@article {pmid42420666,
year = {2026},
author = {Ounjai, S and Liu, H and Zhou, Z and Correia, MP and Creedy, TJ and Andújar, C and Arribas, P and Vogler, AP},
title = {Phylogenetic Authentication of Amplicon Sequence Variants in Single-Specimen Metabarcoding of Tropical Insects.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70178},
pmid = {42420666},
issn = {1755-0998},
support = {//Institute for the Promotion of Teaching Science and Technology/ ; //Biodiversity Initiative of the Natural History Museum/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods/standards ; *Phylogeny ; *Coleoptera/classification/genetics ; Tropical Climate ; *Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA ; Genetic Variation ; DNA, Mitochondrial/genetics ; },
abstract = {High-throughput sequencing (HTS) allows large-scale DNA barcoding of individually tagged specimens ('megabarcoding'), but deep amplicon sequencing produces a mixture of authentic mitochondrial sequences together with nuclear pseudogenes (NUMTs), environmental and cross-sample contaminants, and sequencing artefacts. Standard approaches relying on read clustering or dominant-read selection often fail to classify these types, leading to incorrect taxonomic identifications and species counts. We developed an authentication framework by integrating abundance filtering, phylogenetic placement and taxonomic congruence. The workflow was applied to 18,533 morphospecies of tropical beetles (Coleoptera) from multiple biogeographic regions, which were imaged for family-level identification, prior to individual Illumina barcoding. Sequencing yielded > 36 million reads and 64,544 unique ASVs, which were evaluated against a reference phylogeny of > 13,000 mitogenomes. Authentication succeeded for 86.5% of quality-passing specimens (15,901 ASVs). Non-authentic sequences were technical artefacts (58.0%), environmental contamination including prey DNA (14.2%), intra-individual variants (NUMTs, heteroplasmy; 11.3%) and cross-sample contamination (7.5%). Authentication success and the proportions of failure categories varied markedly across trap types, sampling campaigns, taxonomic groups and sequencing runs. We identified 930 confirmed NUMTs based on consistent co-occurrence patterns and phylogenetic proximity to authenticated haplotypes. Single-specimen HTS data contain substantial biological and technical complexity not resolved by standard filtering methods. Our pipeline-agnostic, phylogenetically informed authentication framework achieves robust recovery of validated barcodes while retaining informative secondary variants, improving the accuracy of molecular ASV data to a standard sufficient for inclusion in barcode reference databases and the phylogenetically informed DNA barcoding of tropical insects.},
}

Animals
*DNA Barcoding, Taxonomic/methods/standards
*Phylogeny
*Coleoptera/classification/genetics
Tropical Climate
*Metagenomics/methods/standards
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA
Genetic Variation
DNA, Mitochondrial/genetics

@article {pmid42421935,
year = {2026},
author = {Memida, T and Jaar, JC and Chen, T and Cao, G and Kuriki, N and Abdolahinia, ED and Okamoto, M and Shindo, S and Yamashita, S and He, X and Suzuki, M and Vardar, S and Kawai, T and Han, X},
title = {Hyperglycemia and systemic inflammation differentially shape immune dysregulation, tissue destruction, and microbiota in experimental periodontitis and peri-implantitis in diabetic mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847456},
pmid = {42421935},
issn = {1664-3224},
mesh = {Animals ; *Peri-Implantitis/immunology/microbiology/pathology/etiology ; *Periodontitis/immunology/microbiology/pathology/etiology ; Mice ; *Hyperglycemia/immunology/microbiology ; *Microbiota/immunology ; *Diabetes Mellitus, Experimental/immunology/complications/microbiology ; *Inflammation/immunology ; Disease Models, Animal ; Cytokines/metabolism ; Male ; },
abstract = {AIM: To investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.

MATERIALS AND METHODS: After implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.

RESULTS: Liraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3[+] Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.

CONCLUSIONS: Diabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.},
}

Animals
*Peri-Implantitis/immunology/microbiology/pathology/etiology
*Periodontitis/immunology/microbiology/pathology/etiology
Mice
*Hyperglycemia/immunology/microbiology
*Microbiota/immunology
*Diabetes Mellitus, Experimental/immunology/complications/microbiology
*Inflammation/immunology
Disease Models, Animal
Cytokines/metabolism
Male

@article {pmid42120930,
year = {2026},
author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X},
title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42120930},
issn = {2045-2322},
support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/complications ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome ; Female ; *Coronary Artery Disease/microbiology/metabolism/complications ; Middle Aged ; Metabolome ; Aged ; Case-Control Studies ; },
abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism/complications
*Metabolomics/methods
Male
*Gastrointestinal Microbiome
Female
*Coronary Artery Disease/microbiology/metabolism/complications
Middle Aged
Metabolome
Aged
Case-Control Studies

@article {pmid42229568,
year = {2026},
author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G},
title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.},
journal = {Environmental research},
volume = {305},
number = {Pt 1},
pages = {124851},
doi = {10.1016/j.envres.2026.124851},
pmid = {42229568},
issn = {1096-0953},
mesh = {*Wetlands ; *Soil Microbiology ; *Soil/chemistry ; *Rain ; *Carbon/metabolism/analysis ; *Microbiota ; Carbon Cycle ; Metagenomics ; *Carbon Sequestration ; },
abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (±40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.},
}

*Wetlands
*Soil Microbiology
*Soil/chemistry
*Rain
*Carbon/metabolism/analysis
*Microbiota
Carbon Cycle
Metagenomics
*Carbon Sequestration

@article {pmid42241983,
year = {2026},
author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M},
title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.},
journal = {International journal of food microbiology},
volume = {459},
number = {},
pages = {111881},
doi = {10.1016/j.ijfoodmicro.2026.111881},
pmid = {42241983},
issn = {1879-3460},
mesh = {*Cheese/microbiology/analysis ; Taste ; *Food Microbiology ; *Microbiota ; Humans ; Bacteria/classification/isolation & purification/genetics ; Volatile Organic Compounds/analysis ; Fungi/isolation & purification/genetics/classification ; Odorants/analysis ; Metagenomics ; },
abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.},
}

*Cheese/microbiology/analysis
Taste
*Food Microbiology
*Microbiota
Humans
Bacteria/classification/isolation & purification/genetics
Volatile Organic Compounds/analysis
Fungi/isolation & purification/genetics/classification
Odorants/analysis
Metagenomics

@article {pmid42302785,
year = {2026},
author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X},
title = {Power and sample-size estimation in human microbiome research.},
journal = {Med (New York, N.Y.)},
volume = {7},
number = {7},
pages = {101174},
doi = {10.1016/j.medj.2026.101174},
pmid = {42302785},
issn = {2666-6340},
mesh = {Humans ; *Microbiota ; Sample Size ; *Research Design ; Metagenomics/methods ; Models, Statistical ; },
abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.},
}

