controls shaping microbiome distributions across the vertical profile and along the degradation gradient. Notably, hydrothermal and microbiome attributes jointly regulated carbon/nitrogen loss during the degradation. Taken together, these findings offer crucial insights into microbiome patterns, carbon/nitrogen loss and biosecurity concerning permafrost degradation under global warming.},
}

*Permafrost/microbiology
*Microbiota/genetics/physiology
Bacteria/genetics/classification
Soil Microbiology
Tibet
Metagenome
Nitrogen/metabolism

@article {pmid42402715,
year = {2026},
author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD},
title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.},
journal = {Plant, cell & environment},
volume = {49},
number = {11},
pages = {7997-8013},
pmid = {42402715},
issn = {1365-3040},
support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; },
mesh = {*Hemiterpenes/metabolism ; *Plant Roots/microbiology/growth & development ; *Butadienes/metabolism ; *Nicotiana/microbiology/growth & development/genetics/metabolism ; Plants, Genetically Modified ; *Microbiota ; *Pentanes/metabolism ; Rhizosphere ; Soil Microbiology ; Biomass ; Bacteria ; },
abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.},
}

*Hemiterpenes/metabolism
*Plant Roots/microbiology/growth & development
*Butadienes/metabolism
*Nicotiana/microbiology/growth & development/genetics/metabolism
Plants, Genetically Modified
*Microbiota
*Pentanes/metabolism
Rhizosphere
Soil Microbiology
Biomass
Bacteria

@article {pmid42444523,
year = {2026},
author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M},
title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {83},
number = {4},
pages = {728-736},
pmid = {42444523},
issn = {1536-4801},
support = {K01 DK135647/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; K23 AT009458/AT/NCCIH NIH HHS/United States ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; R03 DK147916/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; K23 DK135797/DK/NIDDK NIH HHS/United States ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; P30 DK078392/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Crohn Disease/microbiology ; *Irritable Bowel Syndrome/microbiology ; Child ; Female ; *Pancreatitis/microbiology ; Adolescent ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; *Dysbiosis/microbiology ; Case-Control Studies ; Acute Disease ; },
abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.

METHODS: Stool was collected from 120 subjects (AP [n = 30], CD [n = 29], IBS Rome IV [n = 27], and healthy controls [HC, n = 34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.

RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p < 0.0001) and similar to CD (p = 0.97). CD differed from IBS (p = 0.001) and HC (p < 0.0001) while IBS and HC were similar (p = 0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2] = 0.12, p < 0.001), and differences between all conditions in pairwise comparisons (p < 0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC = 0.97), followed by AP (AUC = 0.92), HC (AUC = 0.88), and IBS (AUC = 0.83).

CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.},
}

Humans
*Crohn Disease/microbiology
*Irritable Bowel Syndrome/microbiology
Child
Female
*Pancreatitis/microbiology
Adolescent
Feces/microbiology
*Gastrointestinal Microbiome
Male
*Dysbiosis/microbiology
Case-Control Studies
Acute Disease

@article {pmid42478878,
year = {2026},
author = {Davis, EC and Jackson, CM and Diaz, NS and Susana, J and Nelson, A and Insel, R and Seppo, AE and Järvinen, KM},
title = {Maternal Perinatal Gut Microbiome Is Shaped by Traditional Farming Lifestyle and Associated With Early Childhood Atopic Disease.},
journal = {Allergy},
volume = {81},
number = {10},
pages = {3707-3724},
pmid = {42478878},
issn = {1398-9995},
support = {U01 AI131344/AI/NIAID NIH HHS/United States ; //University of Rochester University Research Award/ ; NIFA 67012-35010//U.S. Department of Agriculture/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; T32 HL066988/HL/NHLBI NIH HHS/United States ; U01 AI131344//National Institute of Allergy and Infectious Diseases/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247//University of Rochester Environmental Health Sciences Center/ ; T32 HL066988/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; Pregnancy ; *Life Style ; *Gastrointestinal Microbiome ; *Hypersensitivity, Immediate/etiology/epidemiology ; *Maternal Exposure/adverse effects ; *Agriculture ; Infant ; Adult ; *Prenatal Exposure Delayed Effects ; Developmental Origins of Health and Disease ; },
abstract = {Maternal exposure to a traditional farming lifestyle during pregnancy is associated with protection against allergic disease in childhood; however, the mechanism remains unclear. Pre-clinical work has demonstrated a role for the maternal gut microbiome in fetal immune programming. Given the diverse microbial exposure on farms, we sought to assess whether the maternal gut microbiome may mediate the relationship between maternal farm exposure and protection against offspring allergic disease. Deep shotgun metagenomic analysis of the perinatal fecal microbiome showed that women from an Old Order Mennonite traditional farming community (OOM, n = 68) harbored a more diverse gut microbiome relative to women from urban/suburban Rochester, NY (ROC, n = 55). We identified several bacterial species differentially abundant between lifestyle groups, including those from Dorea, Anaerobutyricum, Bifidobacterium, and Bacteroides genera, which translated to marked differences in microbiome functional capacity. These differences in the gut microbiome composition were accompanied by targeted metabolite findings indicating higher serum acetate and isobutyrate levels in OOM women that were positively correlated with cord plasma levels and infant systemic IgA concentrations. Among urban women, maternal microbiome composition was associated with early childhood atopic disease outcomes. Specifically, Dorea longicatena and Segatella copri were least abundant in urban mothers whose infants developed atopic disease (atopic dermatitis) or IgE-mediated food allergy alone, respectively, and were most abundant in the OOM mothers. Together, these findings highlight the maternal gut microbiome and metabolites as potential contributors to prenatal farming lifestyle protection against early childhood allergic disease.},
}

Humans
Female
Pregnancy
*Life Style
*Gastrointestinal Microbiome
*Hypersensitivity, Immediate/etiology/epidemiology
*Maternal Exposure/adverse effects
*Agriculture
Infant
Adult
*Prenatal Exposure Delayed Effects
Developmental Origins of Health and Disease

@article {pmid42517538,
year = {2026},
author = {Fehr, D and Flack, N and Masenga, G and Mosha, N and Li, N and White, A and Semango, G and Distler, M and Lang, C and Grimm, F and Scharl, M and Mavura, D and Masenga, JE and Schmid-Grendelmeier, P and Brüggen, MC},
title = {Dietary Habits and Atopic Dermatitis Significantly Influence the Fecal Microbiome.},
journal = {Allergy},
volume = {81},
number = {10},
pages = {3584-3598},
pmid = {42517538},
issn = {1398-9995},
support = {LF-OC-20-000418//LEO Fondet/ ; 0456/2024//Vontobel-Stiftung/ ; //Bruno Bloch Stiftung/ ; },
mesh = {Humans ; *Dermatitis, Atopic/etiology/microbiology/epidemiology ; *Feces/microbiology ; Female ; Male ; *Feeding Behavior ; Case-Control Studies ; Metagenomics/methods ; *Microbiota ; Child, Preschool ; *Gastrointestinal Microbiome ; Child ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) has been associated with microbial gut dysbiosis in children. Data in adults is scarce.

OBJECTIVE: We sought to explore the fecal microbiome composition in AD patients versus healthy controls (HC) and investigate the impact of environmental aspects such as the geographical location and dietary habits.

METHODS: In this case control study, a total of 140 fecal samples from 69 AD patients and 71 HC from Tanzania (TZ) and Switzerland (CH) were analyzed. Illumina shotgun metagenomics sequencing was performed followed by taxonomic profiling, calculation of alpha/beta diversity, and permutational multivariate analysis of variance. Differentially abundant species and genera between AD and HC were evaluated.

RESULTS: Alpha diversity (Shannon Index) did not significantly differ between AD and HC. The presence of AD was identified as a significant source of fecal microbiome variation (Bray-Curtis beta diversity). On the species level, Faecalibacterium taiwanense was more abundant in AD, and Vescimonas sp000435555 in HC. On the genus level, CAG-302 (NCBI: Clostridium) was more abundant in HC. Geographical location was associated with distinct dietary habits. Prevotella was significantly more abundant in TZ, whereas Alistipes and Bacteroides were significantly more abundant in CH.

CONCLUSIONS: The presence of AD significantly impacted the fecal microbiome variation and was associated with a particular microbial composition. The impact of geographical location on the fecal microbiome may be related to nutritional differences. Our data support the rationale of a gut-skin axis and pave the way towards therapeutic approaches modulating the microbiome.},
}

Humans
*Dermatitis, Atopic/etiology/microbiology/epidemiology
*Feces/microbiology
Female
Male
*Feeding Behavior
Case-Control Studies
Metagenomics/methods
*Microbiota
Child, Preschool
*Gastrointestinal Microbiome
Child

@article {pmid42571819,
year = {2026},
author = {Li, S and Cai, M and Chen, L and Liang, J and Luo, X and Meng, J and Cao, Y and Liu, G and Hu, Y and Cai, S and Zou, M},
title = {Serine synergizes with lipopolysaccharide to induce macrophage pyroptosis through extracellular Hsp90α and early skin immune microenvironment disruption in diabetic foot.},
journal = {Metabolism: clinical and experimental},
volume = {184},
number = {},
pages = {156732},
doi = {10.1016/j.metabol.2026.156732},
pmid = {42571819},
issn = {1532-8600},
mesh = {*HSP90 Heat-Shock Proteins/metabolism ; *Macrophages/drug effects/metabolism ; Humans ; *Serine/pharmacology/metabolism ; *Lipopolysaccharides/pharmacology ; *Skin/immunology/metabolism/drug effects ; *Diabetic Foot/metabolism/immunology/pathology/microbiology ; Animals ; Skin Microbiome ; Cellular Microenvironment/drug effects ; Keratinocytes/metabolism/drug effects ; Female ; Male ; Dysbiosis/metabolism ; },
abstract = {BACKGROUND: The pathogenesis of early-stage skin lesions in diabetic foot (DF) remains poorly understood, and cannot be fully explained by conventional theories. Skin microbiota dysbiosis has recently emerged as a critical factor, but the underlying mechanisms remain unclear.

METHODS: In this study, we integrated metabolomics and metagenomics analyses of skin samples to investigate metabolic dysregulation driven by microbial dysbiosis.

RESULTS: We identified elevated serine as a key metabolic alteration strongly correlated with a dysbiotic microbiota structure. Functionally, we demonstrate that abnormal serine accumulation contributes to the dysregulation of the early skin immune microenvironment in the diabetic foot. Mechanistically, our results reveal that excess serine synergizes with lipopolysaccharide (LPS) to stimulate the release of eHsp90α from keratinocytes, which was strictly dependent on the Akt/mTOR/HIF-1α pathway. This released eHsp90α then acts as a damage-associated molecular pattern, promoting both the migration and subsequent pyroptotic cell death of macrophages.

CONCLUSIONS: Collectively, our findings suggest a novel pathogenic axis where a microbiota-host derived metabolite collaborates with a bacterial endotoxin to promote inflammatory cell death, which is closely associated with early skin lesions in DF. This work not only elucidates a new mechanism for DF pathogenesis but also suggests that the serine-eHsp90α-pyroptosis axis may serve as a potential candidate for future therapeutic exploration.},
}

*HSP90 Heat-Shock Proteins/metabolism
*Macrophages/drug effects/metabolism
Humans
*Serine/pharmacology/metabolism
*Lipopolysaccharides/pharmacology
*Skin/immunology/metabolism/drug effects
*Diabetic Foot/metabolism/immunology/pathology/microbiology
Animals
Skin Microbiome
Cellular Microenvironment/drug effects
Keratinocytes/metabolism/drug effects
Female
Male
Dysbiosis/metabolism

@article {pmid42714846,
year = {2026},
author = {Cui, Y and Zhang, B and Jiang, X and Rehemujiang, H and Xu, G and Li, Y and Wang, B},
title = {Perilla seed oil reshapes the rumen microbiome and increases fermentation end-products in vitro.},
journal = {Journal of applied microbiology},
volume = {137},
number = {10},
pages = {},
doi = {10.1093/jambio/lxag233},
pmid = {42714846},
issn = {1365-2672},
support = {2025ZY0108//Central Government-Guided Local Science and Technology Development Fund Project/ ; 326YXQN0947//Natural Science Foundation of China/ ; 324QN289//Natural Science Foundation of China/ ; CARS-37//China Agriculture Research System/ ; },
mesh = {Animals ; *Rumen/microbiology ; Fermentation/drug effects ; *alpha-Linolenic Acid/pharmacology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; *Plant Oils/pharmacology ; RNA, Ribosomal, 16S/genetics ; Animal Feed/analysis ; },
abstract = {AIMS: The effect of Perilla frutescens seed oil (PSO) on an in vitro rumen microbial ecosystem was evaluated by integrating fermentation measurements, microbiome profiling, metagenomics, and untargeted metabolomics.

METHODS AND RESULTS: Rumen inoculum was incubated for 24 h with a control TMR substrate (CK), TMR supplemented with 23.7 mg of Perilla seeds per bottle (PS), or TMR supplemented with 8.5 μL of Perilla seed oil per bottle (PSO), with the PS and PSO treatments providing equivalent amounts of seed oil. Fermentation kinetics and volatile fatty acids were measured, and microbial and metabolic responses were characterized using 16S rRNA gene sequencing, metagenomics, KEGG and CAZy annotation, untargeted metabolomics, and MetOrigin2 source tracing. PSO increased maximum gas production and total volatile fatty acid concentrations while maintaining pH within the physiological range. Community diversity was unchanged, but PSO altered microbial composition, including increases in Firmicutes, Verrucomicrobia, Vagococcus, Clostridium, and Lactobacillus and decreases in Shigella sonnei and Methanosarcina sp. Ant1. PSO also altered microbial functional profiles and increased several lipid- and vitamin-associated metabolites, including linoleic acid, 13-HODE, 9-oxoODE, pantothenic acid, and thiamine, while reducing lactate.

CONCLUSIONS: PSO changed rumen microbial community structure and functional potential in parallel with increased fermentation end-products and extensive metabolic shifts. These in vitro findings identify microbial and metabolic responses that warrant validation in vivo.},
}

Animals
*Rumen/microbiology
Fermentation/drug effects
*alpha-Linolenic Acid/pharmacology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
*Microbiota/drug effects
Fatty Acids, Volatile/metabolism
*Plant Oils/pharmacology
RNA, Ribosomal, 16S/genetics
Animal Feed/analysis

@article {pmid42732816,
year = {2026},
author = {Hao, F and Zhu, W and Tang, A and Chen, Q and Guo, M and Xin, Y and Zhu, X and Zhao, Y and Hu, X and Luo, M and Zhou, N and Qin, K and Zhu, H and Li, W},
title = {Akkermansia muciniphila alleviates osteoporosis by suppressing bone marrow adiposity through the gut microbiota-UDCA-TGR5 axis.},
journal = {Life sciences},
volume = {405},
number = {},
pages = {124676},
doi = {10.1016/j.lfs.2026.124676},
pmid = {42732816},
issn = {1879-0631},
mesh = {Animals ; *Osteoporosis/metabolism/microbiology ; Female ; Rats ; *Gastrointestinal Microbiome/physiology ; *Adiposity ; *Bone Marrow/metabolism ; *Ursodeoxycholic Acid/metabolism ; Rats, Sprague-Dawley ; Ovariectomy ; *Receptors, G-Protein-Coupled/metabolism ; Akkermansia ; Mesenchymal Stem Cells/metabolism ; Signal Transduction ; },
abstract = {Osteoporosis (OP) is characterized not only by progressive bone loss but also frequently by pathological bone marrow adiposity (BMA) expansion. Akkermansia muciniphila (AKK), implicated in lipid metabolic homeostasis, was previously found to be markedly depleted during estrogen deficiency-associated bone loss. However, whether AKK suppresses pathological BMA expansion and the corresponding receptor-mediated mechanisms remain poorly understood. Here, we demonstrated that AKK significantly attenuated bone loss and potently suppressed pathological BMA expansion in ovariectomized rats. Integrated untargeted metabolomics and targeted bile acid profiling revealed that AKK supplementation notably restored ursodeoxycholic acid (UDCA) levels in both serum and feces. Metagenomic analyses showed that AKK reshaped bile salt hydrolase (BSH)-related microbial functions, thereby promoting the intestinal deconjugation of tauroursodeoxycholic acid to generate UDCA. The enhanced UDCA-producing capacity of gut microbiota from the AKK-treated group was abolished by inhibition of microbial BSHs. Consistently, oral UDCA supplementation replenished circulating UDCA levels and reproduced the bone- and marrow-protective effects of AKK. In the host, elevated circulating UDCA activated TGR5-dependent TGF-β/SMAD2 signaling in bone marrow mesenchymal stem cells (BMSCs), thereby suppressing adipogenic differentiation and promoting osteogenesis. These effects were reversed by a TGR5 inhibitor and Tgfbr1 knockdown. Collectively, our study reveals a novel mechanism underlying the anti-osteoporotic effects of AKK, whereby AKK suppresses pathological BMA expansion through the gut microbiota-UDCA-TGR5 signaling axis. These findings provide a potential therapeutic strategy for osteoporosis and bone marrow lipid metabolic dysfunction.},
}

Animals
*Osteoporosis/metabolism/microbiology
Female
Rats
*Gastrointestinal Microbiome/physiology
*Adiposity
*Bone Marrow/metabolism
*Ursodeoxycholic Acid/metabolism
Rats, Sprague-Dawley
Ovariectomy
*Receptors, G-Protein-Coupled/metabolism
Akkermansia
Mesenchymal Stem Cells/metabolism
Signal Transduction

@article {pmid42767176,
year = {2026},
author = {Delican, D and Kılıçkaya, O and Ozden, O and Ensari, Y},
title = {Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity.},
journal = {Bioorganic chemistry},
volume = {182},
number = {},
pages = {110550},
doi = {10.1016/j.bioorg.2026.110550},
pmid = {42767176},
issn = {1090-2120},
mesh = {Humans ; *Asparaginase/pharmacology/metabolism/chemistry/genetics ; *Antineoplastic Agents/pharmacology/chemistry/metabolism ; *Gastrointestinal Microbiome ; Drug Screening Assays, Antitumor ; Structure-Activity Relationship ; Cell Proliferation/drug effects ; Dose-Response Relationship, Drug ; Molecular Structure ; },
abstract = {L-asparaginase is essential for acute lymphoblastic leukemia treatment; however, current Escherichia coli and Erwinia chrysanthemi formulations face significant limitations, including immunogenicity, glutaminase-associated toxicity, and short plasma half-life. The human gut microbiome represents an unexplored reservoir of therapeutic enzymes that may offer superior biocompatibility due to host-commensal co-evolution. We employed a systematic genome-mining approach to screen human gut metagenomic data for novel L-asparaginase candidates. Five candidate enzymes from the genera Bacteroides, Ruminococcus, Clostridium, and Prevotella were identified using virtual screening. These enzymes were subsequently codon-optimized and heterologously expressed in E. coli, thereby validating our computational selection strategy. Biochemical characterization revealed optimal activity at alkaline pH (8.0-9.0), robust performance at physiological temperature (37 °C), and excellent storage stability. Ruminococcus_seq7 exhibited exceptional kinetic properties (Km = 0.53 ± 0.19 mM; Vmax = 78.6 ± 5.59 U/mg), whereas Bacteroides_seq104 showed intermediate kinetics (Km = 2.04 ± 0.57 mM; Vmax = 75.4 ± 5.75 U/mg). These lead candidates demonstrated complementary anti-leukemic profiles: Ruminococcus_seq7 showed broad-spectrum activity against T-cell leukemias (IC50: 5.1-8.6 U/mL for Jurkat, MOLT-4, and THP-1), while Bacteroides_seq104 exhibited remarkable potency against THP-1 cells (IC50 = 0.9 U/mL) and successfully overcame resistance in REH cells (IC50 = 36.9 U/mL). Both enzymes maintained >95% viability in healthy HUVEC cells. This study provides proof-of-concept for the discovery of therapeutic enzyme from the human gut microbiome. The identified L-asparaginases exhibited favorable biochemical properties, potent and selective anti-leukemic activity, and enhanced safety profiles. The absence of glutaminase activity and high biocompatibility position these gut microbiome-derived enzymes as promising biotherapeutic scaffolds for next-generation leukemia treatment, pending further optimization of substrate affinity to meet clinical standards.},
}

Humans
*Asparaginase/pharmacology/metabolism/chemistry/genetics
*Antineoplastic Agents/pharmacology/chemistry/metabolism
*Gastrointestinal Microbiome
Drug Screening Assays, Antitumor
Structure-Activity Relationship
Cell Proliferation/drug effects
Dose-Response Relationship, Drug
Molecular Structure

@article {pmid42841652,
year = {2026},
author = {Voulgari-Kokota, A and Janson, E and Heikamp de Jong, I and Knol, J and van Elburg, R and van der Aa, NE and Hortensius, LM and Dudink, J and de Theije, CGM and Schipper, L and Kozior, M and van de Lagemaat, M and Groenendaal, F and van Bel, F and Wildt-Grootendorst, A and Drost-Verhoef, S and Hennink, A and Obihara, CC and van Hillegersberg-Schilder, JLAM and Dassel, CM and Oudshoorn, JH and Meijssen, CB and de Boer, IP and Illy, KE and Claessens, N and Viergever, MA and Isgum, I and Shetty, S and Wopereis, H and Benders, M and Belzer, C},
title = {Synbiotic supplementation leads to gut microbiome communities with functional capacity linked to better brain white matter development in preterm infants.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743949},
doi = {10.1080/19490976.2026.2743949},
pmid = {42841652},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; *Infant, Premature/growth & development ; *White Matter/growth & development ; *Brain/growth & development ; *Gastrointestinal Microbiome ; *Synbiotics/administration & dosage ; Dietary Supplements ; Male ; Bifidobacterium breve ; Glutamine/administration & dosage ; Female ; Oligosaccharides/administration & dosage ; Neurodevelopment ; Magnetic Resonance Imaging ; Infant ; },
abstract = {Preterm birth, a major cause of brain injury, is often linked to dysregulated gut microbiome development. This association underscores microbial metabolic function as a modifiable target to support neurodevelopment. In this secondary analysis of data derived from a randomized controlled trial (Trial Registration: ISRCTN96620855), we tested whether daily nutritional supplementation with Bifidobacterium breve M-16V, short- and long-chain oligosaccharides, and L-glutamine could steer the gut microbiome of very and extremely preterm infants toward communities that support brain maturation. The gut microbiome was profiled with longitudinal shotgun metagenomics at nine time points during the intervention, which started at 48-72 h after birth and continued until 36 weeks postmenstrual age. Additionally, MRI scans were conducted when infants reached term-equivalent age to evaluate brain maturation. Supplementation promoted the early establishment of Bifidobacterium-rich communities in the test group, with enhanced capacity for amino acid biosynthesis and pyruvate fermentation towards acetate and lactate production. Integration of microbiome data with brain developmental markers post hoc showed that the same functions were markedly reduced in infants with delayed white-matter myelination. By integrating microbiome functional capacity profiling and evaluation of brain maturation via MRI, this study demonstrated that early microbial modulation could influence brain development, positioning the preterm gut microbiome as a clinically actionable target.},
}