Humans
*Microbiota
Sample Size
*Research Design
Metagenomics/methods
Models, Statistical

@article {pmid42335503,
year = {2026},
author = {Liu, LM and Fang, HB and Wang, YF and Zhang, YL and Yu, QQ and Zhang, WY and Liu, J and Miao, H and Zhao, YY},
title = {Niaoduqing particles ameliorated tubulointerstitial fibrosis by suppressing IκB/NF-κB signalling pathway via inhibiting host- and gut microbiota-mediated tryptophan co-metabolism.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128592},
doi = {10.1016/j.micres.2026.128592},
pmid = {42335503},
issn = {1618-0623},
mesh = {Animals ; *Signal Transduction/drug effects ; Rats ; *Tryptophan/metabolism ; *NF-kappa B/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Fibrosis/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Rats, Sprague-Dawley ; Disease Models, Animal ; *I-kappa B Proteins/metabolism ; Bacteria/classification/genetics/drug effects ; Renal Insufficiency, Chronic/drug therapy ; Metabolomics ; Feces/microbiology ; Ureteral Obstruction ; },
abstract = {Tubulointerstitial fibrosis (TIF) is an inevitable outcome of progressive chronic kidney disease (CKD). Niaoduqing particles (NDQ) were developed for the treatment of CKD. However, the molecular mechanisms underlying the effect of NDQ on TIF remain unclear. Fecal gut microbiota (GM) and serum metabolites were analyzed using metagenomics and metabolomics in unilateral ureteral obstruction (UUO)-induced TIF rats. NDQ treatment attenuated UUO-induced TIF in rats in a dose- and time-dependent manner. The increased abundance of eight pathogenic bacteria, including Bacillus wiedmannii, Enterococcus mundtii and Fusobacterium varium, showed strong positive correlations with TID scores, whereas the reduced abundance of two probiotic bacteria, Ruminococcus flavefaciens and Clostridium celatum, showed strong negative correlations with tubulointerstitial damage (TID) scores. NDQ treatment reversed these aberrant microbial alterations, indicating its capacity to remodel GM dysbiosis. TID scores were strongly correlated with host- and GM-mediated tryptophan co-metabolites, including indoxyl sulfate, tryptamine and indole-3-acetic acid, in both TIF- and NDQ-treated TIF rats, and NDQ intervention normalized these metabolic disturbances. Notably, Fusobacterium varium and Enterococcus faecium exhibited strong linear correlations with indoxyl sulfate, indole-3-acetic acid, and indole-3-aldehyde in the TIF rat model. Furthermore, NDQ suppressed IκB/NF-κB signaling pathway in both TIF rats and TGF-β1-induced NRK-52E cells. These inhibitory effects were partially reversed by NF-κB p65 knockdown. This study is the first to demonstrate that NDQ alleviates TIF by reshaping microbial dysbiosis and modulating host- and GM-mediated tryptophan metabolism. These findings support that NDQ mitigates TIF by suppressing IκB/NF-κB signaling pathway through regulation of host-microbiota-derived tryptophan metabolism.},
}

Animals
*Signal Transduction/drug effects
Rats
*Tryptophan/metabolism
*NF-kappa B/metabolism
Male
*Gastrointestinal Microbiome/drug effects
Fibrosis/drug therapy
*Drugs, Chinese Herbal/pharmacology
Rats, Sprague-Dawley
Disease Models, Animal
*I-kappa B Proteins/metabolism
Bacteria/classification/genetics/drug effects
Renal Insufficiency, Chronic/drug therapy
Metabolomics
Feces/microbiology
Ureteral Obstruction

@article {pmid42391940,
year = {2026},
author = {Wang, J and Guo, C and Pu, X},
title = {Metabolic filtering as a putative mechanism linking soil metabolome and microbial community assembly along a lake expansion gradient.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128601},
doi = {10.1016/j.micres.2026.128601},
pmid = {42391940},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Metabolome ; *Lakes/microbiology ; *Soil/chemistry ; *Microbiota/physiology ; Ecosystem ; Multiomics ; Bacteria/classification/metabolism/genetics ; Metabolomics ; Metagenomics ; Tibet ; Salinity ; },
abstract = {Climate-driven lake expansion across the Qinghai-Tibet Plateau induces profound edaphic shifts, but how these abiotic changes shape soil microbial assembly remains unclear. Soil metagenomics and metabolomics were integrated along a 0-10 km spatial gradient at Gahai. Redundancy analysis (RDA) identified moisture (NDWI) and salinity (SI) as primary ecosystem drivers. Structural equation modeling (SEM) provided exploratory evidence consistent with a mediation pathway (P = 0.64, CFI = 1, RMSEA = 0), in which environmental factors potentially influenced microbial community structure indirectly, via reshaping the soil metabolome rather than through a direct path. Moisture availability exerted a strong negative effect on soil metabolic profiles (λ = -0.93), leading to a pronounced negative correlation between the metabolome and microbial community (λ= -0.97). Multi-omics integration attributed this pattern to stress-induced accumulation of defensive metabolites, including Feruloylputrescine and 3-Methylthiopropyl-desulfoglucosinolate. These compounds showed significant negative correlations with dominant genera (e.g., Candidatus Kryptobacter). This "metabolic filtering" is hypothesized to selectively limit the presence of non-adapted taxa based solely on correlational SEM and network analyses, supporting our tentative hypothesis that increasing environmental stress may promote a transition from competitive interactions toward patterns consistent with stronger deterministic filtering. Our exploratory findings suggest that the soil metabolome acts as a functional interface mediating microbial adaptation and strategic resource allocation to lake expansion in this high-altitude saline-alkali system. However, due to regional heterogeneity, these patterns provide a theoretical baseline for plateau lake ecosystems and should be applied with caution to broader geographic areas.},
}

*Soil Microbiology
*Metabolome
*Lakes/microbiology
*Soil/chemistry
*Microbiota/physiology
Ecosystem
Multiomics
Bacteria/classification/metabolism/genetics
Metabolomics
Metagenomics
Tibet
Salinity