Humans
Infant, Newborn
*Infant, Premature/growth & development
*White Matter/growth & development
*Brain/growth & development
*Gastrointestinal Microbiome
*Synbiotics/administration & dosage
Dietary Supplements
Male
Bifidobacterium breve
Glutamine/administration & dosage
Female
Oligosaccharides/administration & dosage
Neurodevelopment
Magnetic Resonance Imaging
Infant

@article {pmid42842295,
year = {2026},
author = {Lin, WY and Chang, YJ and Gill, T and Ching, J and Anderson, D and Creek, DJ and Ayub, Q and Rahman, S and Chong, CW},
title = {Association of microbial pathways predicted/inferred using 16S and shotgun metagenome with faecal metabolite abundances.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001855},
pmid = {42842295},
issn = {2057-5858},
mesh = {*Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Metagenomics/methods ; Humans ; Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; *Bacteria/genetics/classification/metabolism ; Metabolome ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {The gut microbiome is an essential metabolic organ influencing host health through metabolite production. While metabolite production levels can be directly measured by gas or liquid chromatography, they are commonly inferred from the abundance of metagenomic functional pathways. To evaluate the accuracy of these inferences, we established a single, manually curated metabolite-pathway/enzyme mapping list as a standardized biological reference. We then compared liquid chromatography-mass spectrometry (LC-MS)-based faecal metabolites with functional pathways/enzymes inferred from four approaches: 16S rRNA gene amplicons, reference-based shotgun, de novo assembly-based contigs and de novo assembly-based metagenome-assembled genomes (MAGs). Our results demonstrate that predictive accuracy is strongly metabolite-specific and method-dependent rather than a uniform characteristic of metagenomic data. While 16S (9.9%), ref-shotgun (14.2%) and de novo-contigs (5.5%) yielded only a small fraction of well-predicted metabolites, the de novo-MAGs approach significantly outperformed other approaches, achieving a 36.9% well-predicted rate for mapped metabolites. Notably, this approach provided the most robust functional-metabolite associations for indicators of gut health. In conclusion, while microbial functional potential does not always mirror metabolic reality, high-quality genomic binning via MAGs offers a significantly more robust framework for selective metabolite prediction.},
}

*Feces/microbiology/chemistry
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Metagenomics/methods
Humans
Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
*Bacteria/genetics/classification/metabolism
Metabolome
Liquid Chromatography-Mass Spectrometry

@article {pmid42844285,
year = {2026},
author = {Pearman, JK and Sissons, J and Kanyi Kihika, J and Waters, S and Rees, ABH and Howarth, JD and Vandergoes, MJ and Wood, SA},
title = {Divergent microbial functional pathways and declining redundancy in lake sediments across eutrophication gradients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42844285},
issn = {2041-1723},
support = {CAWX2305//Ministry of Business, Innovation and Employment (MBIE)/ ; C05X1707//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; *Geologic Sediments/microbiology/chemistry ; New Zealand ; Phosphorus/metabolism ; Ecosystem ; *Microbiota/genetics ; *Bacteria/metabolism/genetics/classification ; Nitrification ; Denitrification ; Metagenomics ; Nitrogen/metabolism ; },
abstract = {Microbial communities underpin nutrient cycling across aquatic ecosystems and are strongly influenced by human disturbance, yet the implication for functional redundancy remains poorly understood. Lake eutrophication is a global threat to freshwater systems, primarily driven by human activities within lakes and surrounding catchments. We hypothesize that eutrophication alters functional redundancy of key metabolic pathways in lake sediments. To test this, we conducted a national scale metagenomic study of surface sediments from 144 New Zealand lakes spanning a broad nutrient gradient. Increasing eutrophication is associated with reduced taxon-based functional redundancy, the potential of multiple species to perform the same function, indicating a narrower taxa pool supporting core functions. In contrast, abundance-based functional redundancy, characterized by the abundance of organisms that can perform the function, showed pathway-specific responses across trophic gradients. For example, nitrification and denitrification have greater abundance-based functional redundancy under higher nutrient conditions, whereas phosphorus transport shows reduced redundancy. By eroding microbial functional redundancy, eutrophication may increase susceptibility of microbial communities to environmental perturbations, potentially compromising their ability to sustain key metabolic processes. As lakes play key roles in biogeochemical cycles, the lower stability of vital biogeochemical pathways in lake sediments is likely to have an impact across ecosystems globally.},
}

*Lakes/microbiology/chemistry
*Eutrophication
*Geologic Sediments/microbiology/chemistry
New Zealand
Phosphorus/metabolism
Ecosystem
*Microbiota/genetics
*Bacteria/metabolism/genetics/classification
Nitrification
Denitrification
Metagenomics
Nitrogen/metabolism

@article {pmid42844483,
year = {2026},
author = {Carter, MM and Liu, Z and Olm, MR and Martin, M and Sprockett, DD and Ghadermazi, P and Trumble, BC and Kaplan, H and Stieglitz, J and Rodriguez, DE and Relman, DA and Sonnenburg, ED and Gurven, M and Good, BH and Sonnenburg, JL},
title = {Prehistoric global migration of vanishing gut microbes with humans.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42844483},
issn = {1476-4687},
abstract = {The gut microbiome is crucial for health and is affected strongly by lifestyle[1]. Many microorganisms commonly found in non-industrialized populations are disappearing or have become extinct in industrialized populations[2-6]. Studying which microorganisms have been long-term residents of the human gut and may have co-evolved with humans[2,7,8] could provide insights into how microbial biodiversity loss affects human health. However, the genetic complexities of microbial evolution and the plasticity of gut microbiome composition have made it challenging to resolve the evolutionary history of these long-term associations. Here we performed deep metagenomic sequencing of the Tsimane horticulturalists of Bolivia and compared their gut microbiomes with those of the Hadza hunter-gatherers of Tanzania[3]. These two populations, whose ancestors have been separated for tens of thousands of years, share 1,231 microbial species, most of which are rare in or absent from industrialized populations. Population genetic analyses of 636 of the shared species revealed patterns of microbial divergence and gene flow consistent with prehistoric human co-migration, with estimated split times that approximately align with human migration out of Africa and into the Americas. Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia. However, many of these species are now vanishing from industrialized populations and the consequences for human health remain uncertain.},
}

@article {pmid42844624,
year = {2026},
author = {Yoon, J and Lee, B and Yoo, KC and Kwak, MJ and Song, HJ and Hwang, CY and Chung, Y and Kim, K and Kwon, SK and Song, JY and Yoon, HS and Kim, JF},
title = {Novel Antarctic chemolithotroph drives iron biomineralization.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42844624},
issn = {2049-2618},
mesh = {*Iron/metabolism ; *Geologic Sediments/microbiology/chemistry ; Antarctic Regions ; *Biomineralization ; Oxidation-Reduction ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; *Chemoautotrophic Growth ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Iron, the most abundant redox-active metal in the Earth's crust, is coupled to numerous biogeochemical cycles. However, the mechanisms of iron oxidation and the organisms involved remain incompletely understood. Banded iron formations (BIFs) are a major reservoir of iron ore in the Precambrian sedimentary record, yet the biological contribution to their genesis remains a subject of unresolved debate. While large-scale BIF deposition largely ceased after the Proterozoic, microbial activity in modern Holocene sediments under fluctuating redox conditions provides a unique opportunity to examine mechanisms reminiscent of ancient iron cycling. Here, we report the stratigraphic sequence of microbiome profiles recorded in laminated facies with iron-containing crystalline illite in the embayment sediments beneath the Larsen C Ice Shelf (LCIS) in Antarctica during the Holocene.

RESULTS: LCIS sediments record microbial community shifts tightly coupled to environmental changes throughout the Holocene. Metagenomic analyses revealed three dominant microbial phases corresponding to geological facies boundaries. The open marine setting (phase A) showed higher taxonomic richness, whereas the sub-ice shelf sediments (phases B and C) were largely anoxic and characterized by diverse chemolithoautotrophic metabolisms. Keystone taxa including uncultured members of Thermodesulfovibrionia, as well as unique microbial communities and metabolisms, were evident in the aphotic, anoxic seawater; metagenomic analyses further revealed chemolithotrophy. The Thermodesulfovibrionia bacterium, visualized using fluorescence in situ hybridization and designated as "Candidatus Mariimomonas ferrooxydans", formed a novel clade in the phylum Nitrospirota. Metagenome-assembled genome analysis identified a putative outer-membrane Fe(II) oxidase, Cyc2, whose Fe(II)-oxidation activity was experimentally confirmed.

CONCLUSION: Our findings document the interaction between microbiome and environment, illustrating how LCIS sediments preserve a dynamic record of microbial community responses to environmental transitions. These results provide critical insights into microbial iron mineralization, echoing the biogeochemistry of the geologic past, particularly synglacial iron formation during the Neoproterozoic Snowball Earth. Video Abstract.},
}

*Iron/metabolism
*Geologic Sediments/microbiology/chemistry
Antarctic Regions
*Biomineralization
Oxidation-Reduction
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
*Chemoautotrophic Growth
RNA, Ribosomal, 16S/genetics
Phylogeny
Metagenomics/methods
Seawater/microbiology

@article {pmid42845172,
year = {2026},
author = {Xu, Q and Song, Y and Yu, H and Wang, Y and Gu, HF},
title = {Gut Microbiota Modulation by Abelmoschus manihot (L.) Improves Circulating Metabolites and Alleviates Diabetic Nephropathy in db/db Mice.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e5630909},
pmid = {42845172},
issn = {2314-6141},
support = {CPU20200228//Suzhong Pharmaceutical Group Co. Ltd/ ; },
mesh = {Animals ; *Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Abelmoschus/chemistry ; Male ; Metabolomics ; Metabolome/drug effects ; Diabetes Mellitus, Experimental/drug therapy ; *Plant Extracts/pharmacology ; Diabetes Mellitus, Type 2/drug therapy ; Disease Models, Animal ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; },
abstract = {BACKGROUND: Huangkui capsule (HKC), derived from the ethanol extract of Abelmoschus manihot (L.) flowers, is widely used in China for treating kidney diseases, including diabetic nephropathy (DN). Our previous study demonstrated that HKC modulates the intestinal microbiota and circulating metabolites in non-obese diabetic mice, a type 1 diabetes model. To further explore its efficacy, we evaluated HKC in db/db mice, a well-established type 2 diabetes and DN model.

METHODS: An HKC cohort studied in 2022 was compared with historical Ctrl and DN cohorts studied in 2021. Shotgun metagenomic sequencing was performed to characterize intestinal microbiota changes, while liquid chromatography-mass spectrometry (LC-MS)-based plasma metabolomics was used to identify alterations in circulating metabolites. The biological functions of the altered microbiota and plasma metabolites were analyzed, and the potential association between the intestinal microbiome and plasma metabolome was evaluated.

RESULTS: Compared with the historical DN cohort, the HKC cohort had higher abundances of Streptococcaceae, Streptococcus, and Massilimaliae and lower abundances of Alloprevotella and Prevotellamassilia in exploratory comparisons. In the HKC-versus-DN comparison, the archived gene set enrichment analysis reported 15 pathways with nominal positive enrichment. Additionally, 12 plasma metabolites were upregulated and 14 downregulated, including branched-chain amino acids (DL-leucine, DL-valine, D-isoleucine), organic acids (N-methyl-α-aminoisobutyric acid, guanidineacetic acid), and choline.

CONCLUSION: In db/db mice, the cohort receiving A. manihot (L.)-derived HKC had lower urinary albumin-to-creatinine ratio (UACR) and different intestinal microbiota and plasma metabolite profiles than the historical DN cohort, highlighting its therapeutic potential for DN.},
}

Animals
*Diabetic Nephropathies/drug therapy/microbiology/blood/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Abelmoschus/chemistry
Male
Metabolomics
Metabolome/drug effects
Diabetes Mellitus, Experimental/drug therapy
*Plant Extracts/pharmacology
Diabetes Mellitus, Type 2/drug therapy
Disease Models, Animal
Mice, Inbred C57BL
*Drugs, Chinese Herbal/pharmacology

@article {pmid42845237,
year = {2026},
author = {Shannon, E and Devotta, H and Ndwandwe, C and Kim, S and Yao, L and Kareem, L and Walters, A and Korpela, K and Hurley, S and Lunjani, N and Koc, F and Mathur, H and Ambikan, A and Neogi, U and Friess, L and van Sinderen, D and Stanton, C and Venter, C and Walter, J and Hourihane, J and O'Mahony, L},
title = {Gut microbial metabolism of peanuts generates immunoregulatory metabolites.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2743944},
doi = {10.1080/19490976.2026.2743944},
pmid = {42845237},
issn = {1949-0984},
mesh = {Humans ; *Arachis/metabolism/immunology/microbiology/chemistry ; Bifidobacterium/metabolism/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Leukocytes, Mononuclear/immunology ; Fermentation ; Infant ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fatty Acids, Volatile/metabolism ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Interleukin-10/immunology ; Cytokines ; },
abstract = {Early life introduction of potentially allergenic foods such as peanuts is important for the prevention of food allergy. We hypothesized that peanut consumption may indirectly influence the immune system via effects on gut microbiota composition and metabolism. In vitro human fecal fermentations with peanuts were performed. Changes in taxa and metabolism were measured using 16S rRNA gene sequencing and untargeted metabolomics respectively. Ten Bifidobacterium strains were cultured in vitro in the presence of peanuts and human peripheral blood mononuclear cells (PBMCs) were used to assess culture supernatant immunomodulatory effects. Fecal samples were sequenced from children at 12 months (n = 343) using whole genome metagenomic sequencing. An online questionnaire was used to collect dietary data. Human fecal bioreactor fermentation of peanut flour, previously subjected to in vitro simulated gastrointestinal digestion, resulted in significant production of short-chain fatty acids (SCFA), associated with increased relative abundance of Megasphaera and bifidobacteria. 188 metabolites were significantly altered following peanut fermentation. Bifidobacterium longum subspecies longum strain 160 efficiently metabolized peanut associated with secretion of indole-3-lactic acid (ILA). Following growth on peanuts, bifidobacterial supernatants enhanced IL-10 secretion, but reduced TNF-alpha and IL-5 secretion from stimulated PBMCs. Peanut consumption by 12-month-old children was associated with significant changes in gut microbiota composition including increased levels of Prevotella buccae, Megasphaera micronuciformis and Blautia wexlerae. Peanuts are metabolized by microbes generating immunoregulatory metabolites such as SCFAs and ILA. These metabolites may represent one potential mechanism underlying the allergy-protective effects of early peanut consumption, which requires further validation in high-risk allergy cohorts.},
}

Humans
*Arachis/metabolism/immunology/microbiology/chemistry
Bifidobacterium/metabolism/genetics
Feces/microbiology
*Gastrointestinal Microbiome
Leukocytes, Mononuclear/immunology
Fermentation
Infant
*Bacteria/classification/genetics/metabolism/isolation & purification
Fatty Acids, Volatile/metabolism
RNA, Ribosomal, 16S/genetics
Female
Male
Interleukin-10/immunology
Cytokines

@article {pmid41791848,
year = {2026},
author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ},
title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.},
journal = {Gut},
volume = {75},
number = {11},
pages = {2118-2129},
doi = {10.1136/gutjnl-2025-337478},
pmid = {41791848},
issn = {1468-3288},
mesh = {Humans ; Cross-Sectional Studies ; *Colorectal Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Aged ; Colonoscopy ; Feces/microbiology ; Metagenome ; Neoplasm Staging ; },
abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.},
}

Humans
Cross-Sectional Studies
*Colorectal Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
Aged
Colonoscopy
Feces/microbiology
Metagenome
Neoplasm Staging

@article {pmid41806991,
year = {2026},
author = {Martinez-Tellez, B and Schönke, M and Kovynev, A and Garcia-Dominguez, E and Ortiz-Alvarez, L and Verhoeven, A and Gacesa, R and Vich Vila, A and Ducarmon, QR and Jimenez-Pavon, D and Gomez-Cabrera, MDC and Weersma, RK and Smits, WK and Giera, M and Ruiz, JR and Rensen, PC},
title = {Roseburia inulinivorans increases muscle strength.},
journal = {Gut},
volume = {75},
number = {11},
pages = {2130-2142},
doi = {10.1136/gutjnl-2025-336980},
pmid = {41806991},
issn = {1468-3288},
mesh = {Animals ; Humans ; *Muscle Strength/physiology ; Mice ; Female ; Male ; *Eubacteriales/physiology ; *Gastrointestinal Microbiome/physiology ; Muscle, Skeletal/physiology ; Adult ; Aged ; Young Adult ; Hand Strength/physiology ; Mice, Inbred C57BL ; *Probiotics/administration & dosage ; Middle Aged ; },
abstract = {BACKGROUND: Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored.

OBJECTIVE: We aimed to investigate whether specific gut microbial species are associated with muscle strength and to explore underlying mechanisms linking the gut microbiota to muscle health.

DESIGN: We conducted metagenomic analyses in cohorts of younger and older adults extensively phenotyped for muscle strength. Associations were tested between bacterial taxa and performance measures. Causality was assessed by oral supplementation of candidate species in antibiotic-treated mice. Metabolomic profiling and muscle phenotyping were performed to elucidate mechanisms.

RESULTS: The relative abundance of Roseburia inulinivorans, but not other Roseburia species, was positively associated with multiple strength measures including handgrip, leg press and bench press in humans. Supplementation of R. inulinivorans in mice significantly enhanced forelimb grip strength, whereas other Roseburia species had no effect. Metabolomic analyses revealed that R. inulinivorans reduced amino acid concentrations in the caecum and plasma, while activating the purine and pentose phosphate pathway in muscle. These changes coincided with increased muscle fibre size and a shift from type I to type II fibres. Accordingly, we observed that the relative abundance of R. inulinivorans is lower in older adults compared with young adults.

CONCLUSION: R. inulinivorans emerges as a species-specific modulator of muscle strength, linking gut microbiota to muscle metabolism and function. These findings support its potential as a probiotic candidate for nutraceutical interventions targeting age-related muscle-wasting diseases.

TRIAL REGISTRATION NUMBER: NCT02365129.},
}

Animals
Humans
*Muscle Strength/physiology
Mice
Female
Male
*Eubacteriales/physiology
*Gastrointestinal Microbiome/physiology
Muscle, Skeletal/physiology
Adult
Aged
Young Adult
Hand Strength/physiology
Mice, Inbred C57BL
*Probiotics/administration & dosage
Middle Aged

@article {pmid42319773,
year = {2026},
author = {Ali, H and Rieuwpassa, IE and Hamrun, N and Marlina, E and Yulianty, R and Akbar, FH and Siti Hartina Dewang, DA},
title = {Longitudinal effects of antiretroviral therapy on the oral microbiota in people living with HIV: A systematic review.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {73},
number = {3},
pages = {279-287},
doi = {10.1556/030.2026.02910},
pmid = {42319773},
issn = {1588-2640},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; *Microbiota/drug effects ; *Mouth/microbiology ; Longitudinal Studies ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {People living with HIV frequently experience oral microbial dysbiosis, contributing to oral disease burden and reduced quality of life. Although antiretroviral therapy (ART) effectively suppresses viral replication and promotes immune recovery, its longitudinal effects on the oral microbiota remain incompletely understood. This systematic review aimed to evaluate longitudinal changes in oral microbiota composition and diversity in people living with HIV before and after ART initiation. A systematic review was conducted in accordance with PRISMA guidelines and registered in PROSPERO (CRD420251164326). Electronic searches were performed in PubMed, ScienceDirect, Wiley Online Library, DOAJ, and Google Scholar for studies published between 2015 and 2024. Eligible studies included longitudinal human studies reporting pre- and post-ART oral microbiota data using 16S rRNA gene sequencing or metagenomic approaches. Methodological quality was assessed using Joanna Briggs Institute critical appraisal tools. Due to substantial heterogeneity, findings were synthesized narratively. Six longitudinal studies met the inclusion criteria. ART was associated with partial and non-uniform modulation of the oral microbiota. Changes in beta diversity and selective taxonomic shifts were commonly reported, whereas changes in alpha diversity were inconsistent. Taxonomic alterations were more evident at the genus level, while several dominant oral genera remained stable before and after ART. Evidence linking oral microbiota changes with immune recovery was limited. Longitudinal evidence indicates that ART induces selective and heterogeneous changes in the oral microbiota without consistent normalization toward a non-HIV microbial profile, underscoring the importance of integrating oral health into long-term HIV care.},
}

Humans
*HIV Infections/drug therapy/microbiology
*Microbiota/drug effects
*Mouth/microbiology
Longitudinal Studies
*Anti-HIV Agents/therapeutic use
Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics

@article {pmid42321256,
year = {2026},
author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L},
title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42321256},
issn = {2055-5008},
support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; },
mesh = {Animals ; *Methane/metabolism ; Cattle ; *Polyphenols/metabolism/pharmacology ; *Hydrogen/metabolism ; Archaea/metabolism/genetics/classification ; Rumen/microbiology ; Female ; *Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Multiomics ; Animal Feed/analysis ; Microbiota ; },
abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.},
}

Animals
*Methane/metabolism
Cattle
*Polyphenols/metabolism/pharmacology
*Hydrogen/metabolism
Archaea/metabolism/genetics/classification
Rumen/microbiology
Female
*Bacteria/metabolism/genetics/classification
Metagenomics/methods
Multiomics
Animal Feed/analysis
Microbiota

@article {pmid42432696,
year = {2026},
author = {Clarke, MD and Falcione, S and Boghozian, R and Todoran, R and Zhang, Y and Real, MGC and StPierre, A and Joy, T and Jickling, GC},
title = {Metagenomic analysis of blood virome in ischemic stroke reveals an increase in herpesvirus transcripts and host immune activation.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42432696},
issn = {1756-994X},
mesh = {Humans ; *Ischemic Stroke/virology/blood/immunology/genetics ; Female ; *Herpesviridae/genetics ; Male ; *Metagenomics/methods ; *Virome ; Aged ; RNA, Viral/blood/genetics ; Middle Aged ; *Stroke/virology ; Host-Pathogen Interactions/immunology ; },
abstract = {BACKGROUND: Viral infections may influence stroke pathophysiology. Several infections have been linked to increased risk of stroke, however our understanding of these viral interactions with immune and host tissue is limited. We performed a transcriptomic analysis of the blood virome following ischemic stroke to study these interactions.

METHODS: Viruses were measured by RNA sequencing of blood from 37 patients with ischemic stroke and 32 matched controls. RNA reads are aligned against a human reference genome, as well as a comprehensive database of human virus genomes. Host gene expression following stroke is examined in relation to the presence of viral transcripts.

RESULTS: Viral RNAs were detected in the blood samples of both ischemic stroke and control groups. Viral reads with a prevalence > 3% and raw counts > 2 were from a total of 6 viral families. This included several human herpesviruses (HHVs), adenoviruses, and papillomaviruses, as well as human pegivirus, respiratory syncytial virus, and human endogenous retrovirus K (HERV-K). Combined, counts from HHVs were higher in stroke compared to control by a fold change of 2.13. Coinfection with multiple HHVs was more common in stroke, with a 1.23 fold increase in the number of detected herpesviruses. Reads from two viral genes were increased in stroke, UL95 from cytomegalovirus (CMV), and EBNA2 from Epstein-Barr virus (EBV). Genes associated with stroke, including APOE, C3, PDGF, and CXCL2 were differentially expressed in stroke samples which contained high counts of one or both of UL95 and EBNA2.

CONCLUSION: Viral RNAs from multiple families can be detected within the human blood virome. HHV transcripts were the most abundant of viral RNAs detected. Among stroke patients, HHV transcripts were more prevalent, with higher counts, and indicated a higher rate of coinfection with multiple HHV species. Expression of the EBV gene EBNA2 and the CMV gene UL95 may relate to changes in immune gene expression following stroke. Further evaluation is needed to determine the effects that the human virome have on stroke risk, immune response to stroke, and long-term outcome.},
}

Humans
*Ischemic Stroke/virology/blood/immunology/genetics
Female
*Herpesviridae/genetics
Male
*Metagenomics/methods
*Virome
Aged
RNA, Viral/blood/genetics
Middle Aged
*Stroke/virology
Host-Pathogen Interactions/immunology

@article {pmid42437892,
year = {2026},
author = {Chen, Y and Lu, S and Zhao, A and Li, M and Gan, X and Wang, Y and Yang, Y and Huang, M and Wang, Q and Niu, T and Zhou, Y},
title = {Blood mNGS: an effective non-invasive diagnostic tool for Pneumocystis jirovecii pneumonia.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42437892},
issn = {1471-2180},
support = {2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; 82370192//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 2024NSFSC1746//West China Hospital, Sichuan University, the Natural Science Foundation of Sichuan Province/ ; 2022YFC2406804//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/microbiology/blood ; *Pneumocystis carinii/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Male ; Sensitivity and Specificity ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Microbiota ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection. Colonization is prevalent but cannot be reliably distinguished from active infection by conventional methods. Metagenomic next-generation sequencing (mNGS) is a promising diagnostic tool, but the value of blood mNGS for diagnosis, microbial community comparison, and outcome-related associations in PJP remains unclear.

METHODS: We analyzed 73 suspected PJP patients with paired BALF and blood mNGS. Using strict diagnostic criteria, patients were classified as: PJP (n = 50) and P. jirovecii colonization (PJC, n = 23). Bioinformatic analyses compared compartment-specific microbiota. BALF-blood concordance and associations between P. jirovecii load and outcomes were evaluated.

RESULTS: BALF showed higher α-diversity than blood (both Shannon and Simpson, P < 0.001), whereas β-diversity showed no compartmental segregation. BALF identified 216 species versus 43 in blood; however, the top-10 species were concordantly ranked (90% concordance). Blood mNGS distinguished PJP from PJC with an AUC of 0.80 (specificity 95.7%, sensitivity 62.0% at RPM > 4.8), outperforming BALF mNGS (AUC 0.76), blood PCR (AUC 0.64) and BALF PCR (AUC 0.73). Gram-negative bacteria accounted for a large proportion of blood taxa (75% of top 20 taxa), while BALF showed additional fungal taxa including Aspergillus fumigatus. LEfSe identified matrix-specific taxa: oral commensals in PJC-BALF. Blood P. jirovecii load correlated positively with LDH (r = 0.34, P = 0.0035), CRP (r = 0.34, P = 0.0031), and BDG (r = 0.26, P = 0.025), and was higher in non-survivors (P < 0.05).

CONCLUSION: Blood mNGS may serve as a non-invasive, highly specific complementary tool for PJP diagnosis and broader microbiological assessment.},
}

Humans
*Pneumonia, Pneumocystis/diagnosis/microbiology/blood
*Pneumocystis carinii/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Male
Sensitivity and Specificity
Bacteria/classification/genetics/isolation & purification
Middle Aged
Microbiota
Aged, 80 and over

@article {pmid42477236,
year = {2026},
author = {Mohamed, ME and Cheng, S and Staley, C and Rashidi, A and Jurdi, NE and Holtan, SG and Jacobson, PA},
title = {Identification of Microbiome Associations with Tacrolimus Pharmacokinetics in Adult Hematopoietic Cell Transplantation Using Population Pharmacokinetic and Machine Learning.},
journal = {Pharmaceutical research},
volume = {43},
number = {9},
pages = {3125-3144},
pmid = {42477236},
issn = {1573-904X},
support = {1UM1TR004405/TR/NCATS NIH HHS/United States ; P30CA077598/CA/NCI NIH HHS/United States ; 1UM1TR004405/TR/NCATS NIH HHS/United States ; P30CA077598/CA/NCI NIH HHS/United States ; },
mesh = {*Tacrolimus/pharmacokinetics/administration & dosage ; Humans ; *Hematopoietic Stem Cell Transplantation ; *Immunosuppressive Agents/pharmacokinetics/administration & dosage ; Machine Learning ; Female ; Male ; Cytochrome P-450 CYP3A/genetics ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; Biological Availability ; Feces/microbiology ; Administration, Oral ; Aged ; },
abstract = {PURPOSE: Tacrolimus (TAC) is known for its high pharmacokinetic variability which cannot be fully explained by pharmacogenomic (PGx) and clinical variables. We identified gut microbiome associated with TAC pharmacokinetic variability in allogeneic hematopoietic cell transplant (HCT) recipients.

METHODS: In this observational study, metagenomic shotgun sequencing was used to analyze stool microbiome collected within ± 10 days from time of first oral TAC trough at steady state. TAC steady state concentrations (222 IV continuous infusion and 436 oral troughs) were modeled to estimate TAC clearance (CL) and oral bioavailability (F) using nonlinear mixed effects modeling. The effect of clinical covariates, PGx variants and concomitant medications on CL and F were evaluated. Machine learning was used to identify bacterial species associated with variability in F and CL. The identified species were incorporated into the final model, and simulations were conducted to estimate their clinical relevance on oral TAC troughs.

RESULTS: TAC population CL was 6.91 L/h and population F was 64.4%. TAC CL was increased in those with CYP3A5*1 genotype and reduced with voriconazole use and if estimated glomerular filtration rate < 60 ml/min/1.73 m[2]. TAC F increased with laxative use and decreased with corticosteroid use. Limosilactobacillus fermentum had the strongest positive effect on oral TAC troughs while Bacteroides uniformis had the strongest negative effect.

CONCLUSION: Gut microbiome contributes to the inter-patient variability in TAC CL and oral F.},
}

*Tacrolimus/pharmacokinetics/administration & dosage
Humans
*Hematopoietic Stem Cell Transplantation
*Immunosuppressive Agents/pharmacokinetics/administration & dosage
Machine Learning
Female
Male
Cytochrome P-450 CYP3A/genetics
Middle Aged
Adult
*Gastrointestinal Microbiome
Biological Availability
Feces/microbiology
Administration, Oral
Aged

@article {pmid42479457,
year = {2026},
author = {You, J and Khan, RM and Reji, N},
title = {Gut microbiome profiles as predictors of response to chemoradiotherapy in locally advanced rectal cancer.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {73},
number = {3},
pages = {396-404},
doi = {10.1556/030.2026.02874},
pmid = {42479457},
issn = {1588-2640},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome ; Male ; *Chemoradiotherapy ; Female ; Middle Aged ; Prospective Studies ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Aged ; Treatment Outcome ; Adult ; Feces/microbiology ; },
abstract = {This prospective cohort study investigates the predictive role of gut microbiota composition in determining the therapeutic response to neoadjuvant chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (LARC) at Qiqihar Jianhua Hospital. A total of 178 patients underwent standardized CRT protocols and were stratified into responders and non-responders based on pathological tumor regression grades. Gut microbiome profiling was conducted via 16S rRNA amplicon sequencing and shotgun metagenomics at three treatment stages (pre-, mid-, and post-CRT). Responders exhibited significantly higher alpha diversity (Shannon, Chao1) at baseline and maintained greater microbial richness throughout treatment. Taxonomic analysis identified Faecalibacterium, Akkermansia, and Bifidobacterium as enriched in responders, while non-responders showed elevated Clostridium, Escherichia, and Streptococcus. Multivariate regression confirmed Faecalibacterium (OR = 1.16, P = 0.0002) and Akkermansia (OR = 1.27, P = 0.0146) as independent predictors of CRT response. Functional profiling revealed enrichment of anti-inflammatory pathways (butyrate synthesis, tryptophan metabolism) in responders and pro-inflammatory, stress-related functions (lipopolysaccharide biosynthesis, oxidative stress) in non-responders. Exploratory microbiome modulation using probiotics or fecal microbiota transplantation (FMT) targeting Faecalibacterium and Akkermansia demonstrated increased responder rates by 12.5 and 18.2%, respectively. These findings highlight the potential of gut microbiome signatures as non-invasive biomarkers for CRT response prediction and as targets for adjunctive therapeutic strategies. Personalized microbiome-informed treatment may enhance CRT efficacy and reduce unnecessary exposure in non-responders, paving the way for precision oncology in rectal cancer.},
}

Humans
*Rectal Neoplasms/therapy/microbiology
*Gastrointestinal Microbiome
Male
*Chemoradiotherapy
Female
Middle Aged
Prospective Studies
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Aged
Treatment Outcome
Adult
Feces/microbiology

@article {pmid42663459,
year = {2026},
author = {Zhao, J and Chen, X and Wang, X and Cui, Y and Zhuge, J and Fang, H and Hua, Z},
title = {Clinical application of BALF-mNGS in immunocompromised and immunocompetent patients with suspected invasive pulmonary aspergillosis: differentiating infection from colonization, microbiome features, and clinical impact.},
journal = {Microbiology spectrum},
volume = {14},
number = {10},
pages = {e0104526},
doi = {10.1128/spectrum.01045-26},
pmid = {42663459},
issn = {2165-0497},
support = {2023K112//Quzhou Science and Technology Program/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; },
mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/immunology ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; *Microbiota ; Retrospective Studies ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Aspergillus/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; Immunocompetence ; },
abstract = {Invasive pulmonary aspergillosis (IPA) not only causes high morbidity and mortality, especially in immunocompromised patients, but also occurs in immunocompetent individuals. Differentiating infection from colonization is challenging, and bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) may aid diagnosis, microbiome profiling, and clinical assessment. We retrospectively analyzed patients with suspected IPA who underwent BALF-mNGS between December 2021 and March 2025. Patients were classified by immune status. IPA diagnosis was based on EORTC/MSGERC 2020 criteria in immunocompromised patients, while immunocompetent cases were adjudicated using an integrated clinical, radiological, and microbiological assessment. A total of 178 patients were finally included and classified according to immune status into an immunocompromised group (n = 77) and an immunocompetent group (n = 101). Aspergillus_ reads per ten million (RPTM) values were significantly higher in infection versus colonization cases in both groups, with optimal cut-offs of 24 (gray zone: 22-60) for the immunocompromised group and 33 (gray zone: 17-48) for the immunocompetent group. Microbiome analysis revealed distinct community structures between infection and colonization groups, with Aspergillus remaining significantly enriched after false discovery rate (FDR) correction in immunocompromised patients, while no taxa remained significant after FDR correction in immunocompetent patients. BALF-mNGS guided antifungal therapy, avoiding unnecessary treatment in colonized patients, and higher Aspergillus_RPTM was associated with increased 90-day mortality in immunocompromised patients. BALF-mNGS may accurately distinguish Aspergillus infection from colonization and reveal microbial shifts, particularly in immunocompromised patients. It can guide targeted antifungal therapy, avoid unnecessary treatment, and higher Aspergillus_RPTM was associated with 90-day mortality in immunocompromised patients, suggesting its potential value for risk stratification.IMPORTANCEBALF-mNGS with quantitative thresholds improves differentiation between Aspergillus infection and colonization. It reveals distinct lung microbiome patterns under different immune statuses, extending beyond simple pathogen detection. Higher Aspergillus burden is associated with worse outcomes in immunocompromised patients, suggesting its potential value for risk stratification.},
}

Humans
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology/immunology
*Immunocompromised Host
*Bronchoalveolar Lavage Fluid/microbiology
Female
*Microbiota
Retrospective Studies
Male
Middle Aged
High-Throughput Nucleotide Sequencing
Aspergillus/genetics/isolation & purification
Aged
Metagenomics
Adult
Immunocompetence

@article {pmid42671210,
year = {2026},
author = {Stephen, AS and Nagala, V and Fattah, B and Dhadwal, N and Gonzales-Marin, C and Gillam, DG and Bradshaw, DJ and Burnett, GR and Allaker, RP},
title = {Sulfur metabolism and immune-microbial networks across oral niches in periodontal disease.},
journal = {Microbiology spectrum},
volume = {14},
number = {10},
pages = {e0300825},
doi = {10.1128/spectrum.03008-25},
pmid = {42671210},
issn = {2165-0497},
support = {BB/J500239/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; Female ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Microbiota ; RNA, Ribosomal, 16S/genetics ; *Periodontal Diseases/microbiology/immunology/metabolism ; Cytokines/immunology ; Male ; Saliva/microbiology/immunology ; *Sulfur/metabolism ; Hydrogen Sulfide/metabolism ; *Mouth/microbiology/immunology ; Middle Aged ; Adult ; Gingival Crevicular Fluid/immunology ; *Sulfur Compounds/metabolism ; Biofilms/growth & development ; Periodontitis/microbiology/immunology ; Tongue/microbiology/immunology ; Gingivitis/microbiology/immunology ; },
abstract = {Volatile sulfur compounds (VSCs) integrate microbial metabolism with local inflammation in periodontal disease. We profiled five oral niches (saliva, tongue, subgingival, supragingival, and interdental plaque) across clinical health, gingivitis, and periodontitis by combining direct VSC measurements (subgingival and oral headspace H2S/CH3SH), functional cysteine/methionine degradation assays, 16S rRNA profiling, gingival crevicular fluid cytokines, and targeted qPCR. Subgingival H2S concentrations were significantly elevated in periodontitis after adjusting for age, sex, plaque index, and subgingival bacterial load (β = 1.24, P = 0.03), and tracked shifts in community composition and the cytokine milieu. Oral headspace CH3SH increased with disease, whereas headspace H2S showed a bimodal pattern (health and periodontitis). In cysteine assays, subgingival and tongue biofilms were the most efficient H2S producers per mg protein; this ranking was preserved after normalization to total bacteria by qPCR. Metagenome predictions indicated enhanced sulfur metabolism in disease, particularly in subgingival plaque, with relative enrichment of SAM-cycle/methionine biosynthesis pathways in health. Methionine degradation to CH3SH increased with disease severity, shifting from subgingival sites in health to interdental/supragingival plaque in disease, and occurring most frequently in saliva. Correlation networks revealed niche- and diagnosis-specific coupling among VSCs, cytokines, and taxa, including associations of Capnocytophaga, Fusobacterium, Prevotella, and Corynebacterium, with IL-1β, IL-4, IL-8, and MCP-1. Together, these data identify the subgingival crevice as a disproportionate source of sulfide and show that sulfur metabolism is spatially organized and disease-responsive. We show that subgingival H2S as a functional marker that integrates microbial dysbiosis and inflammation.IMPORTANCEWe asked how metabolism, microbes, and immunity fit together during gum disease. Using a systems approach across five oral sites, we combined sulfur metabolite measurements, functional assays, microbiome profiling, and cytokine data, and analyzed them as one network. The result is a comprehensive map showing that sulfur metabolism is spatially organized, disease-responsive, and tightly coupled to local immune signals, with the subgingival niche playing an outsized role. Further, this integrated readout turns sulfur metabolism into a useful window on dysbiosis and inflammation and offers a path toward simple monitoring of periodontal disease, such as point-of-care sensors detecting subgingival hydrogen sulfide or methanethiol, or functional assays in which a methionine rinse is followed by measurement of oral headspace gases to assess microbial sulfur metabolism.},
}

Humans
Female
*Bacteria/genetics/classification/isolation & purification/metabolism
Microbiota
RNA, Ribosomal, 16S/genetics
*Periodontal Diseases/microbiology/immunology/metabolism
Cytokines/immunology
Male
Saliva/microbiology/immunology
*Sulfur/metabolism
Hydrogen Sulfide/metabolism
*Mouth/microbiology/immunology
Middle Aged
Adult
Gingival Crevicular Fluid/immunology
*Sulfur Compounds/metabolism
Biofilms/growth & development
Periodontitis/microbiology/immunology
Tongue/microbiology/immunology
Gingivitis/microbiology/immunology

@article {pmid42690065,
year = {2026},
author = {Langlois, A and Vincent, AT and Lauzon, K and Brouard, J-S and Bueno Dalto, D and Gagnon, N and Talbot, G and Lapointe, J and Poulin-Laprade, D},
title = {Characterization of the gut microbiome and resistome of piglets supplemented with low, moderate, and high concentrations of zinc oxide.},
journal = {Microbiology spectrum},
volume = {14},
number = {10},
pages = {e0005926},
doi = {10.1128/spectrum.00059-26},
pmid = {42690065},
issn = {2165-0497},
support = {GRDI-AMR One Health//Government of Canada, Genomics Research and Development Initiative/ ; Impulse (2022)//Swine and Poultry Infectious Diseases Research Center (CRIPA), Fonds de recherche du Québec 2013; Nature et technologies (FRQNT)/ ; Together for the Next generation (2023)//Swine and Poultry Infectious Diseases Research Center (CRIPA), Fonds de recherche du Québec 2013; Nature et technologies (FRQNT)/ ; },
mesh = {Animals ; *Zinc Oxide/administration & dosage/metabolism ; Swine/microbiology ; *Dietary Supplements/analysis ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation & purification/drug effects/metabolism ; RNA, Ribosomal, 16S/genetics ; Colon/microbiology ; Animal Feed/analysis ; Cecum/microbiology ; Fatty Acids, Volatile/metabolism/analysis ; Weaning ; Metagenomics ; Zinc ; Ileum/microbiology ; Diarrhea/prevention & control/veterinary ; Diet ; },
abstract = {UNLABELLED: The livestock sector is standing out for its substantial use of antimicrobials but is also investing in the development of mitigation strategies. Supranutritional concentrations of zinc (Zn) are served to piglets to prevent post-weaning diarrhea. This practice is detrimental to the piglet's assimilation of nutrients and can impact the environment through the excretion of unassimilated Zn, contributing to the persistence of antibiotic resistance by co-selection. In this study, the ileum and colon microbiome of piglets fed low (175 ppm), moderate (953 ppm), or high (2,991 ppm) concentrations of zinc oxide for 21 days after weaning were investigated using metagenomics and 16S rRNA amplicon sequencing. The pH and volatile fatty acids (VFA) were measured in cecum and colon. The colon resistome was investigated using metagenomics and PCR. The high Zn supplementation led to an increase in pH and a decrease in the VFA in both the cecum and colon. The bacterial diversity in colon was negatively impacted by the high Zn diet, with thriving Clostridiaceae and depletion of beneficial populations (e.g., Lactobacillaceae and Selenomonadaceae). Of concern, higher abundances of blaCTX-M and intI1 were observed in piglets fed with the moderate Zn diet. The findings from this study support the limitation of Zn to low concentrations.

IMPORTANCE: Developing alternatives to antibiotics is imperative to mitigate the global antimicrobial resistance crisis, particularly within the livestock sector, the predominant consumer of these agents. Yet, interventions introduced without due consideration may precipitate unintended consequences. In North American swine production, supranutritional zinc supplementation in pig feed has been adopted to prevent post-weaning diarrhea and sustain profitability. However, excessive zinc disrupts iron and copper metabolism and perturbs mitochondrial homeostasis, impairing energy metabolism, antioxidant defenses, and innate immunity. Moreover, high dietary zinc increases the excretion of this heavy metal, contributing to environmental pollution and fostering antibiotic-resistant bacteria through co-selection. This study provides further evidence supporting the restriction of zinc supplementation to nutritional needs, as supranutritional diets compromised the fermentative capacity of the pig gut microbiome and increased the frequency of clinically relevant antimicrobial resistance markers.},
}

Animals
*Zinc Oxide/administration & dosage/metabolism
Swine/microbiology
*Dietary Supplements/analysis
*Gastrointestinal Microbiome/drug effects
*Bacteria/classification/genetics/isolation & purification/drug effects/metabolism
RNA, Ribosomal, 16S/genetics
Colon/microbiology
Animal Feed/analysis
Cecum/microbiology
Fatty Acids, Volatile/metabolism/analysis
Weaning
Metagenomics
Zinc
Ileum/microbiology
Diarrhea/prevention & control/veterinary
Diet

@article {pmid42708583,
year = {2026},
author = {Yu, H-L and Elsheikha, HM and Wang, H-P and Gao, Y-Q and Liu, R and Ma, H and Jiang, J and Li, Y and Zhang, X-X},
title = {Genome-resolved analysis reveals disruption of gut microbial vitamin B and K2 biosynthesis during Toxoplasma gondii infection in mice.},
journal = {Microbiology spectrum},
volume = {14},
number = {10},
pages = {e0156426},
doi = {10.1128/spectrum.01564-26},
pmid = {42708583},
issn = {2165-0497},
mesh = {Animals ; Mice ; *Toxoplasma/physiology ; *Gastrointestinal Microbiome/genetics ; *Vitamin B Complex/biosynthesis ; Metagenome ; *Toxoplasmosis/metabolism/microbiology/parasitology ; Female ; *Toxoplasmosis, Animal ; *Bacteria/genetics/classification/metabolism/isolation & purification ; },
abstract = {UNLABELLED: Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD[+] precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD[+] metabolism.