@article {pmid42391942,
year = {2026},
author = {Castellano-Hinojosa, A and de Freitas, J and de Carvalho, DU and Monus, BD and González-López, J and Strauss, SL and Albrecht, U},
title = {Compartmental and functional responses of the citrus microbiome and resistome to the systemic delivery of oxytetracycline by trunk injection.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128613},
doi = {10.1016/j.micres.2026.128613},
pmid = {42391942},
issn = {1618-0623},
mesh = {*Oxytetracycline/administration & dosage/pharmacology ; *Microbiota/drug effects ; *Citrus/microbiology/drug effects ; *Plant Diseases/microbiology/prevention & control ; Rhizobiaceae/drug effects ; Plant Roots/microbiology ; Rhizosphere ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Plant Leaves/microbiology ; Liberibacter/drug effects ; Bacteria/classification/genetics/drug effects ; Soil Microbiology ; Fruit/microbiology ; },
abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely limits citrus production worldwide. We investigated how oxytetracycline (OTC) trunk injection affects the citrus holobiont, examining its ability to suppress CLas and improve tree performance while assessing compartment-specific responses of the microbiome and resistome. A field experiment was conducted in CLas-infected sweet orange trees, integrating qPCR pathogen quantification, fruit yield and juice quality measurements, functional pathway analysis, and genome-resolved profiling across leaves, bark, fibrous roots, and the rhizosphere at three time points after injection. OTC reduced CLas abundance in leaves and improved fruit yield and juice quality without altering microbial diversity. No clear OTC-associated shifts in microbial functional pathways were observed in aboveground compartments, and resistome profiles were strongly compartment-dependent but showed no detectable response to OTC treatment. However, pronounced functional shifts were detected in belowground compartments, with consistent reductions in carbon-, nitrogen-, and phosphorus-related pathways and declines in several taxa and metagenome-assembled genomes associated with nutrient turnover. In contrast, stress-tolerance and xenobiotic-responsive microorganisms were enriched. In addition, these belowground responses were associated with low-abundance, rare taxa rather than by changes in alpha diversity or the dominant community, revealing a hidden functional reconfiguration that was concentrated in the root and rhizosphere compartments most relevant to nutrient cycling and long-term soil health. These findings demonstrate that systemically delivered OTC induces targeted, compartment-specific reorganization of microbiome functions rather than broad disruption. By linking physiological improvement with functional and genome-resolved microbial responses, this study highlights the broader ecological consequences of antibiotic interventions in perennial crops.},
}

*Oxytetracycline/administration & dosage/pharmacology
*Microbiota/drug effects
*Citrus/microbiology/drug effects
*Plant Diseases/microbiology/prevention & control
Rhizobiaceae/drug effects
Plant Roots/microbiology
Rhizosphere
*Anti-Bacterial Agents/pharmacology/administration & dosage
Plant Leaves/microbiology
Liberibacter/drug effects
Bacteria/classification/genetics/drug effects
Soil Microbiology
Fruit/microbiology

@article {pmid42398311,
year = {2026},
author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V},
title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128605},
doi = {10.1016/j.micres.2026.128605},
pmid = {42398311},
issn = {1618-0623},
mesh = {*Crops, Agricultural/microbiology/growth & development ; *Microbiota/genetics/physiology ; Biotechnology/methods ; Agriculture/methods ; Bacteria/genetics ; Ecosystem ; Plants/microbiology ; Microbial Consortia ; },
abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.},
}

*Crops, Agricultural/microbiology/growth & development
*Microbiota/genetics/physiology
Biotechnology/methods
Agriculture/methods
Bacteria/genetics
Ecosystem
Plants/microbiology
Microbial Consortia

@article {pmid42419832,
year = {2026},
author = {Chaurasia, A and Ponangi, K},
title = {The microbiome of the head and neck region.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {25-51},
doi = {10.1016/bs.ai.2026.03.002},
pmid = {42419832},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; },
abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.},
}

Humans
*Microbiota/immunology
*Dysbiosis/immunology/microbiology
*Head and Neck Neoplasms/microbiology/immunology
Animals
*Head/microbiology
*Squamous Cell Carcinoma of Head and Neck/microbiology/immunology

@article {pmid42419833,
year = {2026},
author = {Jams, J and Jayasinghe, RD},
title = {Introduction.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {3-23},
doi = {10.1016/bs.ai.2026.03.005},
pmid = {42419833},
issn = {1557-8445},
mesh = {Humans ; *Microbiota ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Biofilms ; Animals ; *Head and Neck Neoplasms/microbiology/etiology/immunology ; Host Microbial Interactions ; Host-Pathogen Interactions ; },
abstract = {Microorganisms colonize nearly all anatomical sites of the human body, with the oral cavity hosting one of the most diverse, accessible, and densely populated microbial ecosystems. The oral microbiome comprises a complex consortium of bacteria, fungi, viruses, archaea, and protozoa that inhabit distinct ecological niches. Each niche provides unique physicochemical conditions that shape microbial composition, structure, and function. In addition to oral and dental sites, oral biofilms frequently develop on dental materials, appliances, and prostheses, where surface characteristics such as roughness, hydrophobicity, and chemical composition further influence microbial adhesion and biofilm maturation, leading to marked differences at species and strain levels. Advances in culture-independent molecular technologies, particularly 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics approaches, have greatly enhanced understanding of oral microbial diversity, functional capacity, and host-microbe interactions beyond the limitations of conventional culture-based methods. In health, the oral microbiome exists in a state of dynamic equilibrium, or eubiosis, which contributes to local and systemic homeostasis. This balance is modulated by host factors such as saliva composition, immune responses, and oral hygiene practices, as well as environmental influences including diet, tobacco use, and alcohol consumption. Disruption of this equilibrium, termed dysbiosis, has been increasingly implicated in the pathogenesis of head and neck cancers. Emerging evidence suggests that microbial dysbiosis may promote carcinogenesis through chronic inflammation, immune modulation, production of carcinogenic metabolites, and direct interactions with epithelial cells. Understanding the microbiology of head and neck cancer therefore provides critical insights into disease initiation, progression, and potential diagnostic and therapeutic strategies.},
}

Humans
*Microbiota
*Dysbiosis/microbiology/immunology
*Mouth/microbiology
Biofilms
Animals
*Head and Neck Neoplasms/microbiology/etiology/immunology
Host Microbial Interactions
Host-Pathogen Interactions