IMPORTANCE: Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD[+] precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD[+]-related metabolism may contribute to host redox adaptation during T. gondii infection.},
}

Animals
Mice
*Toxoplasma/physiology
*Gastrointestinal Microbiome/genetics
*Vitamin B Complex/biosynthesis
Metagenome
*Toxoplasmosis/metabolism/microbiology/parasitology
Female
*Toxoplasmosis, Animal
*Bacteria/genetics/classification/metabolism/isolation & purification

@article {pmid42734355,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Gürkan Yardımcı, G and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {Microbiology spectrum},
volume = {14},
number = {10},
pages = {e0155026},
doi = {10.1128/spectrum.01550-26},
pmid = {42734355},
issn = {2165-0497},
support = {DE028252/DE/NIDCR NIH HHS/United States ; DE029612/DE/NIDCR NIH HHS/United States ; DE029492/DE/NIDCR NIH HHS/United States ; DE030859/DE/NIDCR NIH HHS/United States ; DE031470/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Dental Plaque/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Mouth/microbiology ; *Dysbiosis/microbiology ; *Inflammation/microbiology ; Abscess/microbiology ; Child ; },
abstract = {Across human mucosal sites, dysbiotic inflammatory diseases are characterized by compositional shifts in the resident microbiota, in which commensal-dominated communities give way to pathobiont-enriched communities where "inflammophilic" species often predominate. Effective treatments for these complex polymicrobial infections remain limited, in part, because the ecological mechanisms driving their emergence and persistence are still poorly understood. To address this gap, we analyzed a unique cohort of pediatric patient-matched, disease-free dental plaque and odontogenic abscess specimens, providing a clinically relevant model to examine microbiome transitions from commensal to inflammophilic states. Using complementary community ecology modeling approaches and inferred metagenomic analyses, we identified microbial taxa and functional programs associated with inflammatory selective pressure and dysbiotic community emergence. Dental plaque communities are characterized by anabolic metabolic processes and carbohydrate-derived ATP generation, whereas abscess microbiomes are highly biased for catabolic metabolism, amino acid-derived ATP generation, and antimicrobial resistance. The results suggest that abscess communities are much less reliant upon interspecies metabolic complementation compared to dental plaque communities, which would imply an obligate dependence upon host inflammatory responses to provide the key metabolites required for growth. These findings support a model in which an inflammophilic community ecology is largely the net result of a combination of enhanced resistance to innate immunity and compatibility with the inflammatory nutrient environment. By defining the metabolic requirements and selective pressures governing these dysbiotic transitions, it may be possible to suppress inflammatory dysbiotic diseases using ecologically focused therapeutic strategies that exploit the limited biosynthetic capacity of commensal depleted inflammophilic communities.IMPORTANCEDysbiotic inflammatory diseases are frequently sustained by complex microbial community interactions, but the ecological processes involved remain poorly understood. In this study, we leveraged pediatric patient-matched, disease-free dental plaque and odontogenic abscess clinical specimens to examine how oral microbial communities shift from health-associated to inflammation-associated states. We found that abscess microbiomes are enriched for features consistent with adaptation to inflammatory environments, including antimicrobial resistance, catabolic metabolism, and utilization of host-derived nutrients. These findings support a model in which host inflammation functions as a selective ecological pressure, favoring the establishment of metabolically specialized, inflammophilic microbial communities. By defining the ecological and functional features that distinguish abscess-associated communities from disease-free plaque microbiota, this work provides a framework for understanding inflammatory dysbiosis and for developing ecological strategies to disrupt pathobiont-enriched communities while promoting the restoration of stable, health-associated microbiota.},
}

Humans
*Microbiota
*Dental Plaque/microbiology
*Bacteria/classification/genetics/isolation & purification
*Mouth/microbiology
*Dysbiosis/microbiology
*Inflammation/microbiology
Abscess/microbiology
Child

@article {pmid42820737,
year = {2026},
author = {Liu, T and Smeds, J and Nilsson, M and Öquist, M and Bertilsson, S},
title = {Depth-stratified boreal peatland microbiomes reveal recurring community organization and methane-cycling potential.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {10},
pages = {},
doi = {10.1093/femsec/fiag111},
pmid = {42820737},
issn = {1574-6941},
support = {2020-01327//Swedish Research Council/ ; 2020-01211//Swedish Research Council/ ; 2020-01436//Swedish Research Council/ ; JCK-2016//Kempestiftelserna/ ; },
mesh = {*Methane/metabolism ; *Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sweden ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; Metagenomics ; Metagenome ; Taiga ; Wetlands ; },
abstract = {Microbial communities in peatlands vary with depth, but most studies have been limited in spatial extent or replication, constraining assessment of general community patterns. We characterized microbial community structure and metabolic potential across replicated depth profiles in seven boreal peatlands in Sweden. Combining 16S rRNA gene sequencing and shotgun metagenomics, we identified recurring vertical stratification across sites. Microbial richness declined with depth, and core taxa including Rice Cluster II, Terriglobales, Subgroup 2, Roseiarcus, Methylocystis, and Candidatus Solibacter were shared across locations. Functional gene profiles revealed depth-related reorganization of carbon-cycling potential, with hydrolytic and fermentative functions relatively more abundant near the surface and acetogenic and methanogenic pathways more prominent in deeper anoxic horizons. Gene-centric analyses indicated an important contribution of Rice Cluster II-related methanogens to hydrogenotrophic methanogenesis, while co-occurrence networks identified a depth-conserved syntrophic module centered on this lineage. Environmental variables showed depth-specific associations with microbial communities. Despite geographic separation and site-specific variation among peatlands, recurring depth-resolved microbial assemblages and functional profiles were observed, suggesting that common environmental constraints associated with peat development contribute to broad patterns of microbial community organization and carbon-cycling potential.},
}

*Methane/metabolism
*Soil Microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Sweden
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
Metagenomics
Metagenome
Taiga
Wetlands

@article {pmid42836471,
year = {2026},
author = {Husted, C and Alonso, J and Swofford, R and Stengle, AG and Moreira, LR and Neafsey, DE and Johnston, RA and Baitchman, E and Genereux, DP and Daniels, R and Karlsson, EK},
title = {Population genetics, trait mapping and fungal pathogen surveillance using untargeted sequencing in timber rattlesnakes (Crotalus horridus).},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esag080},
pmid = {42836471},
issn = {1465-7333},
abstract = {Genomic tools are increasingly important for conservation and wildlife health surveillance, yet their use is often constrained by limited resources, sample quality, and the need for minimally invasive approaches. Here we show that untargeted low-coverage sequencing applied to scale-clip DNA can jointly address population structure, genotype-phenotype associations, and pathogen surveillance in timber rattlesnakes (Crotalus horridus), a species threatened by habitat fragmentation, human encroachment, and the emerging fungal pathogen Ophidiomyces ophidiicola. We sequenced 107 snakes sampled from eight populations in the Appalachian Mountains of the northeastern United States to a mean depth of 0.94x per individual. Population differentiation is pronounced and only weakly correlated with geographic distance, and inbreeding coefficients in some populations are high enough to suggest fitness consequences. Genome-wide association analysis identifies a locus for black-to-yellow color morph containing ALDH4A1, a member of a gene family implicated in vertebrate pigmentation but distinct from melanin pathway pigmentation genes. Our untargeted sequencing method also captures host-associated microbes: O. ophidiicola loads are higher in snakes with clinical signs of snake fungal disease, though some asymptomatic individuals carry substantial loads, and skin-associated microbial communities are disrupted in snakes with higher fungal burdens. That all of these inferences derive from the same minimally invasive sampling and sequencing workflow highlights the scalability of this approach for biodiversity conservation.},
}

@article {pmid42838558,
year = {2026},
author = {Dussex, N and Andersson, L and Bergström, U and Johannesson, K and Wallberg, A},
title = {Harnessing macrogenomics to study changing marine ecosystems under global climate change.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2080},
pages = {},
pmid = {42838558},
issn = {1471-2954},
support = {//Swedish Research Council/ ; //FORMAS/ ; },
mesh = {*Climate Change ; *Ecosystem ; *Genomics ; Biodiversity ; Animals ; Oceans and Seas ; Conservation of Natural Resources ; *Aquatic Organisms/genetics ; },
abstract = {Climate change is reshaping marine ecosystems at an accelerating pace. Predicting its impacts on biodiversity and ecosystem functions is therefore crucial to developing effective conservation strategies. Integration of genomic tools, habitat modelling and simulations offers a transformative approach to forecast these impacts. Yet, current frameworks remain limited to single-species analyses. In this review, we discuss future directions in the emerging field of macrogenomics, the analysis of large-scale genomic data across species and time, and show how its integration with environmental data can be applied to understand past and predict future climate-driven ecological shifts across entire marine communities. We demonstrate how applying a macrogenomic framework can provide insights into future responses of marine ecosystems under global climate change by integrating multi-species demographic analyses, metagenomics and signatures of adaptation associated with past climate fluctuations. We also show how macrogenomics combined with predictive approaches can be used to forecast cascading effects of species fluctuations on ecosystem structure and potentially identify ecosystem tipping points. Ultimately, coupling empirical and prediction data offers a powerful approach for ecosystem-based management, improving our ability to predict adaptive responses and extinction risks at relevant scales, and equipping managers and policymakers with actionable insights to prioritize biodiversity conservation strategies.},
}

*Climate Change
*Ecosystem
*Genomics
Biodiversity
Animals
Oceans and Seas
Conservation of Natural Resources
*Aquatic Organisms/genetics

@article {pmid42838980,
year = {2026},
author = {Human, ZR and Hoover, R and Chan, C and Küsel, K and Wegner, CE},
title = {High diversity but limited expression of biosynthetic gene clusters in a peatland microbial community.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42838980},
issn = {2041-1723},
mesh = {*Multigene Family ; *Soil Microbiology ; Metagenome ; Gene Expression Regulation, Bacterial ; Phylogeny ; *Biosynthetic Pathways/genetics ; *Bacteria/genetics/metabolism/classification ; Genetic Variation ; },
abstract = {The in situ relevance of biosynthetic gene clusters (BGCs) remains poorly understood. We apply meta-omics to characterize BGC diversity and activity along a peatland redox gradient. From seven metagenomes, we recover 9,694 BGCs, spanning diverse taxa, most lacking close relatives in reference databases, indicating extensive novelty. Only 9-27% of this potential is expressed in situ, with Acidobacteriota, despite moderate repertoires, accounting for over half of all BGC transcription. Talented producers with up to 24 clusters are largely silent, and expression is inversely related to BGCs per genome. Acidobacteriota, specialized in complex carbon processing potential express a larger proportion of their BGC repertoires than BGC-rich Pseudomonadota, which had shorter doubling times and lower potential for complex carbon processing. At the genome level, the degree of BGC expression is most strongly coupled to carbohydrate-active enzyme expression, particularly glycoside hydrolases, linking secondary metabolism to active carbon processing in peatland microbes. Thus, although BGCs are widespread, BGC expression in situ is integrated into the carbon-cycling activity of individual taxa rather than a shared physiological state.},
}

*Multigene Family
*Soil Microbiology
Metagenome
Gene Expression Regulation, Bacterial
Phylogeny
*Biosynthetic Pathways/genetics
*Bacteria/genetics/metabolism/classification
Genetic Variation

@article {pmid42840241,
year = {2026},
author = {Zhang, H and Zou, W and Wu, W and Xu, J and Ren, L and Liu, M and Sun, D and Liu, J and Yu, Y and Yu, M and Ding, J},
title = {Metagenomic next-generation sequencing reveals airway microbial dysbiosis and functional alterations in Legionella pneumophila pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900957},
pmid = {42840241},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Legionella pneumophila/genetics ; *Legionnaires' Disease/microbiology ; Female ; *Dysbiosis/microbiology ; Community-Acquired Pneumonia/microbiology ; Male ; Aged ; Microbiota ; Middle Aged ; Metagenome ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Legionella pneumonia (LP), primarily caused by Legionella pneumophila, is a clinically important subtype of community-acquired pneumonia (CAP) associated with substantial morbidity and mortality. However, the microbial characteristics and functional profiles of LP remain insufficiently understood.

METHODS: In this study, metagenomic next-generation sequencing (mNGS) was used to compare airway microbial communities between patients with LP and those with non-Legionella CAP.

RESULTS: A total of 60 patients were included, comprising 23 patients with LP patients and 37 patients with non-Legionella CAP patients. Airway microbial diversity and composition differed between groups, although the between-group effect size was modest and residual confounding could not be excluded. The LP group showed higher relative abundance of Legionella pneumophila and selected opportunistic species, whereas several oral commensal-associated species were relatively enriched in non-Legionella CAP. In the pooled 60-patient cohort, selected microbial species were associated with inflammatory and clinical severity markers; these associations were not disease-specific and do not imply causality. Inferred functional profiles also differed between groups. Exploratory machine-learning models showed high internal discriminatory performance, with XGBoost yielding the highest mean AUC, but the small cohort and lack of external validation limit conclusions regarding diagnostic utility.

CONCLUSIONS: In this small retrospective cohort, LP was associated with differences in airway microbial composition and inferred functional potential compared with a heterogeneous non-Legionella CAP group. Because the study was observational, the groups differed in important clinical characteristics, and the pooled association analyses were not disease-specific, the findings should be considered exploratory and hypothesis-generating. The reproducibility and diagnostic value of microbiota-derived features require confirmation in larger, prospectively collected, independent cohorts.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Legionella pneumophila/genetics
*Legionnaires' Disease/microbiology
Female
*Dysbiosis/microbiology
Community-Acquired Pneumonia/microbiology
Male
Aged
Microbiota
Middle Aged
Metagenome
*Respiratory System/microbiology

@article {pmid42832513,
year = {2026},
author = {Yuan, X and Arany, Á and Formanek, A and Moreau, Y and Lähdesmäki, H and Vatanen, T},
title = {LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2741488},
doi = {10.1080/19490976.2026.2741488},
pmid = {42832513},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Models, Statistical ; Metagenome ; Normal Distribution ; },
abstract = {Longitudinal microbiome data are key to understanding the dynamics of microbial communities and their relationships with the host and environment. However, analysis of such data is challenging due to high dimensionality, compositionality, irregular sampling and temporal dependencies on external covariates. Existing analytical approaches typically address only subsets of these challenges, limiting their ability to yield biologically interpretable insights. We introduce LGTM, a probabilistic modeling framework that combines flexible non-linear longitudinal modeling with interpretable topic-based representations of the microbiome. LGTM simultaneously identifies microbial co-abundance patterns ("topics") and models how their proportions change over time and in relation to host and environmental covariates. Using multiple longitudinal human gut microbiome datasets, we demonstrate that LGTM identifies diverse microbial topics whose major patterns are reproducible across runs, while achieving competitive performance in imputation and forecasting tasks. A key strength of the framework is its interpretability: LGTM yields microbial topics with biologically interpretable taxonomic compositions and directly quantifies associations between covariates and microbial dynamics. LGTM is available at https://github.com/yuanx749/lgtm.},
}

Humans
*Gastrointestinal Microbiome
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Models, Statistical
Metagenome
Normal Distribution

@article {pmid42833873,
year = {2026},
author = {Haque, M and Lesker, TR and Rolle-Kampczyk, U and Segers, A and De Vos, WM and Molinaro, A and Basavanapura, T and Chen, Y and Backhaus, M and Mohamed, MR and Jiang, L and Salih, Q and Candels, L and Henricsson, M and Bielecka, A and Lang, S and Tacke, F and Hengstler, JG and Schneider, CV and Demir, M and Strowig, T and von Bergen, M and Schneider, KM and Trautwein, C},
title = {Microbiota-host genetic interactions modulate MASLD risk in PNPLA3[I148M] carriers via ceramides and are reversible by targeted microbial interventions.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338178},
pmid = {42833873},
issn = {1468-3288},
abstract = {BACKGROUND: The factors that determine when genetic susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD) progresses to clinically significant liver injury remain incompletely understood.

OBJECTIVE: We investigated whether disruption of the intestinal host-microbiota interface acts as a contextual modifier that amplifies PNPLA3[I148M] -associated hepatic injury.

DESIGN: We used a dual-hit mouse model combining hepatic Pnpla3[I148M] -expression with Nlrp6-deficiency, a model of impaired intestinal mucosal homeostasis, under western-diet conditions. Multi-omics profiling, including metagenomics, metabolomics and transcriptomics, was integrated with analyses in human cohorts (Lifelines, Charité MASLD, Human Phenotype Project). Microbiota-dependent effects were examined using faecal microbiota transplantation (FMT), antibiotic-mediated depletion and targeted intervention with Akkermansia muciniphila or its membrane protein Amuc_1100.

RESULTS: In mice, the combination of Pnpla3[I148M] expression and impaired intestinal sensing synergistically exacerbated gut-barrier dysfunction and bacterial encroachment, accompanied by increased portal levels of microbiota-associated metabolites, including long-chain ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0)) and bile acids. These changes were associated with hepatic mitochondrial stress and inflammatory responses. Human carriers with advanced MASLD displayed microbial and metabolic signatures consistent with increased gut-derived metabolic signalling. Restoration of eubiotic microbiota via FMT or Amuc_1100 treatment improved intestinal barrier integrity and attenuated hepatic lipid accumulation in experimental models.

CONCLUSION: These findings suggest that gut-derived signals resulting from a disrupted intestinal barrier may act as modifiers of PNPLA3[I148M] -clinical penetrance by amplifying downstream metabolic and inflammatory responses. By identifying these pathways linking environmental context to genetic susceptibility, this study highlights the host-microbiota interface as a potential target for strategies aimed at limiting MASLD progression in genetically at-risk individuals.},
}

@article {pmid42834904,
year = {2026},
author = {Chulenbayeva, L and Rakhmankulova, A and Kamzayeva, N and Kozhakhmetov, S and Terzic, M and Bapayeva, G and Aimagambetova, G 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 Ukybassova, T and Kushugulova, A},
title = {Cervicovaginal microbiome alterations across HPV infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907605},
pmid = {42834904},
issn = {2235-2988},
mesh = {Humans ; Female ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Human Papillomavirus Viruses/classification/genetics ; Cross-Sectional Studies ; Adult ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Dysbiosis ; Papillomaviridae/classification/genetics ; },
abstract = {INTRODUCTION: The cervicovaginal microbiome is a proposed modifier of HPV-associated cervical disease, yet its relationship with viral type heterogeneity, cytological grade, and community state type (CST) remains incompletely understood.

METHODS: This cross-sectional study characterized cervicovaginal microbiome composition and functional potential across HPV infection status, viral type categories (No HPV, HPV High Risk, HPV16, HPV18, HPV Other), cervical cytological grades, and CSTs in 311 non-pregnant women using whole-genome shotgun metagenomic sequencing, integrated diversity analyses, MaAsLin2 differential abundance testing, and HUMAnN 3.0 functional pathway profiling.

RESULTS: HPV-positive samples showed increased bacterial species richness, and a reciprocal Lactobacillus-to-Gardnerella dominance shift compared to HPV-negative samples. HPV Other showed the highest bacterial species richness and distinct taxonomic and predicted functional associations, including higher inferred abundance of siderophore- and lipopolysaccharide-biosynthesis pathways; however, overall species-level community composition did not differ significantly across HPV type groups. CST I and CST II exhibited compositional stability regardless of HPV status, while CST IV showed pronounced Lactobacillus depletion in HPV-positive women. LSIL was associated with lower Fannyhessea vaginae and Alloscardovia omnicolens abundance and higher Phocaeicola vulgatus abundance relative to NILM.

DISCUSSION: These findings indicate that oncogenic potential and dysbiosis severity are not aligned, and that CST type modifies HPV-microbiome interactions.},
}

Humans
Female
*Microbiota
*Papillomavirus Infections/virology/microbiology
*Vagina/microbiology/virology
*Cervix Uteri/microbiology/virology
*Human Papillomavirus Viruses/classification/genetics
Cross-Sectional Studies
Adult
Bacteria/classification/genetics/isolation & purification
Metagenomics
Dysbiosis
Papillomaviridae/classification/genetics

@article {pmid42835245,
year = {2026},
author = {Mujahid, W and Safdar, S and Aftab, A and Tabassum, S and Bakhtiar, SM},
title = {Integrative Metagenomic Analysis Reveals Human Gut Microbiome-Derived Candidate Non-invasive Biomarkers for Type II Diabetes Mellitus.},
journal = {Iranian journal of medical sciences},
volume = {51},
number = {9},
pages = {617-629},
pmid = {42835245},
issn = {1735-3688},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/diagnosis ; Biomarkers/analysis ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics/physiology ; Case-Control Studies ; Bacteroides/genetics ; Dysbiosis/diagnosis ; },
abstract = {BACKGROUND: Type II Diabetes Mellitus (T2DM) is increasingly associated with alterations in the gut microbiome, which influences host metabolism, inflammation, and insulin sensitivity. Metagenomic profiling has emerged as a promising non-invasive strategy for identifying disease-associated microbial signatures. However, distinguishing disease-specific biomarkers from general dysbiosis remains a major challenge. This study aimed to develop an integrative subtractive metagenomic framework to identify candidate disease-specific gut microbial biomarkers.

METHODS: This in silico case-control study used publicly available metagenomics datasets from healthy controls and individuals with T2DM. Assembly-based and read-based taxonomic profiling approaches were integrated. Differential abundance analysis using the Wilcoxon rank-sum test identified key microbial taxa significantly associated with T2DM.

RESULTS: Potential microbial biomarkers were identified as Bacteroides dorei, Bacteroides gracilis, Bacteroides stercoris, Bacteroides ovatus, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Bacteroides xylanisolvens, Eggerthella lenta, Escherichia coli, Faecalibacterium prausnitzii, Parabacteroides distasonis, Ruminococcus torques, and Subdoligranulum. These taxa are involved in gut metabolic homeostasis and may serve as candidate non-invasive biomarkers for T2DM.

CONCLUSION: The results of this study advance understanding of microbiome-disease crosstalk and form the basis for further in vitro and in vivo validation and microbiome-targeted therapeutic approaches. Overall, this integrative metagenomic study supports alteration of microbial ecology in T2DM, validating the use of gut microbiome profiling as a diagnostic and therapeutic tool in metabolic disease research.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/diagnosis
Biomarkers/analysis
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics/physiology
Case-Control Studies
Bacteroides/genetics
Dysbiosis/diagnosis

@article {pmid42364789,
year = {2026},
author = {DiSilvestro, AN and Wesolowski, LT and Williams, BD and Warren, LK and Athrey, G and White-Springer, SH},
title = {Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses.},
journal = {Journal of equine veterinary science},
volume = {166},
number = {},
pages = {106071},
doi = {10.1016/j.jevs.2026.106071},
pmid = {42364789},
issn = {0737-0806},
mesh = {Animals ; Horses ; *Starch/pharmacology/administration & dosage ; *Inflammation/veterinary/etiology/chemically induced ; *Feces/microbiology ; *Physical Conditioning, Animal/adverse effects ; *Dietary Carbohydrates/pharmacology/administration & dosage ; Male ; *Diet/veterinary ; *Animal Feed/analysis ; *Horse Diseases/chemically induced/etiology ; Animal Nutritional Physiological Phenomena ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation.

AIMS/OBJECTIVES: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate.

METHODS: Quarter Horses (mean±SD 16±1mo; 337±30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators were quantified on d0, d21, and surrounding a 2-h submaximal exercise test (SET) on d22.

RESULTS: On d21, CON horses had greater Lactobacillaceae (∼5.7% vs. ∼2.4% in STARCH), while STARCH had greater Lachnospiraceae (∼38% vs. ∼32% in CON) but diet alone did not impact inflammatory markers. On d22, CRP increased at 24h post-SET in all horses (P<0.0001). By 48h, CRP returned to pre-SET in STARCH but remained elevated in CON (P=0.0005), resulting in greater CRP in CON than STARCH at 48h (P=0.02). TNFα increased from pre-SET to 1h in STARCH horses (P=0.02), then returned to pre by 6h. In CON horses, TNFα increased at 24h (P=0.04) and remained elevated at 48h (P=0.0005). Throughout the SET, CON had greater IL-10 than STARCH horses (P=0.005). SAA, IL-4, IL-8, and vascular endothelial growth factor (VEGF)-A were differentially impacted by the SET but were unaffected by diet.

CONCLUSION: Contrary to our hypothesis, fiber-fed horses appeared to elicit a more robust acute inflammatory response to exercise than starch-fed horses despite an altered gastrointestinal microbiome.},
}

Animals
Horses
*Starch/pharmacology/administration & dosage
*Inflammation/veterinary/etiology/chemically induced
*Feces/microbiology
*Physical Conditioning, Animal/adverse effects
*Dietary Carbohydrates/pharmacology/administration & dosage
Male
*Diet/veterinary
*Animal Feed/analysis
*Horse Diseases/chemically induced/etiology
Animal Nutritional Physiological Phenomena
*Microbiota/drug effects

@article {pmid42387526,
year = {2026},
author = {Bing, Y and Yuan, W and Liang, L and Li, J and Chen, Y and Feng, L and Li, X and Li, H and Zhong, J and Wang, L and Tong, Z and Liu, X},
title = {Alterations in the fecal virome and bacteriome-virome interplay in IPAH.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {},
pmid = {42387526},
issn = {1465-993X},
support = {Nos. 82570072, 82170302//Innovative Research Group Project of the National Natural Science Foundation of China/ ; Nos. Ysbz2025004, Ysbz2025005, Ysbz2025006, Ysbz2025007//the Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; },
mesh = {Humans ; *Virome/physiology ; *Feces/microbiology/virology ; Female ; Male ; *Familial Primary Pulmonary Hypertension/diagnosis/microbiology/virology/metabolism ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; *Bacteria/metabolism/genetics ; Case-Control Studies ; },
abstract = {BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening cardiovascular disorder characterized by complex multisystem disturbances. Although alterations in the gut microbiota have been reported in IPAH, how the gut virome interacts with bacterial communities and host metabolism remains unclear.

METHODS: We enrolled 28 patients with IPAH and 30 age-matched healthy controls (HCs). Fecal viromes and bacteriomes were profiled by metagenomic sequencing, and serum metabolomic data were integrated to construct virus-bacterium-metabolite interaction networks. Random forest models were used to evaluate the diagnostic potential of virome features.

RESULTS: IPAH patients exhibited markedly reduced gut virome diversity (Shannon, Simpson, and Pielou indices, p < 0.05) and distinct community structures from HCs (p < 0.01). A total of 499 differential viral operational taxonomic units (vOTUs) were identified, accompanied by extensive reorganization of interaction networks. At the phylum level, Hofneiviricota was enriched and Phixviricota depleted, both correlating with clinical indicators. Virus-bacterium associations were markedly increased in IPAH (44,894 vs. 17,920, r > 0.5). Notably, vOTU2967, vOTU1924, and vOTU4522 were elevated and inversely related to Bacteroides, whose depletion was associated with increased lactic acid levels. Mediation analysis confirmed significant indirect virus-bacterium-metabolite effects (p < 0.05). Random forest models based on vOTUs or viral families effectively distinguished IPAH patients from controls, highlighting the exploratory potential of gut virome features for mechanistic insights.

CONCLUSIONS: IPAH is characterized by reduced virome diversity, altered viral taxa, and reorganized virus-bacterium-metabolite networks. These findings suggest that gut viruses may influence disease progression by modulating bacterial metabolism, providing a potential avenue for biomarker discovery and therapeutic intervention.},
}

Humans
*Virome/physiology
*Feces/microbiology/virology
Female
Male
*Familial Primary Pulmonary Hypertension/diagnosis/microbiology/virology/metabolism
*Gastrointestinal Microbiome/physiology
Adult
Middle Aged
*Bacteria/metabolism/genetics
Case-Control Studies

@article {pmid42429615,
year = {2026},
author = {Jiang, K and Xiong, F and Peng, Y and Meng, L and Wang, X and Xu, Y and Tang, T and Gao, H},
title = {Intermittent Fasting Restores Cardiac Lipid Homeostasis in Diabetic Cardiomyopathy in Association With Akkermansia Muciniphila and 1-methyl-L-histidine.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {55},
pages = {e76528},
pmid = {42429615},
issn = {2198-3844},
support = {22274115//National Natural Science Foundation of China/ ; 21974096//National Natural Science Foundation of China/ ; LZ26C010002//Zhejiang Provincial Natural Science Foundation of China/ ; LQN26C010004//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; *Diabetic Cardiomyopathies/metabolism/microbiology ; *Histidine/analogs & derivatives/metabolism ; *Intermittent Fasting ; Homeostasis/physiology ; *Lipid Metabolism/physiology ; Akkermansia ; *Gastrointestinal Microbiome/physiology ; Male ; *Myocardium/metabolism ; Diabetes Mellitus, Experimental/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Fasting ; },
abstract = {Diabetic cardiomyopathy (DCM) is a major cardiovascular complication of diabetes with limited effective interventions. Using a streptozotocin-induced insulin-deficient, type 1 diabetes-like DCM mouse model, we show that intermittent fasting (IF) improves cardiac function and attenuates myocardial remodeling. Antibiotic-mediated microbiota depletion largely abolished these benefits, whereas fecal microbiota transplantation from IF-treated donors recapitulated cardioprotection, supporting a causal role of the gut microbiota. Metagenomic profiling identified Akkermansia muciniphila (A. muciniphila) as a prominent IF-responsive taxon, and A. muciniphila supplementation alleviated cardiac injury without obvious improvement in glycaemia. Integrated serum and heart metabolomics identified 1-methyl-L-histidine as a microbiota-associated metabolite reduced in diabetes but restored by IF and A. muciniphila. In vitro and ex vivo assays further supported an L-anserine-linked microbial route for 1-methyl-L-histidine generation. Importantly, oral 1-methyl-L-histidine supplementation recapitulated key cardioprotective effects, remodeled cardiac lipid homeostasis, and reduced lipid peroxidation and oxidative injury. Together, these findings support a gut microbiota-metabolite-lipid axis associated with IF-related cardioprotection in DCM and highlight microbial metabolites as tractable targets to complement dietary intervention.},
}

Animals
Mice
*Diabetic Cardiomyopathies/metabolism/microbiology
*Histidine/analogs & derivatives/metabolism
*Intermittent Fasting
Homeostasis/physiology
*Lipid Metabolism/physiology
Akkermansia
*Gastrointestinal Microbiome/physiology
Male
*Myocardium/metabolism
Diabetes Mellitus, Experimental/metabolism
Mice, Inbred C57BL
Disease Models, Animal
*Fasting

@article {pmid42432469,
year = {2026},
author = {Liu, L and Fu, M and Peng, J and Duan, T and Ma, X and Liu, H and Sha, R and Yang, Y and Yan, H and Jia, R and Li, X and An, X and Liu, Y and Lu, Q},
title = {Bio-valorization of Caragana korshinskii forage via a synthetic microbial community.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42432469},
issn = {1471-2180},
mesh = {Fermentation ; Bacillus subtilis/metabolism ; *Caragana/metabolism/microbiology/chemistry ; *Microbiota ; *Microbial Consortia/physiology ; Lignin/metabolism ; Aspergillus niger/metabolism ; *Animal Feed/microbiology/analysis ; },
abstract = {Caragana korshinskii represents a critical ecological and feed resource in arid regions, yet its utilization is severely impeded by the recalcitrant lignocellulose barrier. This study established a cross-kingdom synthetic microbial community (SynCom) to synergistically overcome this bottleneck, integrating Lactobacillus plantarum for rapid acidification with the fibrolytic enzyme secretion of Bacillus subtilis and the oxidative delignification potential of Aspergillus niger. We integrated microbiome profiling and functional prediction to decode the fermentation dynamics and metabolic mechanisms. Results demonstrated that the SynCom (LBA) treatment engineered a robust fermentation system, achieving a significantly higher in vitro dry matter digestibility (49.68%) and neutral detergent fiber digestibility (25.65%) compared to the control (P < 0.05). This enhancement was driven by a directed shift in the microbiome, where Lactobacillus abundance surged to > 95%, effectively suppressing spoilage genera like Staphylococcus and Weissella via competitive exclusion. Metagenomic prediction revealed that the SynCom upregulated key metabolic modules, specifically pyruvate metabolism and amino acid biosynthesis pathways, facilitating rapid acidification and protein preservation. These findings delineate a coordinated degradation-fermentation-preservation process driven by a rationally assembled synthetic consortium, offering a promising and sustainable bio-valorization strategy for converting high-fiber woody biomass into high-quality livestock feed.},
}

Fermentation
Bacillus subtilis/metabolism
*Caragana/metabolism/microbiology/chemistry
*Microbiota
*Microbial Consortia/physiology
Lignin/metabolism
Aspergillus niger/metabolism
*Animal Feed/microbiology/analysis

@article {pmid42477955,
year = {2026},
author = {Fariba, E and Rosanna, V and Domenico, C and Gaetano, S and Mauro, L and Lucio, LR},
title = {Oral and Pancreatobiliary Microbiota in Cancer: A Systematic Review of Compositional Alterations and Their Clinical Implications.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {55},
number = {9},
pages = {1008-1018},
doi = {10.1111/jop.70172},
pmid = {42477955},
issn = {1600-0714},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology ; *Microbiota ; *Dysbiosis/microbiology/complications ; *Mouth/microbiology ; *Pancreas/microbiology ; },
abstract = {BACKGROUND: Associations between microbial dysbiosis and malignancies of the pancreatobiliary system have been described in recent studies. As a result of the limited number of studies that have been done specifically on the malignancies of the biliary tract, information regarding oral, biliary and tumour-related microbial alterations was combined to provide an overview of the microbial changes that may occur.

METHODS: Studies that involved observations on the composition or presence of dysbiosis of the microbiota from oral (saliva, oral rinse, dental plaque) or other non-oral specimens (bile, pancreatic tissue, duodenal tissue and bacteria-derived extracellular vesicles from plasma) in patients with pancreatobiliary malignancies were considered. The risk of bias was evaluated using the Newcastle-Ottawa Scale (NOS) for case-control study designs and the JBI Checklist for cross-sectional studies.

RESULTS: There were a total of 16 studies involving 1426 participants that were conducted using both case-control and cross-sectional study designs. Samples were collected from saliva, oral wash, bile, pancreatic and duodenal tissues and bacterial extracellular vesicles isolated from plasma samples. The most common method used was 16S rRNA sequencing, and two used shotgun metagenomics. In all the studies, patients with pancreatobiliary cancers, especially PDAC, had a significantly higher abundance of opportunistic microbes like Streptococcus, Veillonella, Fusobacterium, Prevotella and a lower abundance of commensal bacteria like Neisseria and Corynebacterium. There was overlap of microbial profile in the oral cavity and tumour/bile compartments in a few studies.

CONCLUSIONS: Although the current data is preliminary and observational in nature, there are consistent findings linking microbiota dysbiosis with cancers of the pancreatobiliary region within both oral and non-oral body sites. Causality has not been established yet. The use of microbial signatures as a basis for biomarker development is a promising research direction.},
}

Humans
*Pancreatic Neoplasms/microbiology
*Microbiota
*Dysbiosis/microbiology/complications
*Mouth/microbiology
*Pancreas/microbiology

@article {pmid42751774,
year = {2026},
author = {Shao, J and Hung, W and Yin, P and Huang, P and Zhao, W and Yu, L and Tian, F and Chen, W and Xu, J and Zhai, Q and Li, J and Zhao, J},
title = {Efficacy of Bifidobacterium animalis subsp. lactate BL-99 in relieving functional constipation: a randomized placebo-controlled clinical trial.},
journal = {Food & function},
volume = {17},
number = {19},
pages = {8691-8701},
doi = {10.1039/d5fo03175c},
pmid = {42751774},
issn = {2042-650X},
mesh = {Humans ; *Constipation/microbiology/drug therapy/therapy ; Female ; *Probiotics/therapeutic use/administration & dosage ; *Bifidobacterium animalis/physiology ; Double-Blind Method ; Male ; Middle Aged ; Adult ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; Treatment Outcome ; Aged ; },
abstract = {Current therapies for functional constipation (FC) often exhibit limited long-term efficacy. Probiotics, particularly Bifidobacterium animalis subsp. lactis BL-99 (BL-99), may offer a novel approach to alleviate FC symptoms. This randomized, double-blind, placebo-controlled trial (No. WXSY-YXLL-AF/SC-11/01.0) enrolled 41 FC patients who completed the full 6-week study. Participants were randomly assigned to receive either BL-99 (1 × 10[11] colony-forming units per day) or placebo for 4 weeks in this population trial. After completing the 4-week intervention period, administration was discontinued and participants entered a 2-week observation following-up period for continued monitoring. Primary endpoint data collected after trial completion were the changes in the Patient Assessment of Constipation Symptoms (PAC-SYM, 12-item scale) score, evaluated on the first day (0 day), the 28th day (week 4), and the 42th day (week 6). Secondary outcomes included fecal metagenomic profiling to evaluate gut microbiota alterations. After 4 weeks of intervention, the BL-99 group demonstrated significant reductions in PAC-SYM scores compared to the placebo, particularly in domains of "abdominal discomfort" (Δ = 1.8 vs. 0.9, p = 0.007) and "pain during defecation" (Δ = 2.1 vs. 1.0, p = 0.003). These improvements persisted at the 2-week post-treatment follow-up (p < 0.05). Metagenomic analysis revealed that BL-99 enriched Bifidobacterium and Faecalibacterium while suppressing Clostridium species, shifting gut microbiota composition closer to that of the healthy controls. Functional annotation highlighted significant downregulation of infection-related pathways (e.g., bacterial invasion and LPS biosynthesis) and metabolic disease-associated pathways (e.g., insulin resistance) in the BL-99 group (q < 0.05). This trial suggests that 4-week BL-99 supplementation effectively alleviates FC symptoms, partially through microbiota modulation and metabolic pathway regulation. The sustained post-treatment effects warrant further investigation into its long-term benefits.},
}

Humans
*Constipation/microbiology/drug therapy/therapy
Female
*Probiotics/therapeutic use/administration & dosage
*Bifidobacterium animalis/physiology
Double-Blind Method
Male
Middle Aged
Adult
Feces/microbiology
Gastrointestinal Microbiome/drug effects
Treatment Outcome
Aged

@article {pmid42776001,
year = {2026},
author = {Ma, C and Geng, R and Hou, Q and Wang, Q and Xue, T and Wen, L and Yang, J and Hu, J},
title = {Inulin ameliorates sarcopenic obesity: critical roles of gut microbiota and bile acid metabolism.},
journal = {Food & function},
volume = {17},
number = {19},
pages = {8808-8824},
doi = {10.1039/d5fo05320j},
pmid = {42776001},
issn = {2042-650X},
mesh = {Animals ; *Inulin/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Obesity/drug therapy/metabolism ; Male ; *Bile Acids and Salts/metabolism ; *Sarcopenia/drug therapy/metabolism ; Liver/metabolism/drug effects ; Muscle, Skeletal/metabolism/drug effects ; Mice, Inbred C57BL ; Prebiotics ; Humans ; },
abstract = {The concurrent manifestation of muscle wasting and excessive adiposity, termed Sarcopenic Obesity (SO), represents a growing public health challenge. Inulin, a widely used prebiotic, has been shown to improve metabolic disorders, but its specific effects on SO and the mechanisms governing the gut-liver-muscle axis remain underexplored. This study evaluated the therapeutic potential of inulin in db/db mice exhibiting SO features. Our data indicate that inulin supplementation effectively curbed weight gain and fat deposition while preserving lean mass. Crucially, it ameliorated systemic hyperglycemia and dyslipidemia. In the liver, inulin attenuated steatosis by potentiating the AMPK/PPARα oxidative pathway; in skeletal muscle, it reversed atrophy by enhancing myogenic factors (MyoD and MyHC I) and suppressing atrophic ligases (Atrogin-1 and MuRF1). Mechanistically, inulin restored intestinal barrier integrity, thereby reducing serum lipopolysaccharide (LPS) and proinflammatory cytokine levels. Metagenomic sequencing and targeted metabolomics revealed that inulin restructured the gut microbiota composition, characterized by an enrichment of Ligilactobacillus, Prevotella and Bifidobacterium, and modulated the bile acid (BA) profile. Crucially, protein quantification confirmed that inulin significantly upregulated the expression of core bile acid receptors (FXR and TGR5) in both colonic and hepatic tissues. These findings demonstrate that inulin ameliorates SO through an integrated mechanism involving gut microbiota remodeling, BA-FXR/TGR5 receptor activation, and intestinal barrier reinforcement to harmonize the gut-liver-muscle axis, highlighting its potential as a functional food ingredient for managing SO.},
}

Animals
*Inulin/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
*Obesity/drug therapy/metabolism
Male
*Bile Acids and Salts/metabolism
*Sarcopenia/drug therapy/metabolism
Liver/metabolism/drug effects
Muscle, Skeletal/metabolism/drug effects
Mice, Inbred C57BL
Prebiotics
Humans

@article {pmid42785314,
year = {2026},
author = {Somerville, V and Meola, M and Nunes-Richards, A and Bengtsson-Palme, J and Neukamm, J and Majander, K and Pla-Díaz, M and Turgay, M and Moineau, S and Haueter, M and Berthoud, H and von Ah, U and Lüdin, P and Schuenemann, VJ and Shani, N},
title = {Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking.},
journal = {Current biology : CB},
volume = {36},
number = {19},
pages = {4870-4882.e4},
doi = {10.1016/j.cub.2026.08.023},
pmid = {42785314},
issn = {1879-0445},
mesh = {*Cheese/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis/genetics ; Switzerland ; *Bacteria/genetics/classification ; *Food Microbiology ; Dairying ; Fermentation ; },
abstract = {The history of cheesemaking is deeply intertwined with the evolution of microbial communities, from spontaneous fermentation to modern, standardized practices. The rapid technological changes of the last century likely induced profound alterations in cheese microbial communities, yet this remains largely underexplored. Using shotgun metagenomics and 16S rRNA amplicon sequencing, we examined microbial community changes in Raclette du Valais, a traditional Swiss cheese, using preserved wheels from 1875 to 2017 from the same Alpine dairy. Our results reveal that significant differences in microbial community composition coincide with changes in production practices. The oldest cheese harbored a distinct bacterial community, dominated by Lactiplantibacillus paraplantarum, Streptococcus thermophilus, Pseudolactococcus laudensis, and gut-associated taxa. Antibiotic-resistance genes mirrored historical antibiotic use, lactic acid bacteria domestication predated the studied period, and bacteriophage genera from 1875 were already comparable to those of modern cheese factories. These findings highlight how human practices have shaped cheese microbiomes over time.},
}

*Cheese/microbiology
*Microbiota
RNA, Ribosomal, 16S/analysis/genetics
Switzerland
*Bacteria/genetics/classification
*Food Microbiology
Dairying
Fermentation

@article {pmid42827448,
year = {2026},
author = {Imokhai, PO and Metellus, R and Karsten, M and Alhoda, M and Gandhi, S and Ogbuefi, C and Carranza, S and Zhang, J and Lee, D and Brooks, A},
title = {An interdisciplinary scoping review of the emerging impact of periocular skincare products on the ocular surface microbiome and tear film stability.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1898798},
pmid = {42827448},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Tears/drug effects/chemistry ; *Cosmetics/adverse effects ; *Eye/microbiology/drug effects ; Personal Care Products ; Bacteria/classification/drug effects ; Meibomian Gland Dysfunction ; Meibomian Glands/drug effects ; },
abstract = {BACKGROUND: The healthy ocular surface microbiome consists of Actinobacteria, Proteobacteria, and Firmicutes phyla, with Corynebacterium, Propionibacterium, and Staphylococcus as dominant genera. This microbial environment is essential for maintaining immune homeostasis and barrier integrity.

OBJECTIVE: To synthesize existing evidence on how periocular skincare and cosmetic products affect the ocular surface microbiome, tear film stability, and downstream ocular surface disease.

METHODS: A systematic literature search was conducted across PubMed, Cochrane Library, Embase, Web of Science, and Scopus using Boolean MeSH term strategies. Studies from 2010 to present evaluating microbial composition of the ocular surface and the effects of exogenous exposures (cosmetics, contact lenses, medications) were included.

RESULTS: Preservatives (benzalkonium chloride, parabens), surfactants, retinoids, and essential oils (tea tree oil/terpinene-4-ol) disrupt the ocular surface through non-selective microbial depletion, epithelial cytotoxicity, and lipid emulsification. These mechanisms contribute to meibomian gland dysfunction (MGD), blepharitis, and evaporative dry eye - all associated with characteristic dysbiotic microbiome shifts. Advanced sequencing technologies, including 16S rRNA gene sequencing and shotgun metagenomics, reveal taxon-level changes and functional alterations linked to inflammation and tear film instability.

CONCLUSIONS: Periocular product ingredients represent an underappreciated source of ocular surface dysbiosis. Regulatory gaps under current FDA and MoCRA frameworks limit ingredient-level safety evaluation. Future longitudinal studies using functional metagenomics, metabolomics, and standardized microbiome-specific testing pipelines are urgently needed.},
}

Humans
*Microbiota/drug effects
*Tears/drug effects/chemistry
*Cosmetics/adverse effects
*Eye/microbiology/drug effects
Personal Care Products
Bacteria/classification/drug effects
Meibomian Gland Dysfunction
Meibomian Glands/drug effects

@article {pmid42828686,
year = {2026},
author = {Kazarina, A and Vaškevica, A and Senkāne, DE and Zayakin, P and Hušča, S and Vīksne, K and Pirsko, V and Sokolovska, L and Sergejeva, N and Nakurte, I and Pastare, L and Ruhl, S},
title = {Salivary microbiome responses to chlorhexidine and Coriandrum sativum essential oil mouthwashes in patients with periodontitis in a randomized 2-week clinical trial.},
journal = {Clinical oral investigations},
volume = {30},
number = {10},
pages = {},
pmid = {42828686},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Saliva/microbiology ; *Chlorhexidine/pharmacology ; *Microbiota/drug effects ; *Oils, Volatile/pharmacology ; Female ; Male ; *Periodontitis/drug therapy/microbiology ; *Coriandrum/chemistry ; Adult ; Middle Aged ; Porphyromonas gingivalis/drug effects ; },
abstract = {OBJECTIVES: To compare the short-term salivary microbiome effects of a Coriandrum sativum essential oil (CSEO) mouthwash, chlorhexidine (CHX) as a benchmark comparator, and water in patients with periodontitis.