@article {pmid42420265,
year = {2026},
author = {Vilar Geraldi, M and Dwibedi, C and Jaiswal, R and Gregori, G and Zhou, X and Lv, B and Zheng, Y and Wang, X and Wu, H and Axelsson, KF and Bäckhed, F and Tremaroli, V and Lorentzon, M},
title = {Gut microbiota associates with frailty in older women.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42420265},
issn = {2041-1723},
support = {2023-01976, 2023-01976, 2022-06725, 2018-05973, 2024-03723,//Vetenskapsrådet (Swedish Research Council)/ ; Lorentzon, 2023-2024//Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse (King Gustaf V and Queen Victoria's Foundation of Freemasons)/ ; 2024-0104//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; Lorentzon, 2016//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {Humans ; Female ; Aged ; *Frailty/microbiology/mortality ; Aged, 80 and over ; *Gastrointestinal Microbiome/genetics/physiology ; Sweden/epidemiology ; Frail Elderly ; Bacteria/classification/genetics/isolation & purification ; Cohort Studies ; },
abstract = {Frailty is a multifactorial geriatric condition linked to increased mortality and adverse health outcomes and is associated with gut microbiome features that differ from those observed in healthy ageing. We analyze gut metagenomic profiles in relation to estimated frailty severity and frailty-related clinical outcomes assessed with an internally developed and validated Frailty Mortality Index (FMI) in the SUPERB cohort, comprising 2,081 Swedish women aged 75-80 years. The FMI is a composite measure that integrates functional, physiological and psychological dimensions associated with frailty and mortality risk, and shows stronger associations with mortality compared to the Charlson Comorbidity Index in the SUPERB cohort. The FMI is inversely associated with microbial diversity, gene richness, and predicted functional capacity, which are linked to physical function, mortality and fall-related injuries. A total of 404 bacterial species are significantly associated with FMI, and most show concordant associations in a Chinese cohort of 1,448 older adults. Here we show microbial signatures linked to frailty and mortality across different continents.},
}

Humans
Female
Aged
*Frailty/microbiology/mortality
Aged, 80 and over
*Gastrointestinal Microbiome/genetics/physiology
Sweden/epidemiology
Frail Elderly
Bacteria/classification/genetics/isolation & purification
Cohort Studies

@article {pmid41935631,
year = {2026},
author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , },
title = {Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {7},
pages = {101848},
pmid = {41935631},
issn = {2589-5559},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; Homeostasis ; Male ; Female ; *Liver Diseases, Alcoholic/metabolism ; Cross-Sectional Studies ; Liver/metabolism ; Middle Aged ; Feces/chemistry ; Adult ; },
abstract = {BACKGROUND & AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.

METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n = 462), alongside matched healthy controls (n = 148), and validated key findings in two independent ALD cohorts (n = 34 and n = 52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.

RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F = 69.9, p = 8.6e-66) and feces (inprimis, cholic acid: F = 5.5, p = 1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multistep dehydroxylation pathway (including baiB) increased, whereas those in the reduction arm (baiN) were depleted. In patients with ALD, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.

CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.

IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive ALD progression. Additionally, our study identifies specific bacterial species influencing BA concentrations in ALD using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating ALD.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bile Acids and Salts/metabolism
Homeostasis
Male
Female
*Liver Diseases, Alcoholic/metabolism
Cross-Sectional Studies
Liver/metabolism
Middle Aged
Feces/chemistry
Adult

@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell & environment},
volume = {49},
number = {8},
pages = {5703-5719},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
mesh = {*Indoleacetic Acids/metabolism ; *Rhizosphere ; *Salt Tolerance/physiology ; *Triticum/microbiology/physiology/metabolism ; *Bacillus cereus/physiology ; Plant Roots/microbiology/metabolism ; *Microbiota/physiology ; *Plant Proteins/metabolism ; Biological Transport ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}

*Indoleacetic Acids/metabolism
*Rhizosphere
*Salt Tolerance/physiology
*Triticum/microbiology/physiology/metabolism
*Bacillus cereus/physiology
Plant Roots/microbiology/metabolism
*Microbiota/physiology
*Plant Proteins/metabolism
Biological Transport

@article {pmid42086631,
year = {2026},
author = {Moon, K and Kang, I and Cho, JC},
title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42086631},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; },
mesh = {*Fresh Water/virology ; *Aquaculture ; *Genome, Viral ; *Virome ; *Metagenome ; Republic of Korea ; Bacteriophages/genetics ; },
abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.},
}

*Fresh Water/virology
*Aquaculture
*Genome, Viral
*Virome
*Metagenome
Republic of Korea
Bacteriophages/genetics

@article {pmid42115271,
year = {2026},
author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W},
title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42115271},
issn = {2045-2322},
support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; },
mesh = {Humans ; Multiomics ; *Anorexia/microbiology/metabolism ; *Gastrointestinal Microbiome ; Child, Preschool ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Infant ; Case-Control Studies ; Metagenomics/methods ; Feces/microbiology ; *Metabolome ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.},
}

Humans
Multiomics
*Anorexia/microbiology/metabolism
*Gastrointestinal Microbiome
Child, Preschool
Male
Female
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Infant
Case-Control Studies
Metagenomics/methods
Feces/microbiology
*Metabolome
Bacteria/genetics/classification

@article {pmid42119966,
year = {2026},
author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC},
title = {Metagenomic characterization of bacterial communities on beach macroplastics: Insights into antimicrobial resistance and virulence.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {405},
number = {},
pages = {128213},
doi = {10.1016/j.envpol.2026.128213},
pmid = {42119966},
issn = {1873-6424},
mesh = {*Bacteria/genetics/classification ; *Drug Resistance, Bacterial/genetics ; Virulence ; *Bathing Beaches ; Metagenomics ; India ; Drug Resistance, Microbial/genetics ; *Microbiota ; Seashore ; Metagenome ; },
abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1264-2046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.},
}

*Bacteria/genetics/classification
*Drug Resistance, Bacterial/genetics
Virulence
*Bathing Beaches
Metagenomics
India
Drug Resistance, Microbial/genetics
*Microbiota
Seashore
Metagenome

@article {pmid42140378,
year = {2026},
author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA},
title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {590},
number = {},
pages = {121086},
doi = {10.1016/j.cca.2026.121086},
pmid = {42140378},
issn = {1873-3492},
mesh = {Humans ; Male ; *Prostatic Neoplasms/metabolism/therapy/diagnosis/blood ; *Biomarkers, Tumor/metabolism/blood ; *Gastrointestinal Microbiome ; *Prostate/metabolism ; },
abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.},
}

Humans
Male
*Prostatic Neoplasms/metabolism/therapy/diagnosis/blood
*Biomarkers, Tumor/metabolism/blood
*Gastrointestinal Microbiome
*Prostate/metabolism

@article {pmid42157110,
year = {2026},
author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F},
title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42157110},
issn = {1471-2229},
support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Microbial Consortia ; Bacteria/genetics ; Fungi ; },
abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.

RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.

CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype × microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.},
}

*Solanum lycopersicum/microbiology/growth & development
*Rhizosphere
*Microbiota
*Soil Microbiology
*Microbial Consortia
Bacteria/genetics
Fungi

@article {pmid42417135,
year = {2026},
author = {Walker, WB and Neven, LG},
title = {eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {4},
pages = {},
pmid = {42417135},
issn = {1536-2442},
support = {//Washington State Department of Agriculture Specialty Crops Block/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA, Environmental/analysis ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Sequence Analysis, DNA ; Insecta/genetics/classification ; Extrachromosomal DNA ; },
abstract = {Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*DNA, Environmental/analysis
High-Throughput Nucleotide Sequencing/methods
Biodiversity
Sequence Analysis, DNA
Insecta/genetics/classification
Extrachromosomal DNA

@article {pmid42417728,
year = {2026},
author = {Välikangas, T and Fritze, H and Pitkänen, JM and Peltoniemi, K and Järvi-Laturi, E and Christensen, TR and Väisänen, M and Lämsä, J and Paavola, R and Hultman, J},
title = {Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag072},
pmid = {42417728},
issn = {1574-6941},
abstract = {Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect soil microorganisms involved in methane (CH4) cycling and nitrous oxide (N2O) production/reduction. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH4 flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH4 fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.},
}

@article {pmid42418234,
year = {2026},
author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC},
title = {Evolving strategies for virus discovery.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
pmid = {42418234},
issn = {2057-5858},
mesh = {*Viruses/genetics/isolation & purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.},
}

*Viruses/genetics/isolation & purification/classification
Genome, Viral
*Metagenomics/methods
*Virome/genetics
Artificial Intelligence
Computational Biology/methods

@article {pmid42418242,
year = {2026},
author = {Robinson, JM and Guentas, L and Breed, MF},
title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001777},
pmid = {42418242},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; },
abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.},
}

*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Ecology

@article {pmid42419262,
year = {2026},
author = {Gelsinger, DR and Wang, HH},
title = {Toward precision microbiome therapeutics: From black box to blueprint.},
journal = {Cell host & microbe},
volume = {34},
number = {7},
pages = {1157-1161},
doi = {10.1016/j.chom.2026.06.014},
pmid = {42419262},
issn = {1934-6069},
mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/physiology/genetics ; Bacteria/genetics ; Animals ; Gene Editing ; *Precision Medicine/methods ; Microbiota ; },
abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.},
}

Humans
Metagenomics
*Gastrointestinal Microbiome/physiology/genetics
Bacteria/genetics
Animals
Gene Editing
*Precision Medicine/methods
Microbiota

@article {pmid42135633,
year = {2026},
author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X},
title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42135633},
issn = {1471-2180},
support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; },
mesh = {*Phytophthora/physiology/pathogenicity ; *Soil Microbiology ; *Microbiota/genetics ; *Nicotiana/microbiology/parasitology ; *Plant Diseases/microbiology ; Rhizosphere ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Shotgun Sequencing ; },
abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.

RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.

CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.},
}

*Phytophthora/physiology/pathogenicity
*Soil Microbiology
*Microbiota/genetics
*Nicotiana/microbiology/parasitology
*Plant Diseases/microbiology
Rhizosphere
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Metagenome
Shotgun Sequencing

@article {pmid42143215,
year = {2026},
author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ},
title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42143215},
issn = {1471-2180},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Drinking Water/microbiology ; *Biofilms/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Geologic Sediments/microbiology ; *Microbiota/genetics ; Metagenomics ; Water Supply ; Seasons ; Water Microbiology ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.

RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.

CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.},
}

*Drinking Water/microbiology
*Biofilms/growth & development
*Bacteria/classification/genetics/isolation & purification
*Geologic Sediments/microbiology
*Microbiota/genetics
Metagenomics
Water Supply
Seasons
Water Microbiology
Whole Genome Sequencing

@article {pmid42217383,
year = {2026},
author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W},
title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.},
journal = {Water research},
volume = {303},
number = {},
pages = {126182},
doi = {10.1016/j.watres.2026.126182},
pmid = {42217383},
issn = {1879-2448},
mesh = {*Sulfates/metabolism ; *Sulfur ; *Rivers ; *Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Plastics ; Mining ; Oxidation-Reduction ; },
abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.},
}

*Sulfates/metabolism
*Sulfur
*Rivers
*Geologic Sediments/microbiology/chemistry
*Microbiota
*Plastics
Mining
Oxidation-Reduction

@article {pmid42251226,
year = {2026},
author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR},
title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.},
journal = {Journal of natural medicines},
volume = {80},
number = {4},
pages = {1301-1338},
pmid = {42251226},
issn = {1861-0293},
support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; },
mesh = {Humans ; *Biological Products/chemistry/metabolism/pharmacology ; *Microbiota ; Biosynthetic Pathways ; },
abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.},
}

Humans
*Biological Products/chemistry/metabolism/pharmacology
*Microbiota
Biosynthetic Pathways

@article {pmid42284942,
year = {2026},
author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.},
journal = {Water research},
volume = {303},
number = {},
pages = {126258},
doi = {10.1016/j.watres.2026.126258},
pmid = {42284942},
issn = {1879-2448},
mesh = {*Microbiota ; Risk Assessment ; Biodegradation, Environmental ; Multiomics ; Sulfur/metabolism ; },
abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.},
}

*Microbiota
Risk Assessment
Biodegradation, Environmental
Multiomics
Sulfur/metabolism

@article {pmid42398615,
year = {2026},
author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J},
title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153356},
doi = {10.1016/j.ijbiomac.2026.153356},
pmid = {42398615},
issn = {1879-0003},
abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.},
}

@article {pmid42399943,
year = {2026},
author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W},
title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42399943},
issn = {1743-422X},
support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; },
abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.},
}

Humans
*Virome
*Autoimmune Diseases/virology/blood
*Metagenomics
Female
*Viruses/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Lupus Erythematosus, Systemic/virology

@article {pmid42400260,
year = {2026},
author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S},
title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2695485},
pmid = {42400260},
issn = {1949-0984},
mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.},
}

Animals
Caenorhabditis elegans/microbiology/metabolism
Humans
*Dopamine/metabolism
*Gastrointestinal Microbiome
*Vitamin B 6/metabolism/biosynthesis
*Parkinson Disease/microbiology/metabolism/genetics
Mice
Pyridoxal Phosphate/metabolism
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism
Phenotype
Escherichia coli/genetics/metabolism
alpha-Synuclein/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Male
Mice, Inbred C57BL
Feces/microbiology
Disease Models, Animal

@article {pmid42404879,
year = {2026},
author = {Dai, P and Feng, J and Cao, J and Fan, D},
title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828633},
pmid = {42404879},
issn = {1664-3224},
mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.

METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.

RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-κB, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).

CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.},
}

Humans
Multiomics
*Pancreatitis/metabolism/microbiology/immunology
Metabolomics
Gene Expression Profiling
*Host Microbial Interactions/immunology
Biomarkers
Metabolic Reprogramming
*Gastrointestinal Microbiome/immunology
Acute Disease
Female
Transcriptome
Male
Metabolome

@article {pmid42409501,
year = {2026},
author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D},
title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119678},
doi = {10.1016/j.foodres.2026.119678},
pmid = {42409501},
issn = {1873-7145},
mesh = {Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Swine ; *Food Microbiology ; *Microbiota ; Bacteria/metabolism/classification/genetics ; *Red Meat/microbiology/analysis ; *Pork Meat/microbiology/analysis ; Food, Processed ; Food Handling/methods ; },
abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.},
}

Animals
*Metabolomics/methods
*Metagenomics/methods
Swine
*Food Microbiology
*Microbiota
Bacteria/metabolism/classification/genetics
*Red Meat/microbiology/analysis
*Pork Meat/microbiology/analysis
Food, Processed
Food Handling/methods

@article {pmid42414020,
year = {2026},
author = {Clister, D and Chandra, QM and Tan, MW and Gunawan, MC and Bibi, A and Ahmed, A and Bastian, M and Meesakul, P and Cao, S and Kim, B and Nurkolis, F and Syahputra, RA},
title = {Microbiome-Based Precision Interventions in Type 2 Diabetes Mellitus: Mechanisms, Modulators, and Translational Opportunities.},
journal = {The Journal of nutrition},
volume = {156},
number = {7},
pages = {101596},
doi = {10.1016/j.tjnut.2026.101596},
pmid = {42414020},
issn = {1541-6100},
mesh = {*Diabetes Mellitus, Type 2/therapy/microbiology ; Humans ; *Precision Medicine ; Probiotics ; *Gastrointestinal Microbiome ; Prebiotics ; Fecal Microbiota Transplantation ; Synbiotics ; Dysbiosis ; Animals ; *Microbiota ; },
abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disease driven by insulin resistance, chronic low-grade inflammation, and impaired glucose regulation. Although pharmacological options have advanced, sustained glycemic control remains elusive due to heterogeneity in disease progression and therapeutic response. Precision medicine offers a framework to individualize interventions, with the gut microbiota emerging as a central determinant of host metabolic and immune regulation. Dysbiosis has been implicated in T2DM through altered microbial metabolites-including short-chain fatty acids, bile acids, branched-chain amino acids, and indole derivatives-that shape insulin sensitivity, inflammatory pathways, and glucose homeostasis. This review critically examined microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and personalized nutrition, alongside advances in metagenomics and machine learning for biomarker discovery. By integrating mechanistic and translational insights, we highlight opportunities and challenges in implementing microbiome-based precision interventions, underscoring their potential to transform T2DM management.},
}

*Diabetes Mellitus, Type 2/therapy/microbiology
Humans
*Precision Medicine
Probiotics
*Gastrointestinal Microbiome
Prebiotics
Fecal Microbiota Transplantation
Synbiotics
Dysbiosis
Animals
*Microbiota

@article {pmid41045876,
year = {2025},
author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M},
title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180614},
doi = {10.1016/j.scitotenv.2025.180614},
pmid = {41045876},
issn = {1879-1026},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; Germany ; Biomass ; *Extracellular Polymeric Substance Matrix ; *Microbiota ; Archaea ; Bacteria ; *Environmental Monitoring ; },
abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.},
}

*Geologic Sediments/microbiology/chemistry
*Rivers/microbiology/chemistry
Germany
Biomass
*Extracellular Polymeric Substance Matrix
*Microbiota
Archaea
Bacteria
*Environmental Monitoring

@article {pmid41412727,
year = {2026},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {75},
number = {8},
pages = {1505-1519},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
mesh = {Animals ; *Diet, Western/adverse effects ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/etiology ; Mice ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Deoxycholic Acid/metabolism ; Swine ; Disease Models, Animal ; Female ; Feces/microbiology ; Cell Proliferation ; Colon/microbiology ; Mice, Inbred C57BL ; Germ-Free Life ; Eubacteriales ; },
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.

OBJECTIVE: Investigate the causal role of BAs produced by 7αDH+ gut bacteria in CRC.

DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7αDH+ bacteria or a genetically modified strain to demonstrate causality.

RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7αDH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7αDH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.

CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7αDH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}

Animals
*Diet, Western/adverse effects
Humans
*Colorectal Neoplasms/microbiology/metabolism/etiology
Mice
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
Deoxycholic Acid/metabolism
Swine
Disease Models, Animal
Female
Feces/microbiology
Cell Proliferation
Colon/microbiology
Mice, Inbred C57BL
Germ-Free Life
Eubacteriales

@article {pmid42106412,
year = {2026},
author = {Guo, L and Holyoak, GR and DeSilva, U},
title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42106412},
issn = {2045-2322},
mesh = {Animals ; Female ; Horses/virology ; *Uterus/virology/microbiology ; *Virome/genetics ; Phylogeny ; Microbiota ; Genome, Viral ; Bacteriophages/genetics ; },
abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.},
}

Animals
Female
Horses/virology
*Uterus/virology/microbiology
*Virome/genetics
Phylogeny
Microbiota
Genome, Viral
Bacteriophages/genetics

@article {pmid42108251,
year = {2026},
author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J},
title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42108251},
issn = {2045-2322},
support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; },
mesh = {Animals ; *Feces/virology ; *Metagenomics/methods ; *Virome/genetics ; *Felidae/virology ; Risk Assessment ; Animals, Wild/virology ; *Zoonoses/virology ; Phylogeny ; DNA Viruses/genetics ; *Viruses/genetics/classification ; },
abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.},
}

Animals
*Feces/virology
*Metagenomics/methods
*Virome/genetics
*Felidae/virology
Risk Assessment
Animals, Wild/virology
*Zoonoses/virology
Phylogeny
DNA Viruses/genetics
*Viruses/genetics/classification

@article {pmid42108276,
year = {2026},
author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK},
title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42108276},
issn = {2045-2322},
support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; },
mesh = {*Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Oxygen/metabolism ; *Chemoautotrophic Growth ; Metagenomics ; Metabolomics ; *Microbiota ; },
abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.},
}

*Carbon Dioxide/metabolism
*Bacteria/metabolism/genetics/classification
*Oxygen/metabolism
*Chemoautotrophic Growth
Metagenomics
Metabolomics
*Microbiota

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0411725},
pmid = {42148573},
issn = {2165-0497},
support = {AM22SCBPCA1133//Center for Produce Safety/ ; },
mesh = {*Pyrus/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; *Food Storage/methods ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Fruit/microbiology ; Metagenomics ; Food Preservation/methods ; Food Microbiology ; },
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}

*Pyrus/microbiology
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
*Food Storage/methods
RNA, Ribosomal, 16S/genetics
Microbiota/genetics
Fruit/microbiology
Metagenomics
Food Preservation/methods
Food Microbiology