MATERIALS AND METHODS: In this randomized three-arm trial, participants with periodontitis rinsed twice daily for 14 days with water, CSEO, or 0.12% CHX. Preclinical anti-Porphyromonas gingivalis and fibroblast cytotoxicity assays informed CSEO concentration selection. Shotgun metagenomic sequencing was performed on 54 saliva libraries, two per participant, from 27 participants sampled at baseline and week 2 (H2O n = 9, CSEO n = 8, CHX n = 10). Alpha diversity, within-subject Bray-Curtis change, and differential abundance were analysed longitudinally.

RESULTS: Both active agents inhibited P. gingivalis in vitro, with CHX showing greater potency. In the clinical trial, no statistically detectable difference between CSEO and water was observed for the primary species-level Bray-Curtis outcome (q = 0.413), alpha diversity (all q ≥ 0.259), or differential abundance. CHX showed greater species-level Bray-Curtis change than water (q = 0.020), lower species-level Simpson diversity (q = 0.014), and broad taxonomic restructuring.

CONCLUSIONS: Under the tested formulation and exposure conditions, CSEO did not produce a statistically detectable group-level salivary microbiome shift relative to water. CHX provided a benchmark for broad ecological perturbation. The CSEO null finding does not exclude modest or heterogeneous effects in a larger cohort.

CLINICAL RELEVANCE: No clinical benefit can be inferred from the absence of a detectable CSEO-associated microbiome shift. Larger studies integrating clinical, inflammatory, and direct functional outcomes are needed.

TRIAL REGISTRATION: ISRCTN79156900, retrospectively registered on 11 May 2026.},
}

Humans
*Mouthwashes/pharmacology
*Saliva/microbiology
*Chlorhexidine/pharmacology
*Microbiota/drug effects
*Oils, Volatile/pharmacology
Female
Male
*Periodontitis/drug therapy/microbiology
*Coriandrum/chemistry
Adult
Middle Aged
Porphyromonas gingivalis/drug effects

@article {pmid42830277,
year = {2026},
author = {Feng, T and Shang, J and Ma, Y and Li, J and Qin, Y and Zhang, J and Cheng, S and Zhang, G and Xie, H},
title = {Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42830277},
issn = {1471-2180},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Apiaceae/microbiology/growth & development ; *Plants, Medicinal/microbiology/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.},
}

*Rhizosphere
*Soil Microbiology
*Metagenomics/methods
*Apiaceae/microbiology/growth & development
*Plants, Medicinal/microbiology/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification

@article {pmid42830300,
year = {2026},
author = {Nguyen, TT and Steen, IH and Stokke, R},
title = {Diverse biosynthetic pathways in Arctic hydrothermal biofilms.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42830300},
issn = {2041-1723},
support = {315427//Norges Forskningsråd (Research Council of Norway)/ ; },
mesh = {*Biofilms ; *Biosynthetic Pathways/genetics ; Arctic Regions ; *Archaea/genetics/metabolism ; *Hydrothermal Vents/microbiology ; *Bacteria/genetics/metabolism ; Metagenome ; Multigene Family ; Metagenomics ; Microbiota/genetics ; Peptide Synthases/genetics/metabolism ; Protein Processing, Post-Translational ; },
abstract = {Biosynthetic gene clusters (BGCs) which encode diverse secondary metabolites are ubiquitous across microbiomes and support critical ecological functions. They also serve as attractive targets for new drug discovery. Here we combined genome-resolved metagenomics with long-read Nanopore RNA sequencing, yielding 1016 bacterial and 124 archaeal medium-to-high quality MAGs from previously unchartered microbial communities in Arctic hydrothermal vent biofilms. We identified 2965 BGCs from 870 metagenome-assembled genomes (MAGs) comprising a distinctive and rich diversity of BGCs, with ribosomally synthesized and post-translationally modified peptides (RiPPs) predominating across all samples. RiPPs and non-ribosomal peptide synthetases (NRPs), also known to encode metabolites with antimicrobial potential, are represented among the most expressed transcripts. Terpenes, though less expressed, contribute to microbial signaling and defense. Notably, we identify hydrogen cyanide (HCN) synthesis pathways in archaeal genomes, challenging the view that cyanogenesis is restricted to bacteria and eukaryotes. Our findings demonstrate that microbial adaptation to extreme environments favors RiPP-based biosynthesis and that HCN may play a role in archaeal ecological interactions. Moreover, microbial communities in Arctic hydrothermal vent biofilms provide a rich reservoir of unique bioactive compounds, with implications for drug discovery.},
}

*Biofilms
*Biosynthetic Pathways/genetics
Arctic Regions
*Archaea/genetics/metabolism
*Hydrothermal Vents/microbiology
*Bacteria/genetics/metabolism
Metagenome
Multigene Family
Metagenomics
Microbiota/genetics
Peptide Synthases/genetics/metabolism
Protein Processing, Post-Translational

@article {pmid42830672,
year = {2026},
author = {Carew, M and Chung, J and Hehir, G and Hoffmann, A and Coleman, R},
title = {Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70213},
doi = {10.1111/1755-0998.70213},
pmid = {42830672},
issn = {1755-0998},
support = {LP200100381//Australian Research Council/ ; },
mesh = {Animals ; *Invertebrates/classification/genetics ; *DNA Barcoding, Taxonomic/methods/standards ; *Biodiversity ; Australia ; Fresh Water ; *Metagenomics/methods/standards ; },
abstract = {DNA metabarcoding of freshwater macroinvertebrate samples can provide rapid and accurate identification of species diversity. Processing samples where macroinvertebrates are not separated from net contents can substantially reduce time and cost. We devised and tested a standardised method for processing combined kick/sweep samples using DNA metabarcoding to provide accurate estimates of macroinvertebrate species diversity. Kick and sweep samples were collected from 10 sites across Greater Melbourne known to vary in catchment land use, macroinvertebrate abundance and diversity as well as the type and volume of sampling debris. A sieving, blending and DNA extraction protocol was developed to reduce large debris, rocks and sand in samples, and to concentrate macroinvertebrates for metabarcoding. Variable percentages of the dry weight of samples from each site were used as a source of DNA for metabarcoding. We found that the macroinvertebrate species diversity recovered was mostly consistent when processing different percentages (20%-40%) of dry weight, but a minimum dry weight would be recommended for samples with low total dry weight. We present a method with a laboratory and bioinformatic workflow that enables the cost-effective and reliable processing of large volume samples, like those encountered in freshwater bioassessment. This metabarcoding approach has potential to be applied to any invertebrate biodiversity analysis where invertebrates are not separated from sampling debris, regardless of volume and composition, and used on samples varying in species abundance, diversity and density.},
}

Animals
*Invertebrates/classification/genetics
*DNA Barcoding, Taxonomic/methods/standards
*Biodiversity
Australia
Fresh Water
*Metagenomics/methods/standards

@article {pmid42831335,
year = {2026},
author = {Atayan, AA and Belov, YV and Kuznetsov, MR and Sinyavin, GV and Chernookov, AI and Belykh, EN and Yumasheva, VA and Parfenov, IM},
title = {[Current knowledge of pathophysiology of ischemia-induced intestinal wall damage: comprehensive analysis of pathogenesis and perspectives].},
journal = {Khirurgiia},
volume = {},
number = {10},
pages = {71-79},
doi = {10.17116/hirurgia202610171},
pmid = {42831335},
issn = {0023-1207},
mesh = {Humans ; *Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis ; Intestinal Barrier Function ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; *Intestines/blood supply/physiopathology ; *Intestinal Mucosa/metabolism/physiopathology/pathology ; *Ischemia/physiopathology ; Oxidative Stress ; },
abstract = {Intestinal ischemia is still one of the most complex pathological processes and characterized by high mortality and difficulties in early diagnosis. The article presents modern data on pathophysiological mechanisms of ischemia-induced intestinal wall damage. Etiological factors, molecular basis of ischemia-reperfusion injury, role of intestinal microbiota and innovative approaches to diagnosis and therapy are considered. Particular attention is paid to the paradoxical role of reperfusion. Indeed, the last one causes almost 70% of structural damages through activation of NADPH oxidase (NOX-4) and mitochondrial dysfunction. Metagenomic studies revealed a critical decrease in microbiota diversity (Shannon index 1.5-2.0) and butyrate deficiency. This directly correlates with violation of intestinal barrier function. In addition, the authors discuss clinical implications of new data, including probiotics and fecal microbiota transplantation. The article highlights the need for interdisciplinary approach involving microbiologists, clinicians and bioinformaticians to develop personalized strategies to reduce mortality and improve treatment outcomes.},
}

Humans
*Reperfusion Injury/physiopathology/etiology/metabolism/diagnosis
Intestinal Barrier Function
*Gastrointestinal Microbiome/physiology
Fecal Microbiota Transplantation/methods
*Intestines/blood supply/physiopathology
*Intestinal Mucosa/metabolism/physiopathology/pathology
*Ischemia/physiopathology
Oxidative Stress

@article {pmid42832260,
year = {2026},
author = {Song, X and Jia, S and Chen, L and Cao, C and Chen, Z and Hang, L and Jiang, H and Chen, Z},
title = {Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001847},
pmid = {42832260},
issn = {2057-5858},
mesh = {Antarctic Regions ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; Phylogeny ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Oceans and Seas ; Metagenomics ; Biodiversity ; },
abstract = {Antarctic deep-sea ecosystems harboured unique and metabolically versatile micro-organisms that sustained key biogeochemical processes under extreme polar conditions. However, the genomic diversity and ecological functions of these sedimentary or deep-sea microbial communities remained largely unexplored. Here, we constructed a comprehensive deep-sea microbial dataset of the Antarctic Ocean (dsMDAO) by integrating three newly sequenced Prydz Bay sediment metagenomes with 22 publicly available datasets (9 seawater and 13 sediment samples), spanning water depths of ~300-3500 m. Genome binning yielded 186 metagenome-assembled genomes spanning 19 phyla, including 175 bacteria and 11 archaea, a substantial proportion of which represent previously uncharacterized species. Meanwhile, reads mapping with the available standard Kraken2 database (k2_standard) enabled the expansion of species richness of the dsMDAO database. Furthermore, functional annotation revealed diverse metabolic and ecological potentials, including carbon, nitrogen and sulphur cycling, as well as secondary metabolite biosynthesis, virulence-associated defence and cold-adaptation mechanisms. Sediment microbiomes exhibited higher phylogenetic and functional diversity, enriched in Thaumarchaeota and Chloroflexi, whereas seawater communities were dominated by Proteobacteria with more competitive biosynthetic and interaction potentials. Co-occurrence analyses further indicated complex and competitive networks in seawater versus modular and cooperative assemblages in sediments, reflecting distinct ecological strategies. Collectively, dsMDAO provides the first genome-resolved dataset of Antarctic deep-sea microbiota, revealing the hidden taxonomic and functional diversity that underpins ecosystem resilience in polar oceans. This resource lays a foundation for future ecological, evolutionary and biotechnological exploration of Antarctic microbial dark matter.},
}

Antarctic Regions
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification
Metagenome
Phylogeny
*Microbiota/genetics
Geologic Sediments/microbiology
Oceans and Seas
Metagenomics
Biodiversity

@article {pmid42832270,
year = {2026},
author = {Almatrafi, R and Alqurainy, N and Hakami, M and Ajina, R and Alrabiah, S and Arafah, AM and Alotibi, RS and Aldriwesh, MG},
title = {Gut microbiome and healthy ageing: a systematic review of literature.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {10},
pages = {},
doi = {10.1099/mic.0.001779},
pmid = {42832270},
issn = {1465-2080},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Healthy Aging/physiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Aged ; Aging ; Centenarians ; Aged, 80 and over ; Longevity ; },
abstract = {The gut microbiome undergoes compositional and functional changes with ageing. However, microbial signatures specifically associated with healthy ageing, independent of age-related diseases, remain poorly defined. This systematic review aimed to identify compositional and functional features of the gut microbiome associated with healthy ageing. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, a systematic search was conducted using PubMed, Web of Science and ScienceDirect for studies published up to January 2026. The search strategy focused on gut microbiome, ageing and healthy terms. Risk of bias was assessed using the Newcastle-Ottawa Scale. Gut microbiome composition was reviewed across five predefined age groups, while the functional pathways were reviewed for older adults and centenarians. The included studies represented several regions, including recognized longevity hotspots, although geographic representation remained limited. Most studies used 16S rRNA gene sequencing (n=24; 58.5%), followed by shotgun metagenomics (n=13; 31.7%), both (n=3; 7.4%) or metaproteomics (n=1; 2.4%). Enrichment of specific taxa such as Akkermansia, Alistipes and Parabacteroides was consistently reported in centenarians, alongside distinct patterns in older adults and long-lived individuals. Functional profiling suggested differences in pathways related to amino acid catabolism, vitamin biosynthesis and pathways potentially linked to immune modulation, inflammatory processes and gut barrier support. This review provides the first structured synthesis of gut microbiome signatures associated with healthy ageing across the lifespan, highlighting consistent functional traits and the need for a wider geographic representation in future research. It supports standardized, multi-omics framework to identify robust biomarkers and potential microbiome-based interventions for promoting healthy ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Healthy Aging/physiology
*Bacteria/classification/genetics/isolation & purification
Metagenomics
RNA, Ribosomal, 16S/genetics
Aged
Aging
Centenarians
Aged, 80 and over
Longevity

@article {pmid42426884,
year = {2026},
author = {Lei, Y and Xu, Y and Yan, Y and Zhang, J and Zhang, T and Huang, J and Huang, Y and Zhong, J and Wang, X and Zhang, K and Chen, Y},
title = {Multi-omics and functional validation reveal that Methanobrevibacter-derived L-3-aminoisobutyrate alleviates subclinical mastitis in dairy goats via the HSPA1B-p65 signaling pathway.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42426884},
issn = {2049-2618},
mesh = {Animals ; *Mastitis/veterinary/microbiology/therapy ; Female ; Goats ; Signal Transduction ; *Methanobrevibacter/metabolism/genetics ; Gastrointestinal Microbiome ; Multiomics ; Lactation ; Metabolomics ; Milk/metabolism ; Metagenomics ; *Goat Diseases/microbiology ; },
abstract = {BACKGROUND: Subclinical mastitis (SCM) is prevalent in dairy livestock and compromises milk quality and lactation performance. Although often attributed to bacterial infection, many cases lack identifiable pathogens, suggesting alternative mechanisms. While evidence supports a gut-mammary gland axis, the microbial drivers and microbiota-derived metabolites linking gut dysbiosis to SCM remain unclear. Here, we aimed to identify SCM-associated gut microbial markers, prioritize candidate therapeutic metabolites and define the underlying mechanism.

RESULTS: Based on differences in somatic cell count (SCC) and inflammatory phenotypes across a cohort of 167 mid-lactation Saanen dairy goats, we selected 6 healthy and 6 SCM goats for downstream analyses. By integrating metagenomics, metabolomics, cross-species fecal microbiota transplantation (FMT) and functional validation in vitro and in vivo, we found that SCM was accompanied by reduced milk yield and heightened inflammatory signatures. Compared with the Healthy group, SCM goats exhibited marked remodelling of the gut microbiota, with enrichment of opportunistic taxa (Eubacterium and Blautia) and a pronounced depletion of archaeal Methanobrevibacter spp. Notably, FMT from SCM donors recapitulated mammary inflammatory phenotypes in mice, supporting a causal contribution of gut dysbiosis to mammary inflammation. Joint metagenomic functional profiling and metabolomics further identified the branched-chain amino-acid-derived metabolite L-3-aminoisobutyrate (BAIBA) as significantly enriched in the gut of healthy goats. Moreover, Methanobrevibacter spp. harboured key enzyme genes (vorA, vorB and vorD) implicated in BAIBA biosynthesis. In an LPS-challenged MAC-T model, BAIBA attenuated mammary epithelial inflammation by activating endoplasmic reticulum protein quality control programmes and restoring HSPA1B expression, thereby suppressing NF-κB activation and reducing pro-inflammatory cytokine production. Finally, in naturally infected goats, intramammary administration of BAIBA lowered SCC, highlighting translational potential.

CONCLUSIONS: This study identifies BAIBA as a microbiota-derived metabolite that protects against SCM by restraining mammary inflammation via the HSPA1B-NF-κB axis, establishing a mechanistic gut-mammary link and highlighting a potential non-antibiotic intervention strategy. Video Abstract.},
}

Animals
*Mastitis/veterinary/microbiology/therapy
Female
Goats
Signal Transduction
*Methanobrevibacter/metabolism/genetics
Gastrointestinal Microbiome
Multiomics
Lactation
Metabolomics
Milk/metabolism
Metagenomics
*Goat Diseases/microbiology

@article {pmid42612504,
year = {2026},
author = {Liu, Y and Zhang, C and Zhang, Y and Pang, J and Zhang, J and Li, J and Shi, H and He, X and Kang, Y and Shen, J},
title = {Multivariable-adjusted multi-omics signatures reveal gut microbial functional alterations and metabolic dysregulation in intrinsic capacity decline.},
journal = {The journal of nutrition, health & aging},
volume = {30},
number = {10},
pages = {100945},
pmid = {42612504},
issn = {1760-4788},
mesh = {Humans ; Female ; Multiomics ; *Aging/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; Male ; Biomarkers/blood ; Metabolomics ; *Metabolome ; Metagenomics ; Carnitine/metabolism ; },
abstract = {BACKGROUND: Intrinsic capacity (IC) decline is inherently correlated with aging, yet distinguishing specific IC-related biomarkers from general physiological aging markers remains a significant challenge. We aimed to identify multi-omics signatures associated with IC decline after adjustment for relevant covariates and to explore the functional pathways potentially involved in IC decline.

METHODS: We analyzed 110 fecal (metagenomics) and 121 serum (untargeted metabolomics) samples from older adults at Beijing Hospital. Multivariable models were applied adjusting for age, sex, Charlson Comorbidity Index (CCI), fish intake, and fruit intake frequency. Differential analyses and network-based mediation approaches were used to assess microbiome-metabolome-IC associations.

RESULTS: After multivariable adjustment, 57 bacterial species and 56 serum metabolites were associated with IC status. The normal IC group showed enrichment of multiple taxa, including Lactobacillus zeae and Paenibacillus glucanolyticus. IC decline was associated with concurrent alterations in amino acid and carnitine-related metabolic pathways, including changes in L-serine, Cysteine, N6,N6,N6-trimethyl-L-lysine, and carnitine C5-OH. Network-based mediation analysis identified overlapping associations among senescence-related metabolites (N1,N8-diacetylspermidine), dietary-derived microbial products (3-(3-hydroxyphenyl)-3-hydroxypropanoic acid), and secondary bile acids (3-epideoxycholic acid), suggesting a structured microbiome-metabolome architecture linked to IC variation.

CONCLUSIONS: This study identifies a multi-omics signature associated with IC decline after adjustment for major demographic, clinical, and dietary factors. The findings reveal concurrent alterations in circulating metabolites related to nutrient and carnitine metabolism, alongside compositional and functional differences in the gut microbiome. Together, these parallel findings characterize a multi-omics profile associated with functional decline. These results provide hypotheses for future validation in longitudinal studies.},
}

Humans
Female
Multiomics
*Aging/physiology/metabolism
*Gastrointestinal Microbiome/physiology
Feces/microbiology
Male
Biomarkers/blood
Metabolomics
*Metabolome
Metagenomics
Carnitine/metabolism

@article {pmid42628247,
year = {2026},
author = {Millar, CL and Chopra, MP and Morgan, X and Green, EA and Wolfe, A and Pierce, KA and Gao, L and Blesso, CN and Dufour, AB and Kiel, DP and Lipsitz, LA},
title = {A pilot study of daily blueberry intake modulates the gut microbiota enzyme commissions in older, sedentary adults with mild depressive symptoms.},
journal = {The journal of nutrition, health & aging},
volume = {30},
number = {10},
pages = {100958},
pmid = {42628247},
issn = {1760-4788},
support = {P30 AG048785/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Female ; Pilot Projects ; *Blueberry Plants ; Aged ; *Depression/microbiology ; Sedentary Behavior ; Feces/microbiology/chemistry ; Double-Blind Method ; Male ; Fruit ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/analysis/metabolism ; },
abstract = {BACKGROUND: Fiber and anthocyanins in blueberries have potential to modify the gut microbiome and metabolites that are relevant to depression in older adults.

OBJECTIVE: Our objective was to preliminarily determine the effect of blueberry consumption on the gut microbiome, metabolites, and depressive symptoms.

DESIGN: Sedentary, older adults (≥65y) with mild depressive symptoms were enrolled in a randomized, double-blind, parallel-arm, placebo-controlled pilot study. Participants consumed 48 g/day of blueberry powder (∼2 cups of fresh berries) or placebo for 3 months. Metagenomic sequencing measured the abundance of fecal bacterial species and genes, liquid chromatography/mass spectrometry evaluated gut-derived fecal short chain fatty acids (SCFA), and validated questionnaires evaluated depressive symptoms before and after the intervention.

PARTICIPANTS: Eighteen participants who were predominantly female and white completed the intervention (Placebo Group, n = 8, mean age: 75 ± 6; Blueberry Group, n = 10, mean age: 71 ± 4).

RESULTS: Measures of species abundance, MetaCyc pathways, and metabolites did not change. There were statistically significant in the gene abundance of several Enzyme Commissions (EC) of the gut microbiome within the Blueberry Group-including EC 3.6.3.31 Polyamine Transporting ATPase, which is involved in the production of the neurotransmitter, gamma-aminobutyric acid (GABA).