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0377525},
pmid = {42148581},
issn = {2165-0497},
support = {//Guizhou Province 2020 Science and Technology Support Plan Project/ ; },
mesh = {Fermentation ; Multiomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism/analysis ; Metagenomics ; China ; Microbiota ; Metagenome ; Metabolomics ; *Archaea/genetics/classification/metabolism/isolation & purification ; },
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

Fermentation
Multiomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism/analysis
Metagenomics
China
Microbiota
Metagenome
Metabolomics
*Archaea/genetics/classification/metabolism/isolation & purification

@article {pmid42148582,
year = {2026},
author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L},
title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0346925},
pmid = {42148582},
issn = {2165-0497},
support = {2023AH051003//Scientific Research Project of Universities in Anhui Province/ ; SKLTOF20210113//Open Fund of State Key Laboratory of Tea Plant Biology and Utilization/ ; },
mesh = {*Bacillus/metabolism/genetics/physiology ; *Catechin/metabolism/biosynthesis ; *Camellia sinensis/microbiology/metabolism ; Rhizosphere ; Secondary Metabolism ; Plant Leaves/metabolism/microbiology/chemistry ; Soil Microbiology ; Microbiota ; },
abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.},
}

*Bacillus/metabolism/genetics/physiology
*Catechin/metabolism/biosynthesis
*Camellia sinensis/microbiology/metabolism
Rhizosphere
Secondary Metabolism
Plant Leaves/metabolism/microbiology/chemistry
Soil Microbiology
Microbiota

@article {pmid42187250,
year = {2026},
author = {Liu, X and Kwok, L-Y and Zhang, W},
title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0024426},
pmid = {42187250},
issn = {2165-0497},
support = {2024ZY0168//Central Guiding Local Science and Technology Development Fund Project/ ; NMGIRT2411//Program of Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; 2025QN03001//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/metabolism/etiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Stroke/complications/microbiology/metabolism ; Male ; Fungi/classification/genetics/isolation & purification/metabolism ; Female ; Aged ; Feces/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Metabolomics ; },
abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.

IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.},
}

Humans
*Diabetes Mellitus, Type 2/complications/microbiology/metabolism
*Metabolome
*Gastrointestinal Microbiome
*Cognitive Dysfunction/microbiology/metabolism/etiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Stroke/complications/microbiology/metabolism
Male
Fungi/classification/genetics/isolation & purification/metabolism
Female
Aged
Feces/microbiology
Metagenomics
High-Throughput Nucleotide Sequencing
Metabolomics

@article {pmid42206864,
year = {2026},
author = {Zhao, R and Biddle, JF},
title = {Community structure and methylation of microbes in an artificially forced sediment core.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0353325},
pmid = {42206864},
issn = {2165-0497},
support = {//W. M. Keck Foundation/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification/metabolism ; *DNA Methylation ; Metagenome ; *Microbiota/genetics ; Epigenesis, Genetic ; Phylogeny ; },
abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.},
}

*Geologic Sediments/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification/metabolism
*DNA Methylation
Metagenome
*Microbiota/genetics
Epigenesis, Genetic
Phylogeny

@article {pmid42214368,
year = {2026},
author = {Karmarkar, B and Dhotre, D},
title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0321425},
pmid = {42214368},
issn = {2165-0497},
mesh = {*Gliadin/metabolism ; *Celiac Disease/microbiology/metabolism ; Humans ; *Stenotrophomonas maltophilia/enzymology/genetics ; Caco-2 Cells ; *Gastrointestinal Microbiome ; *Prolyl Oligopeptidases/metabolism/genetics ; Intestinal Barrier Function ; Peptides/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.

IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.},
}

*Gliadin/metabolism
*Celiac Disease/microbiology/metabolism
Humans
*Stenotrophomonas maltophilia/enzymology/genetics
Caco-2 Cells
*Gastrointestinal Microbiome
*Prolyl Oligopeptidases/metabolism/genetics
Intestinal Barrier Function
Peptides/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid42214386,
year = {2026},
author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG},
title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.},
journal = {mBio},
volume = {17},
number = {7},
pages = {e0071126},
doi = {10.1128/mbio.00711-26},
pmid = {42214386},
issn = {2150-7511},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage ; Infant ; *Metabolome/drug effects ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Female ; Male ; Longitudinal Studies ; Amoxicillin/therapeutic use/adverse effects ; Metagenomics ; },
abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.

IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage
Infant
*Metabolome/drug effects
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/drug effects
Feces/microbiology/chemistry
Female
Male
Longitudinal Studies
Amoxicillin/therapeutic use/adverse effects
Metagenomics

@article {pmid42214685,
year = {2026},
author = {Jiang, TA and Prioult, G and Quann, E},
title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.},
journal = {The Journal of nutrition},
volume = {156},
number = {7},
pages = {101621},
doi = {10.1016/j.tjnut.2026.101621},
pmid = {42214685},
issn = {1541-6100},
mesh = {*Polyphenols/metabolism/pharmacokinetics ; Humans ; *Synbiotics ; Biotransformation ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; },
abstract = {BACKGROUND: Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health but are constrained by poor bioavailability. Only 5%-10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract, while the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits due to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways.

OBJECTIVES: This review aimed to synthesize recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and to evaluate how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes, as well as the potential of targeted synbiotic strategies to enhance metabolite production.

METHODS: We conducted a narrative synthesis of recent literature examining microbial conversion pathways of dietary bioactives and their associated physiological effects, with a specific focus on interindividual variability in metabolite production and emerging evidence on synbiotic interventions combining probiotics with selected bioactive precursors.

RESULTS: Production of microbial metabolites varied markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes (metabotypes) that influenced clinical and nutritional responsiveness. Evidence showed that microbially derived metabolites were key mediators of systemic benefits. Studies evaluating targeted synbiotics demonstrated the capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging.