CONCLUSION: While there were no statistically significant differences in changes in depressive symptoms between groups, the magnitude of reduction in depressive symptom severity appeared greater, with smaller variability in the Blueberry Group, which was paired with minor changes in the gut microbial ECs. Our data are preliminary and warrant additional studies to investigate the link between blueberries, the gut-microbiome, and mood in older adults.},
}

Humans
Female
Pilot Projects
*Blueberry Plants
Aged
*Depression/microbiology
Sedentary Behavior
Feces/microbiology/chemistry
Double-Blind Method
Male
Fruit
*Gastrointestinal Microbiome
Fatty Acids, Volatile/analysis/metabolism

@article {pmid42825217,
year = {2026},
author = {Zhu, Y and Zhang, J and Wei, Y and Zhou, S and Qin, X},
title = {Biochar application alters soil properties and microbial gene profiles in a continuous cassava cropping system.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21731},
pmid = {42825217},
issn = {2167-8359},
mesh = {*Manihot/growth & development ; *Soil Microbiology ; Rhizosphere ; *Charcoal/pharmacology ; *Soil/chemistry ; Nitrogen/metabolism ; Metagenome ; *Microbiota/genetics ; Nitrogen Cycle ; },
abstract = {Continuous cassava cropping can lead to soil degradation and disturbances in soil microbial functions, threatening the sustainability of cassava production systems. To address these challenges, this study examined the effects of biochar on soil physicochemical properties and microbial functional profiles in a continuous cassava cropping system. Two biochar application rates (0 and 3 Mg ha[-1]) were applied, and metagenomic sequencing was conducted to evaluate microbial community composition and functional genes related to carbon and nitrogen cycling in rhizosphere and bulk soils. The results demonstrated that biochar was associated with higher soil pH, soil organic matter, and available nutrient content, with a stronger effect in rhizosphere soil. Biochar application altered the genetic potential of microbial communities, particularly in the rhizosphere soil. In terms of functional categories, biochar was related to higher gene abundances in "homologous recombination" and "DNA replication" categories (Kyoto Encyclopedia of Genes and Genomes (KEGG) database), as well as the "replication, recombination, and repair" category (evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database) in rhizosphere soil. Biochar also affected the abundance of carbon cycling genes, particularly in the rhizosphere. The abundance of the aerobic respiration-related gene coxA was increased, while the abundance of the anaerobic fermentation gene L-lactate dehydrogenase (LDH) was decreased. Additionally, in rhizosphere soil, biochar significantly increased the abundance of norB (denitrification), GDH2 (nitrogen mineralization), and nifD (nitrogen fixation), while decreasing the abundance of genes involved in nitrogen assimilation (gltB), assimilatory nitrate reduction (nirA), nitrogen mineralization (cynS), and nitrogen uptake (nrtA, nasF, cynA, nrtC, and nasD). Together, these results suggest that biochar application may enhance nutrient availability and reshape microbial functional potential primarily in the cassava rhizosphere, providing field evidence for biochar use in continuous cassava cropping.},
}

*Manihot/growth & development
*Soil Microbiology
Rhizosphere
*Charcoal/pharmacology
*Soil/chemistry
Nitrogen/metabolism
Metagenome
*Microbiota/genetics
Nitrogen Cycle

@article {pmid42826561,
year = {2026},
author = {Zhang, Y and Wu, H and Zhang, X and Wu, Y and Hysen, L and Liu, Y and Zhang, H and Yang, J and Fu, L and Xiao, M and Lu, L and Zhang, Z and Zhang, J and Zhu, D},
title = {Protected area management contexts are associated with variation in Tibetan macaque gut microbiota and antibiotic resistomes.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120878},
doi = {10.1016/j.ecoenv.2026.120878},
pmid = {42826561},
issn = {1090-2414},
abstract = {Protected areas (PAs) are central to global biodiversity conservation and differ in their management contexts and associated patterns of human activity, yet differences in wildlife gut microbiota and antibiotic resistomes across PAs remain poorly understood. This study employed metagenomic analyses to compare the gut microbiota and resistomes of Tibetan macaques (Macaca thibetana) across three PAs in China with differing management contexts: Emeishan Scenic Area (EMS), where ecotourism is prominent; the Tangjiahe sector of Giant Panda National Park (TJH), where ecotourism is permitted but regulated; and Mabian Dafengding National Nature Reserve (MB), where tourist access is prohibited but livelihood-related resource use persists. Results showed that the MB population was characterized by higher gut microbial diversity and antibiotic resistance gene (ARG) abundance, with broader repertoires of potential pathogen taxa and high-risk ARGs. In contrast, potential pathogen signals in EMS and TJH were dominated by a single taxon, while EMS also showed a high-abundance signal of high-risk ARGs dominated by erm(B). Study area, gut microbiota and mobile genetic element (MGE) profiles were independently associated with gut ARG composition. This study provides a new perspective for global wildlife conservation and supports incorporating microbiota and resistome surveillance into protected-area management.},
}

@article {pmid42322606,
year = {2026},
author = {Sinha, A and Qian, A and Boutin, T and Maurice, CF},
title = {Prophage induction contributes to alterations in the gut phageome during intestinal inflammation.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {117491},
doi = {10.1016/j.celrep.2026.117491},
pmid = {42322606},
issn = {2211-1247},
mesh = {*Prophages/classification/metabolism ; *Gastrointestinal Microbiome ; Virome ; Dextran Sulfate ; Animals ; Mice ; Colitis/chemically induced/immunology/microbiology/virology ; T-Lymphocytes ; Mice, Inbred C57BL ; Datasets as Topic ; Metagenome ; Biodiversity ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology ; Germ-Free Life ; *Bacteria/growth & development/metabolism/virology ; },
abstract = {Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial communities. During homeostasis, gut phage communities are longitudinally stable and lysogenic replication is dominant. In chronic gut inflammatory disorders, such as inflammatory bowel diseases (IBDs), there are alterations in phage diversity, which may result from changes in phage replication cycles. Here, we use a combination of in vitro, simplified community, and whole-community bioinformatics approaches to investigate whether prophage induction contributes to these alterations. We identify several compounds associated with gut inflammation that induce prophages from commensal gut bacterial isolates. Analyzing data from two mouse models of colitis, we observe that shifts in the composition of temperate phages occur over the course of inflammation, supporting a switch from lysogenic to lytic replication. Collectively, our observations support the idea that prophage induction contributes to alterations in the phageome associated with intestinal inflammation.},
}

*Prophages/classification/metabolism
*Gastrointestinal Microbiome
Virome
Dextran Sulfate
Animals
Mice
Colitis/chemically induced/immunology/microbiology/virology
T-Lymphocytes
Mice, Inbred C57BL
Datasets as Topic
Metagenome
Biodiversity
*Inflammatory Bowel Diseases/metabolism/microbiology/pathology/virology
Germ-Free Life
*Bacteria/growth & development/metabolism/virology

@article {pmid42814154,
year = {2026},
author = {Sivarajan, D and Pothayi, V and Devasia, SC and Ramachandran, B},
title = {Photoperiod driven modulation of behavior, gut microbiota, and brain transcriptomics in zebrafish.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {10},
pages = {},
pmid = {42814154},
issn = {1432-2013},
support = {CSIR-UGC-JRF-905/2018//CSIR-UGC/ ; ECR/2018/002479//DST-SERB/ ; },
mesh = {Animals ; *Zebrafish/physiology ; *Brain/metabolism/physiology ; *Photoperiod ; *Gastrointestinal Microbiome/physiology ; *Transcriptome ; Circadian Rhythm/physiology ; *Behavior, Animal/physiology ; },
abstract = {Circadian rhythms regulate physiological and behavioural processes, with the light-dark cycle acting as the principal environmental cue synchronising the biological clock; disruption of this cue can affect brain function and behaviour. Using zebrafish (Danio rerio) as a translational model, we examined how chronic photoperiod alteration, applied from the larval stage to adulthood, affects exploratory activity, anxiety-like behaviour, aggression, and social preference, and whether these changes are paralleled by shifts in gut microbiota composition and brain transcriptomic profile. Zebrafish were reared under three photoperiod regimes: 14L/10D (control), 20L/4D (extended light), and 4L/20D (extended dark), followed by behavioural, gut metagenomic, and brain transcriptomic analyses. Extended darkness (4L/20D) reduced anxiety-like behaviour, whereas extended light (20L/4D) increased aggression both extended photoperiods altered social behaviour, but with distinct behavioural profiles. Gut microbiota in the 20L/4D group showed phylum-level co-dominance of Actinomycetota and Pseudomonadota, including a greater presence of potentially pathogenic taxa, while the 4L/20D group was dominated by Bacillota. Brain transcriptome profiling, based on a single pooled sample per condition, identified transcripts showing the largest expression differences in each group: in 20L/4D, transcripts linked to phototransduction (gnat1, saga, pde6ga, exorh), ribosomal function (rpl13a, rpl9, knop1), melatonin synthesis (asmt), calcium signalling (plcb4a), and glycolysis (eno1a) were elevated; in 4L/20D, transcripts linked to neuroprotection (nr4a1), DNA repair and chromatin remodelling (fance, uimc1, histh1l), synaptic plasticity (serpina10a), neurodevelopment (six6a), and cell-cycle regulation (btg2) were elevated. These findings indicate that photoperiod shapes zebrafish behaviour, gut microbial composition, and brain gene expression, providing a hypothesis-generating basis for future studies incorporating biological replication.},
}

Animals
*Zebrafish/physiology
*Brain/metabolism/physiology
*Photoperiod
*Gastrointestinal Microbiome/physiology
*Transcriptome
Circadian Rhythm/physiology
*Behavior, Animal/physiology

@article {pmid42817813,
year = {2026},
author = {Wang, L and Yu, S and Huang, J and Meng, Y and Zhao, C and Gan, Y and Hu, W and Yang, Y},
title = {Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70579},
doi = {10.1111/mec.70579},
pmid = {42817813},
issn = {1365-294X},
support = {2023YFD1801900//National Key Research and Development Program of China/ ; 2025KYPT0066//National Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; 32460897//National Natural Science Foundation of China/ ; Q2022002//'Grassland Talents' Youth Innovation and Entrepreneurship Talent Project of Inner Mongolia Autonomous Region/ ; 2025-Gui-Yan-1-36//Hohhot R&D Investment Incentive Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; Birds/microbiology/virology ; *Ecosystem ; Bacteria/genetics/classification ; *Biodiversity ; Arthropod Vectors/microbiology/virology ; Fungi/genetics/classification ; Phylogeny ; Grassland ; Sequence Analysis, DNA ; Virome ; Viruses/classification/genetics ; },
abstract = {Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.},
}

Animals
*Microbiota/genetics
Birds/microbiology/virology
*Ecosystem
Bacteria/genetics/classification
*Biodiversity
Arthropod Vectors/microbiology/virology
Fungi/genetics/classification
Phylogeny
Grassland
Sequence Analysis, DNA
Virome
Viruses/classification/genetics

@article {pmid42824003,
year = {2026},
author = {Qi, G and Wu, Z and Chen, J and Zhang, D and Wang, Q},
title = {Gut microbiota characteristics of gastric cancer patients across distinct pathological stages and their associations with tumor and paratumor mucosal microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1897107},
pmid = {42824003},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; China ; Aged ; Feces/microbiology ; Metagenomics ; Neoplasm Staging ; Dysbiosis ; },
abstract = {Gastric cancer (GC) is closely associated with microbial dysbiosis; however, the spatial-temporal characteristics of the gut, paracancerous, and intratumoral microbiomes, as well as their interrelationships during tumor progression, remain insufficiently defined. This study aimed to characterize these microbiomes in 85 GC patients from Northwest China using shotgun metagenomic sequencing and functional annotation. Clinical samples included feces, tumor tissues, and paratumor mucosal tissues (≥5 cm from the tumor margin), enabling comprehensive profiling of microbial composition at the phylum, genus, and species levels, as well as functional pathway analysis. The results showed that the microbial community was dominated by Firmicutes and Bacteroidetes (combined relative abundance >75%), maintaining structural stability across tumor stages II-IV (Stage I n=2 is only descriptively reported and excluded from formal statistical testing), thereby supporting the "core microbiota resilience" hypothesis. PERMANOVA revealed that tumor stage had a statistically significant yet modest effect on community structure (R[2] = 0.039, P = 0.032). MaAsLin2 identified stage-associated differential genera: Roseburia and Megamonas decreased with advancing stage, whereas Lactobacillus and Enterobacter were enriched in advanced stages (III/IV). Functional pathway analysis revealed stage-specific metabolic remodeling: Stage II was enriched in DNA repair, glycolysis, aromatic amino acid, and nucleotide biosynthesis pathways; Stage IV showed enrichment in protein deamination/demethylation, pyruvate fermentation, and coenzyme metabolism pathways. Correlation analysis further revealed a characteristic pattern of "pathogen enrichment and beneficial bacteria depletion." Fusobacterium nucleatum and Helicobacter pylori exhibited strong positive correlations with GC, whereas short-chain fatty acid-producing bacteria such as Roseburia and Faecalibacterium prausnitzii showed significant negative correlations, particularly in paracancerous tissues. We established multi-layered taxonomic correlation profiles based on intra-cohort microbial shifts, in which Bacteroides stercoris and Bifidobacterium pseudocatenulatum exhibited the most pronounced stage-related abundance changes in the fecal microbiota across tumor stages. Overall, this study systematically delineates the structural stability, stage-specific functional remodeling, and interrelated dynamics of gut, paracancerous, and intratumoral microbiomes in gastric cancer. These findings provide descriptive baseline data of cross-compartment microbiome variation within gastric cancer patients across tumor stages, which only deliver preliminary correlative clues of GC-related microbial shifts and require further multi-cohort verification with non-cancer control populations.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
Female
Male
*Bacteria/classification/genetics/isolation & purification
Middle Aged
China
Aged
Feces/microbiology
Metagenomics
Neoplasm Staging
Dysbiosis

@article {pmid42248819,
year = {2026},
author = {Peng, D and Zhou, J and Xiong, M and Chen, Y and Zhang, Y and Hu, Y and Yang, Y and Xu, J and Zheng, Y and Xu, D},
title = {Gut Microbiota Dysbiosis Drives Lethal Bacterial Enteritis in Sturgeons: Insights From Ex Vivo Cultivation and Metagenomic Investigations.},
journal = {Journal of fish diseases},
volume = {49},
number = {11},
pages = {e70218},
doi = {10.1111/jfd.70218},
pmid = {42248819},
issn = {1365-2761},
support = {D-8006-25-0392//Shanghai Aquatic Wildlife Conservation and Research Center/ ; K2025-02-08-00-12-F00043//Shanghai Municipal Commission of Agriculture and Rural Affairs/ ; },
mesh = {Animals ; *Enteritis/veterinary/microbiology ; *Fish Diseases/microbiology ; *Dysbiosis/veterinary/microbiology ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Bacteria/isolation & purification/genetics/pathogenicity/classification ; *Bacterial Infections/veterinary/microbiology ; },
abstract = {The Chinese sturgeon (Acipenser sinensis) and Yangtze sturgeon (A. dabryanus) are critically endangered flagship species. To investigate the intestinal microbial changes associated with bacterial enteritis in captive populations, we integrated bacterial isolation with metagenomic sequencing to characterize both healthy and maladjusted gut microbiomes. Healthy sturgeons exhibited a stable microbiota dominated by the beneficial Cetobacterium. In contrast, enteritis was consistently associated with severe dysbiosis, characterized by the depletion of these commensals and the massive expansion of opportunistic pathogens, notably Aeromonas and Citrobacter. Culture-based analyses identified A. veronii, C. freundii and Plesiomonas shigelloides as the dominant cultivable bacteria from diseased individuals; these isolates harboured diverse virulence traits and were multidrug-resistant. Crucially, both sturgeon species showed highly similar microbial responses and pathogenic profiles during enteritis. These findings indicate that sturgeon enteritis is closely correlated with a dysbiosis-driven syndrome. Establishing the healthy baseline provides a critical theoretical foundation for screening autochthonous probiotics and developing targeted pathogen control strategies. Furthermore, the striking cross-species commonality validates the Yangtze sturgeon as a viable surrogate model for advancing disease management and conservation in the difficult-to-breed Chinese sturgeon.},
}

Animals
*Enteritis/veterinary/microbiology
*Fish Diseases/microbiology
*Dysbiosis/veterinary/microbiology
*Fishes/microbiology
*Gastrointestinal Microbiome
Metagenomics
Bacteria/isolation & purification/genetics/pathogenicity/classification
*Bacterial Infections/veterinary/microbiology

@article {pmid42417977,
year = {2026},
author = {Yu, SJ and Stanley, D and Van, TTH and Steel, JC and Bajagai, YS},
title = {Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {42417977},
issn = {1432-0614},
support = {PRO-017656//AgriFutures Australia/ ; },
mesh = {Animals ; Humans ; *Chickens/microbiology ; *Metagenomics ; Swine/microbiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; Host Specificity ; Zoonoses/microbiology ; },
abstract = {Integrating human, animal, and environmental health is crucial for combating infectious diseases, as an estimated 60 to 75% of emerging infectious diseases originate from zoonotic sources globally. In this study, we analysed 1274 shotgun metagenomic faecal samples of humans, pigs, and chickens collected across multiple countries to estimate levels of microbial sharing at the species-level genome bins (SGBs) resolution. We confirm that host species, rather than geography, significantly structures the gut microbial community, as shown by alpha and beta diversity analyses. Despite this high host specificity, we identified substantial cross-host sharing of SGBs, including taxa recognised as pathogens such as Escherichia coli, Clostridium perfringens, Clostridium innocuum, Clostridium disporicum, Enterococcus species, and Streptococcus alactolyticus. Core taxa were predominantly host-specific, while non-core taxa were more frequently shared across humans, pigs, and chickens. LEfSe analysis identified distinctive microbial signatures for each host, further supporting differences in community composition. These findings demonstrate that unrelated and geographically distant humans and livestock can harbour highly similar microbial populations with pathogenic potential. This work provides molecular evidence supporting the need for integrated One Health surveillance to better detect, manage, and prevent zoonotic and reverse zoonotic transmission events across interconnected human, animal, and environmental systems. KEY POINTS: • There is substantial cross-host sharing of species-level genome bins, including potential pathogens • Core taxa are predominantly host-specific • Non-core taxa are more likely to be shared across humans, pigs, and chickens.},
}

Animals
Humans
*Chickens/microbiology
*Metagenomics
Swine/microbiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification/pathogenicity
*Gastrointestinal Microbiome/genetics
Host Specificity
Zoonoses/microbiology

@article {pmid42587158,
year = {2026},
author = {Sinha, T and Brushett, S and Fernández-Pato, A and Garmaeva, S and Andreu-Sánchez, S and Spreckels, JE and Mallon, CA and Kuzub, N and Gois, MB and Wu, J and Kruk, M and Jankipersadsing, SA and Dekens, JAM and Gacesa, R and Vila, AV and Bang, C and Perenboom, C and Franke, A and Tytgat, HLP and Mottaz, SC and Peters, L and de Jonge, A and Verkade, HJ and Swertz, MA and Wijmenga, C and Kuipers, F and Scherjon, S and Sikkema, J and Sprikkelman, AB and de Kroon, MLA and Prins, JR and Gordijn, SJ and Koppelman, GH and Reijneveld, SA and , and Fu, J and Yassour, M and Kurilshikov, A and Zhernakova, A},
title = {Maternal influences on infant gut microbiome and health.},
journal = {Nature},
volume = {658},
number = {8134},
pages = {218-229},
pmid = {42587158},
issn = {1476-4687},
mesh = {Humans ; Female ; Infant ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Pregnancy ; Vagina/microbiology ; Milk, Human/microbiology ; Diet ; Adult ; Delivery, Obstetric ; Netherlands ; Infant, Newborn ; *Mothers ; *Infant Health ; Breast Feeding ; Smoking ; Male ; },
abstract = {The establishment of the infant gut microbiome is critical for later health[1,2], yet how it is shaped by maternal and early-life factors remains unclear. Here we metagenomically sequenced 4,526 longitudinal faecal samples from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT, spanning 12 weeks of pregnancy to 1 year postpartum. We integrated these data with 474 clinical and exposure variables, and with ultra-deep sequencing of breast milk and vaginal microbiomes. We observe that the maternal gut microbiome undergoes only subtle changes during pregnancy and postpartum, influenced by diet, infections and pre-pregnancy smoking. The maternal gut microbiome is a major reservoir for infant gut strains, with only occasional transmission from vaginal and breast milk microbiomes. Mother-infant gut strain sharing is time dependent, and higher maternal gut species abundance increases the likelihood of strain transmission. We find that the maternal gut microbiome is a predictor of infant eczema. Mode of delivery and feeding mode primarily shaped the infant gut microbiome and its functional profiles, with maternal exposures also having a role. Of 585 vaginally delivered infants, 155 were born at home, but home delivery was only moderately associated with infant gut microbiome composition, similar to other birth parameters such as duration of pushing and ruptured membranes. Overall, we highlight the central role of the mother and her microbiome in shaping the infant gut ecosystem and early health outcomes.},
}

Humans
Female
Infant
Feces/microbiology
*Gastrointestinal Microbiome/physiology/genetics
Pregnancy
Vagina/microbiology
Milk, Human/microbiology
Diet
Adult
Delivery, Obstetric
Netherlands
Infant, Newborn
*Mothers
*Infant Health
Breast Feeding
Smoking
Male

@article {pmid42767308,
year = {2026},
author = {Zhao, Y and Zheng, M and An, J and Xiu, W and Yao, J and Qi, Z and Wu, H and Lv, Y and Liu, X},
title = {Characterization and soil remediation performance of a natural polycyclic aromatic hydrocarbon-degrading bacterial consortium (PD1).},
journal = {Environmental research},
volume = {308},
number = {Pt 2},
pages = {125717},
doi = {10.1016/j.envres.2026.125717},
pmid = {42767308},
issn = {1096-0953},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; *Microbial Consortia ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent and toxic soil contaminants that pose significant risks to environmental and human health. In this study, a natural PAHs-degrading microbial consortium (PD1) was enriched from coal gangue backfill soil using phenanthrene as the sole carbon source. PD1 features Acidovorax and Pigmentiphaga as the dominant functional genera. The consortium achieved 70% phenanthrene removal within 3 days in liquid culture and demonstrated robust soil remediation performance, with 74.7% and 89.5% removal within 3 and 9 days, respectively, significantly outperforming native conditions. PD1 also degraded fluoranthene, pyrene, and benzo[a]anthracene, and exhibited strong tolerance to As(III) at concentrations up to 50 mg/L, while maintaining stable activity during long-term storage at 4°C. Metagenomic and metatranscriptomic analyses, together with the tentative annotation of two early-stage intermediates, supported a proposed major route for PHE degradation in PD1. The cooperative interactions among various functional microorganisms within the consortium drive the efficient degradation of PHE. These results establish PD1 as a robust, synergistic consortium with strong potential for the bioremediation of PAHs-contaminated soils.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Soil Pollutants/metabolism
*Soil Microbiology
Biodegradation, Environmental
*Bacteria/metabolism/genetics
*Microbial Consortia

@article {pmid42813505,
year = {2026},
author = {Huang, S and Sun, S and Zhao, Z and Gao, D and Zhang, W and Zhou, N and Jin, Y and Jin, B and Sun, D},
title = {Associations of Gut Microbiota Composition and Fecal Metabolomic Profiles in Patients With Acquired Premature Ejaculation: A Cross-Sectional Pilot Study.},
journal = {American journal of men's health},
volume = {20},
number = {5},
pages = {15579883261493263},
doi = {10.1177/15579883261493263},
pmid = {42813505},
issn = {1557-9891},
mesh = {Humans ; Male ; Pilot Projects ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Premature Ejaculation/microbiology/metabolism ; Metabolomics ; Case-Control Studies ; *Metabolome ; },
abstract = {Premature ejaculation (PE) is a prevalent male sexual disorder with an incompletely understood pathogenesis and limited effective therapeutic strategies. Although the gut microbiota has been implicated in several diseases, its association with PE remains unclear. Metabolomic analyses and metagenomic sequencing were performed to compare the intestinal microbiota profiles between 20 patients with PE and 20 healthy controls, investigating the association between PE and gut microbiota. Comprehensive analysis revealed distinct microbial signatures between PE and control groups. The PE group exhibited significantly reduced relative abundances of Bifidobacteriaceae bacterium, Blautia, Coprobacillus, Ruminococcus sp. ctHOG1, Siphoviridae, and Alistipes. Metabolomic profiling identified 150 upregulated and 73 downregulated metabolites between the two groups. Kyoto encyclopedia of genes and genomes pathway enrichment analysis indicated significant enrichment of several potential signaling pathways in the PE group. This study characterized distinct gut microbiota features in patients with PE compared with healthy controls and investigated microbiota-associated pathways potentially related to PE through integrated metabolomics analysis. The findings provide preliminary insights into microbiome-associated alterations in PE.},
}

Humans
Male
Pilot Projects
Adult
*Feces/microbiology/chemistry
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Premature Ejaculation/microbiology/metabolism
Metabolomics
Case-Control Studies
*Metabolome

@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {31-44},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
mesh = {Animals ; *Ruminants/virology ; *Gastrointestinal Tract/virology ; *Virome/genetics ; Metagenome ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; },
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.

OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.

METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).

RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.

CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}

Animals
*Ruminants/virology
*Gastrointestinal Tract/virology
*Virome/genetics
Metagenome
*Viruses/genetics/classification
*Gastrointestinal Microbiome/genetics

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {285-295},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
mesh = {Animals ; *Cecum/microbiology/drug effects/metabolism ; Male ; Mice ; Humans ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Metabolomics/methods ; Liver/metabolism/drug effects ; Microbiota ; Multiomics ; *Carbon ; },
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

Animals
*Cecum/microbiology/drug effects/metabolism
Male
Mice
Humans
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Metabolomics/methods
Liver/metabolism/drug effects
Microbiota
Multiomics
*Carbon

@article {pmid41539600,
year = {2026},
author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z},
title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.},
journal = {Journal of advanced research},
volume = {88},
number = {},
pages = {77-89},
doi = {10.1016/j.jare.2026.01.022},
pmid = {41539600},
issn = {2090-1224},
mesh = {Animals ; *Tryptophan/metabolism ; *Chickens/growth & development/microbiology/metabolism ; *Immunoglobulin A, Secretory/metabolism ; *Gastrointestinal Microbiome ; Cecum/microbiology/metabolism ; Probiotics ; Metagenome ; },
abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.

OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.

METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.

RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.

CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.},
}

Animals
*Tryptophan/metabolism
*Chickens/growth & development/microbiology/metabolism
*Immunoglobulin A, Secretory/metabolism
*Gastrointestinal Microbiome
Cecum/microbiology/metabolism
Probiotics
Metagenome

@article {pmid42155010,
year = {2026},
author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN},
title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {212},
number = {10},
pages = {2455-2466},
doi = {10.1093/ajrccm/aamag249},
pmid = {42155010},
issn = {1535-4970},
support = {R01 HL162659/HL/NHLBI NIH HHS/United States ; UO1HL128964//NIH/NHLBI/ ; R01HL162659//IPF Foundation, and Veracyte Inc/ ; //NHLBI/ ; K23HL150301//Drews Sarcoidosis Research Fund/ ; R01HL176659//Drews Sarcoidosis Research Fund/ ; UH3 HL145266//Drews Sarcoidosis Research Fund/ ; R01HL130796//Drews Sarcoidosis Research Fund/ ; R01HL153028//Drews Sarcoidosis Research Fund/ ; R35HL176572//Drews Sarcoidosis Research Fund/ ; R35GM16312//Drews Sarcoidosis Research Fund/ ; //NIGMS/ ; },
mesh = {Humans ; *Idiopathic Pulmonary Fibrosis/mortality/microbiology/drug therapy/physiopathology ; Female ; Male ; *Gastrointestinal Microbiome ; Severity of Illness Index ; Aged ; Middle Aged ; Pyridones/therapeutic use ; },
abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the role of gut microbiota in IPF pathogenesis is unknown.

OBJECTIVES: Determine associations between gut microbiota, disease severity, and lung transplant-free survival in IPF.

METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n = 411). CleanUP-IPF investigated the clinical efficacy of long-term antimicrobials in IPF. 16S ribosomal RNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models, and Cox regression models.

MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted diffusing capacity of lung for carbon monoxide). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (hazard ratio [HR] = 0.34; 95% CI, 0.14-0.87; P = .02) in patients not assigned to antimicrobial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long-term cotrimoxazole had worse survival (HR = 6.09; 95% CI, 1.36-27.27; P = .02). Survival in pirfenidone-treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.

CONCLUSIONS: In exploratory post hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.},
}

Humans
*Idiopathic Pulmonary Fibrosis/mortality/microbiology/drug therapy/physiopathology
Female
Male
*Gastrointestinal Microbiome
Severity of Illness Index
Aged
Middle Aged
Pyridones/therapeutic use

@article {pmid42242497,
year = {2026},
author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and , and Segre, JA and Sereti, I and Kong, HH},
title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.},
journal = {The Journal of investigative dermatology},
volume = {146},
number = {10},
pages = {2840-2849.e7},
pmid = {42242497},
issn = {1523-1747},
support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; ZIA AR041220/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Skin Microbiome/immunology ; *HIV Infections/immunology/drug therapy/microbiology/complications ; *Skin/microbiology/immunology ; Female ; Male ; Adult ; CD4-Positive T-Lymphocytes/immunology ; *Lymphopenia/immunology/microbiology/drug therapy ; Middle Aged ; *T-Lymphocytopenia, Idiopathic CD4-Positive/immunology/microbiology/drug therapy ; Human Papillomavirus Viruses/isolation & purification/immunology ; Longitudinal Studies ; *Microbiota/immunology ; },
abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia, a rare clinical syndrome with an obscure cause, and people living with HIV are 2 etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to examine the multi-kingdom taxonomic diversity of skin microbiomes in patients with idiopathic CD4 lymphopenia and people living with HIV who were followed longitudinally before and after initiation of antiretroviral therapy. Compared with healthy individuals, the skin microbiomes of patients with idiopathic CD4 lymphopenia and antiretroviral therapy-naïve people living with HIV showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy controls. In people living with HIV, high-oncogenic-risk human papillomaviruses persisted after 2 months of antiretroviral therapy but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.},
}

Humans
*Skin Microbiome/immunology
*HIV Infections/immunology/drug therapy/microbiology/complications
*Skin/microbiology/immunology
Female
Male
Adult
CD4-Positive T-Lymphocytes/immunology
*Lymphopenia/immunology/microbiology/drug therapy
Middle Aged
*T-Lymphocytopenia, Idiopathic CD4-Positive/immunology/microbiology/drug therapy
Human Papillomavirus Viruses/isolation & purification/immunology
Longitudinal Studies
*Microbiota/immunology

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenome ; Salinity ; *Archaea/classification/genetics/isolation & purification/metabolism ; Biodiversity ; *Extremophiles/genetics/classification/isolation & purification ; India ; Phylogeny ; *Seawater/microbiology/chemistry ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism
Metagenome
Salinity
*Archaea/classification/genetics/isolation & purification/metabolism
Biodiversity
*Extremophiles/genetics/classification/isolation & purification
India
Phylogeny
*Seawater/microbiology/chemistry

@article {pmid42554630,
year = {2026},
author = {Tandon, A and Bais, AK and Shrinet, J and Tripathi, V and Gupta, D},
title = {Effect of alcohol and smoking on methamphetamine users' oral microbiome and metabolome.},
journal = {The American journal of drug and alcohol abuse},
volume = {52},
number = {4},
pages = {442-454},
doi = {10.1080/00952990.2026.2697752},
pmid = {42554630},
issn = {1097-9891},
mesh = {Humans ; *Microbiota/drug effects ; Female ; *Methamphetamine ; *Metabolome/drug effects ; *Mouth/microbiology ; Male ; *Alcohol Drinking/metabolism ; Adult ; *Amphetamine-Related Disorders/microbiology/metabolism ; Metabolomics ; *Tobacco Smoking/metabolism ; },
abstract = {Background: The oral microbiome comprises the microbial communities inhabiting the oral cavity, whereas the oral metabolome reflects the small molecules generated by host and microbial metabolic activity. These systems may provide insight into substance-related physiological disruption, including altered inflammation, immune signaling, and host - microbial interactions. Although the individual effects of methamphetamine, alcohol, and smoking have been explored, their combined impact on these systems remains largely unexplored.Objectives: To investigate the metabolic and microbiome alterations associated with chronic methamphetamine use in individuals with alcohol and tobacco use.Methods: High-throughput metabolomic and microbiome datasets from methamphetamine users (Males:168, Females: 50), stratified by self-reported tobacco smoking and alcohol use, were analyzed using integrative bioinformatics approaches, including multivariate and pathway enrichment analyses, to identify dysregulated metabolic pathways and microbial alterations across defined subgroups.Results: The study revealed significant upregulation in metabolites like prostaglandin E2 (log-2-fold-change: 2.63, Cohen's D: |~0.881|, p-val: 7.1 × 10[-10]) and glutamylisoleucine (log-2-fold-change: 1.42, Cohen's D: |~0.88|, p-val: 2.5 × 10[-2]). Microbes such as Bacteroides (log-2-fold-change: -4.91, Cohen's D: |~1.95|, p-val: 1.3 × 10[-4]) and Brachymonas (log-2-fold-change: -2.47, Cohen's D: |~1.09|, p-val: 5.8 × 10[-3]) were significantly downregulated. This suggests that long-term concurrent methamphetamine use, alcohol consumption, and smoking are associated with alterations in microbial and metabolic pathways related to oxidative stress, glutathione metabolism, and neuroactive signaling.Conclusions: The oral microbiome and metabolomic profiles may serve as accessible indicators of substance-related biological disruption. They may also help identify clinically relevant targets for monitoring risk, guiding personalized interventions, and developing informed strategies to support recovery.},
}

Humans
*Microbiota/drug effects
Female
*Methamphetamine
*Metabolome/drug effects
*Mouth/microbiology
Male
*Alcohol Drinking/metabolism
Adult
*Amphetamine-Related Disorders/microbiology/metabolism
Metabolomics
*Tobacco Smoking/metabolism

@article {pmid42647084,
year = {2026},
author = {Díaz-Díaz, LM and Estremera-Rodriguez, L and Rojas-Correa, M and Quintana, MDC and Madziar, C and Hickey, DC and Vargas Robles, D and Méndez, Y and Santiago, A and Bermudez, D and Olendzki, B and Torres, EA and Maldonado-Contreras, A},
title = {Diet quality, gut microbiome, and inflammatory signatures in Puerto Rican adults with Crohn disease: a multidimensional analysis.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {10},
pages = {1993-2003},
doi = {10.1093/ibd/izag161},
pmid = {42647084},
issn = {1536-4844},
support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
mesh = {Humans ; Female ; Male ; *Crohn Disease/microbiology ; Adult ; Puerto Rico/epidemiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diet/standards ; Middle Aged ; Feces/chemistry/microbiology ; *Inflammation ; Biomarkers/analysis ; Young Adult ; C-Reactive Protein/analysis ; },
abstract = {BACKGROUND AND AIMS: Diet is increasingly recognized as a modifiable factor influencing gut microbiome and outcomes in Crohn disease (CD), yet data in underrepresented populations remain limited. We evaluated diet quality, dietary patterns, gut microbiome composition, inflammatory markers, and patient-reported outcomes in adults with CD from Puerto Rico.

METHODS: We conducted a cross-sectional analysis of 60 adults with CD enrolled prior to dietary intervention in a parent study. Dietary intake was assessed using 24-hour recalls and evaluated using the Healthy Eating Index-2015 (HEI-2015), Alternative Healthy Eating Index-2010 (AHEI-2010), and exploratory dietary pattern analysis. The gut microbiome was assessed by shotgun metagenomic sequencing. Clinical outcomes included fecal calprotectin, C-reactive protein (CRP), a 96-cytokine panel, short Crohn Disease Activity Index (sCDAI), and short Inflammatory Bowel Disease Questionnaire (sIBDQ). Associations were evaluated using unadjusted and adjusted models with false discovery rate (FDR) correction.

RESULTS: Overall diet quality was poor and characterized by low intake of fruits, vegetables, whole grains, and fiber, alongside high intake of saturated fat, added sugars, and animal-derived protein. Four dietary patterns were identified: vegetable-rich, dairy-rich, fruit-rich, and coffee/sweetener-rich. Participants adhering to the fruit-rich pattern exhibited the highest diet quality scores. Higher HEI-2015 scores were associated with greater gut microbial diversity and differences in overall microbiome composition. Participants with greater adherence to the vegetable-rich pattern showed modest increases in microbial diversity. Exploratory analyses suggested that higher fruit intake and adherence to a fruit-rich dietary pattern were associated with lower fecal calprotectin and CRP levels, whereas adherence to a vegetable-rich pattern was associated with better health-related quality of life (HRQoL) and adherence to a coffee/sweetener-rich pattern was associated with a worse symptom burden. However, no associations between dietary metrics and inflammatory markers, cytokines, or clinical outcomes remained significant after FDR correction. Most participants were in clinical remission despite substantial impairment in HRQoL.

CONCLUSIONS: Adults with CD in Puerto Rico exhibited poor diet quality that was associated with gut microbial diversity and exploratory differences in clinical outcomes. While these findings support the influence of diet on the microbiome and clinical outcomes, larger longitudinal studies are needed to determine whether dietary improvements can influence disease outcomes this underrepresented population.},
}

Humans
Female
Male
*Crohn Disease/microbiology
Adult
Puerto Rico/epidemiology
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Diet/standards
Middle Aged
Feces/chemistry/microbiology
*Inflammation
Biomarkers/analysis
Young Adult
C-Reactive Protein/analysis

@article {pmid42806510,
year = {2026},
author = {Singh, S and Sharma, VK and Shrivastav, D and Kushwaha, JM and Mishra, MK and Beg, MMA},
title = {From Rhizosphere to Resistance: Microbe-Plant Interactions in Eco-Smart Biocontrol.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70398},
pmid = {42806510},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Plant Diseases/prevention & control/microbiology ; Pest Control, Biological/methods ; Soil Microbiology ; Plant Roots/microbiology ; *Biological Control Agents ; Microbiota ; Multiomics ; Crops, Agricultural/microbiology ; Fungi ; *Plants/microbiology ; },
abstract = {The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.},
}

*Rhizosphere
*Plant Diseases/prevention & control/microbiology
Pest Control, Biological/methods
Soil Microbiology
Plant Roots/microbiology
*Biological Control Agents
Microbiota
Multiomics
Crops, Agricultural/microbiology
Fungi
*Plants/microbiology

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811876,
year = {2026},
author = {Bo, T and Liu, X and Liu, M and Shen, W and Zhang, X and Guo, H and Wen, J},
title = {Winter Caching of Artemisia frigida Is Associated With Host Physiological and Gut Microbial Variation in Brandt's Voles.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70576},
doi = {10.1111/mec.70576},
pmid = {42811876},
issn = {1365-294X},
support = {32470487//National Natural Science Foundation of China/ ; 32201278//National Natural Science Foundation of China/ ; 2023FY100305//Science & Technology Fundamental Resources Investigation Program/ ; 5242016//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {Animals ; *Arvicolinae/physiology/microbiology/genetics ; Seasons ; *Artemisia ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Hypothalamus/metabolism ; Cold Temperature ; Transcriptome ; Lipid Metabolism/genetics ; },
abstract = {Seasonal variation in food resources represents a major ecological challenge for wild herbivores, yet how naturally selected dietary resources become associated with host and microbial responses remains poorly understood. During winter, Brandt's voles (Lasiopodomys brandtii) cache large amounts of Artemisia frigida, suggesting that this plant may have ecological significance beyond its nutritional value. However, the biological basis underlying this seasonal food preference remains unclear. Here, using Brandt's voles as a model system, we investigated whether the naturally selected winter food A. frigida was associated with coordinated variation in host physiology and gut microbial organization under cold conditions. By integrating physiological phenotyping, hypothalamic neuroendocrine analyses, adipose tissue transcriptomics, shotgun metagenomics and metagenomic binning, we characterized host and microbial responses across multiple biological levels. Dietary A. frigida was associated with altered hypothalamic AgRP expression, increased UCP1 expression in BAT and transcriptional changes related to lipid metabolism and thermogenic pathways during cold exposure. Supplement of A. frigida was associated with changes in gut microbial community structure, enrichment of specific bacterial taxa and shifts in predicted microbial functional potential. Genome-resolved analyses further reconstructed 277 non-redundant metagenome-assembled genomes, enabling assessment of microbial ecological variation associated with seasonal food conditions. Together, our findings provide molecular ecological evidence linking winter caching of A. frigida with coordinated variation in host physiology and gut microbial organization, highlighting seasonal dietary resources as an overlooked component of ecological variation in wildlife.},
}

Animals
*Arvicolinae/physiology/microbiology/genetics
Seasons
*Artemisia
*Gastrointestinal Microbiome/genetics
Metagenomics
Hypothalamus/metabolism
Cold Temperature
Transcriptome
Lipid Metabolism/genetics

@article {pmid42320811,
year = {2026},
author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L},
title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and Enhances with αPD-1 therapy.},
journal = {International journal of biological macromolecules},
volume = {377},
number = {},
pages = {153116},
doi = {10.1016/j.ijbiomac.2026.153116},
pmid = {42320811},
issn = {1879-0003},
mesh = {Animals ; *Polygonatum/chemistry ; *Polysaccharides/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Molecular Weight ; Cell Line, Tumor ; Humans ; Immune Checkpoint Inhibitors/pharmacology ; Cell Proliferation/drug effects ; Female ; },
abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-associated mechanisms and potentiates anti-PD-1 therapy.

MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.

RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-α reduced. In vitro, butyrate enhanced T-cell production of IFN-γ, IL-2 and granzyme-B and counteracted IFN-γ-induced PD-L1 expression. In vivo, PSP-H reduced tumor HDAC activity and increased histone acetylation while inducing adaptive STAT1/PD-L1 upregulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H + anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.

CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by reprogramming systemic immunity while inducing targetable adaptive resistance.},
}

Animals
*Polygonatum/chemistry
*Polysaccharides/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Mice
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Molecular Weight
Cell Line, Tumor
Humans
Immune Checkpoint Inhibitors/pharmacology
Cell Proliferation/drug effects
Female

@article {pmid42410398,
year = {2026},
author = {Xiang, X and Zhu, Y and Wang, T and Cheng, K and Ming, Y},
title = {Association between salivary microbiota-related amino acid metabolic dysregulation and tacrolimus-induced gingival overgrowth following kidney transplantation.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {42410398},
issn = {1472-6831},
support = {81771722//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Kidney Transplantation ; *Gingival Overgrowth/chemically induced/microbiology ; *Tacrolimus/adverse effects ; *Immunosuppressive Agents/adverse effects ; *Microbiota ; *Amino Acids/metabolism ; *Saliva/microbiology/metabolism ; Female ; Male ; Middle Aged ; Case-Control Studies ; Adult ; },
abstract = {BACKGROUND: Kidney transplant (KT) recipients require lifelong immunosuppressive therapy to prevent allograft rejection. Drug-induced gingival overgrowth (DIGO) is a notable adverse effect of tacrolimus, for which effective preventive or therapeutic strategies are lacking. Dysbiosis of the oral microbiota has been implicated as a major risk factor for DIGO. However, its mechanistic role remains poorly understood.

RESULTS: Twenty KT recipients with newly diagnosed DIGO while receiving tacrolimus were enrolled, along with 20 matched controls with stable graft function. Salivary samples were collected and subjected to metagenomic and untargeted metabolomic profiling. Taxonomic analysis revealed greater microbial heterogeneity in DIGO patients compared to more interconnected communities observed in controls. Periodontitis-associated taxon, including Porphyromonas gingivalis, were enriched in the DIGO group. Multiple differentially expressed microbial genes and metabolites were identified, predominantly enriched in disordered amino acid metabolic pathways. Key metabolites-such as L-proline, carnosine, choline, 5-aminolevulinic acid, and spermidine-showed strong associations with DIGO-related taxon.

CONCLUSION: A strong association was observed between salivary microbial composition, metabolic profiles, and DIGO. The identified microbiota and metabolite alterations suggest a potential link between amino acid metabolic dysregulation and gingival fibroblast-related pathways in DIGO. These findings provide new insights into the biological features of DIGO and offer a foundation for future mechanistic and therapeutic studies.},
}

Humans
*Kidney Transplantation
*Gingival Overgrowth/chemically induced/microbiology
*Tacrolimus/adverse effects
*Immunosuppressive Agents/adverse effects
*Microbiota
*Amino Acids/metabolism
*Saliva/microbiology/metabolism
Female
Male
Middle Aged
Case-Control Studies
Adult

@article {pmid42532775,
year = {2026},
author = {Nealon, NJ},
title = {Next-Generation Sequencing in Companion Animal Practice for Infectious Disease Diagnostics and Characterizing Normal Microbiomes.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {56},
number = {6},
pages = {1323-1336},
doi = {10.1016/j.cvsm.2026.06.005},
pmid = {42532775},
issn = {1878-1306},
mesh = {Animals ; *High-Throughput Nucleotide Sequencing/veterinary/methods ; *Microbiota/genetics ; *Pets/microbiology ; *Communicable Diseases/veterinary/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Cats ; },
abstract = {The purpose of this article is to review and compare the most common and emergent next-generation sequencing methodologies used in small animal veterinary practice, with a focus on their applications to bacterial diagnostics and assessment of the healthy gut microbiome. These methodologies include whole genome sequencing, amplicon sequencing, shotgun metagenomic sequencing, and transcriptomics. Understanding the benefits and limitations of each methodology will help small animal practitioners to make informed decisions for their patients and maximize the utility of each test as part of a complete patient health assessment.},
}

Animals
*High-Throughput Nucleotide Sequencing/veterinary/methods
*Microbiota/genetics
*Pets/microbiology
*Communicable Diseases/veterinary/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics
Cats