CONCLUSIONS: Metabolite-guided synbiotics represent a promising paradigm for precision nutrition by enhancing the consistency and efficacy of bioactive compound metabolism. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate the translation of microbiota-targeted interventions into practice.},
}

*Polyphenols/metabolism/pharmacokinetics
Humans
*Synbiotics
Biotransformation
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism

@article {pmid42218921,
year = {2026},
author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X},
title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.},
journal = {Molecular phylogenetics and evolution},
volume = {223},
number = {},
pages = {108650},
doi = {10.1016/j.ympev.2026.108650},
pmid = {42218921},
issn = {1095-9513},
mesh = {Animals ; *Symbiosis/genetics ; Phylogeny ; *Nematoda/microbiology/genetics ; *Microbiota/genetics ; Gene Transfer, Horizontal ; *Coxiellaceae/genetics/classification ; Wolbachia/genetics/classification ; Genome, Bacterial ; Sequence Analysis, DNA ; Metagenome ; Genomics ; Evolution, Molecular ; *Bacteroidetes/genetics/classification ; },
abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.},
}

Animals
*Symbiosis/genetics
Phylogeny
*Nematoda/microbiology/genetics
*Microbiota/genetics
Gene Transfer, Horizontal
*Coxiellaceae/genetics/classification
Wolbachia/genetics/classification
Genome, Bacterial
Sequence Analysis, DNA
Metagenome
Genomics
Evolution, Molecular
*Bacteroidetes/genetics/classification

@article {pmid42233654,
year = {2026},
author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H},
title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0318325},
pmid = {42233654},
issn = {2165-0497},
support = {2024AB034//Science and Technology Bureau of Xinjiang Production and Construction Corps/ ; CZ004311//Science Fund for Distinguished Young Scholars of Xinjiang Autonomous Region/ ; 202358//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; },
mesh = {Animals ; *Camelus/microbiology/growth & development ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Age Factors ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.},
}

Animals
*Camelus/microbiology/growth & development
*Bacteria/genetics/classification/isolation & purification/drug effects
*Gastrointestinal Microbiome/genetics
Anti-Bacterial Agents/pharmacology
Age Factors
Feces/microbiology
*Drug Resistance, Bacterial/genetics
Metagenomics

@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0113225},
pmid = {42262077},
issn = {2165-0497},
mesh = {Animals ; Female ; Swine/blood/microbiology ; Pregnancy ; Multiomics ; *Reproduction/physiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Litter Size ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Serum/chemistry ; },
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}

Animals
Female
Swine/blood/microbiology
Pregnancy
Multiomics
*Reproduction/physiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Litter Size
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Metabolomics
Metagenomics
*Serum/chemistry

@article {pmid42276012,
year = {2026},
author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T},
title = {IgG4-related disease has a specific intestinal microbiota signature.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106326},
pmid = {42276012},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; },
abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.

METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).

FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.

INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.

FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.},
}

Humans
*Gastrointestinal Microbiome
Female
RNA, Ribosomal, 16S/genetics
Male
*Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology
Middle Aged
Flow Cytometry
Aged
Immunoglobulin G
Adult
Cross-Sectional Studies
Feces/microbiology
Metagenomics/methods

@article {pmid42331262,
year = {2026},
author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R},
title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.},
journal = {Genomics},
volume = {118},
number = {4},
pages = {111282},
doi = {10.1016/j.ygeno.2026.111282},
pmid = {42331262},
issn = {1089-8646},
mesh = {Humans ; *Cholesteatoma/microbiology ; *Ear Canal/microbiology/pathology ; Metagenomics ; *Microbiota ; *Metagenome ; Actinobacteria/genetics/isolation & purification ; Bacillota/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification ; },
abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.

METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.

RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).

CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.},
}

Humans
*Cholesteatoma/microbiology
*Ear Canal/microbiology/pathology
Metagenomics
*Microbiota
*Metagenome
Actinobacteria/genetics/isolation & purification
Bacillota/genetics/isolation & purification
Proteobacteria/genetics/isolation & purification

@article {pmid42341885,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.},
journal = {Diabetes research and clinical practice},
volume = {238},
number = {},
pages = {113373},
doi = {10.1016/j.diabres.2026.113373},
pmid = {42341885},
issn = {1872-8227},
mesh = {Humans ; Female ; Male ; *Diabetes Mellitus, Type 1/blood/microbiology/complications/epidemiology ; Adult ; *Glycemic Control ; *Gastrointestinal Microbiome/physiology ; *Dyslipidemias/epidemiology/blood/etiology ; Food, Processed ; Middle Aged ; Italy/epidemiology ; *Atherosclerosis/epidemiology ; *Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism ; *Fast Foods/adverse effects ; Continuous Glucose Monitoring ; },
abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).

METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.

RESULTS: Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).

CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

Humans
Female
Male
*Diabetes Mellitus, Type 1/blood/microbiology/complications/epidemiology
Adult
*Glycemic Control
*Gastrointestinal Microbiome/physiology
*Dyslipidemias/epidemiology/blood/etiology
Food, Processed
Middle Aged
Italy/epidemiology
*Atherosclerosis/epidemiology
*Blood Glucose/metabolism
Glycated Hemoglobin/metabolism
*Fast Foods/adverse effects
Continuous Glucose Monitoring

@article {pmid42387381,
year = {2026},
author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B},
title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42387381},
issn = {1471-2180},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.

RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq. Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.

CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.},
}

*RNA, Ribosomal, 16S/genetics
*Computational Biology/methods
*Gene Library
Humans
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Sequence Analysis, DNA/methods
Metagenomics/methods
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid42387604,
year = {2026},
author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY},
title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.},
journal = {Infectious diseases of poverty},
volume = {15},
number = {1},
pages = {},
pmid = {42387604},
issn = {2049-9957},
support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; },
mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; },
abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.

METHODS: Female BALB/c mice and Sprague Dawley rats (n = 10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.

RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P < 0.05) while Bacteroidetes increased (P < 0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P < 0.05) but decreased in rats (P < 0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P < 0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.

CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.},
}

Animals
Female
*Angiostrongylus cantonensis/physiology
Rats, Sprague-Dawley
*Strongylida Infections/parasitology/microbiology/metabolism
Rats
*Gastrointestinal Microbiome
Mice
Mice, Inbred BALB C
RNA, Ribosomal, 16S/genetics/analysis
Biomarkers
Feces

@article {pmid42389510,
year = {2026},
author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F},
title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1760700},
pmid = {42389510},
issn = {2235-2988},
mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation & purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; },
abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.

METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).

KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.

CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.},
}

Humans
Male
*Methylobacterium/genetics/classification/isolation & purification/physiology
*Prostatic Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Retrospective Studies
Microbiota/genetics
Prostate/microbiology/pathology

@article {pmid42390270,
year = {2026},
author = {Varona, NS and Schellenberg, L and Barnes, W and Scholten, Y and Haas, AF and Silveira, C},
title = {Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0039526},
doi = {10.1128/msystems.00395-26},
pmid = {42390270},
issn = {2379-5077},
abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in carbon cycling within marine environments. In coral reefs, dissolved organic matter (DOM) released by benthic primary producers such as algae fuels heterotrophic microbial growth, which can be detrimental to corals. This microbialization process has been associated with the abundance and replication strategies of bacteriophages, but the direct relationship between reef DOM composition and bacteriophage communities remains unclear. Here, we combine metabolomics, metagenomes, and viromes to demonstrate that phage communities have significant relationships with DOM composition on the reefs of Curaçao, Southern Caribbean. While total viral abundances did not significantly correlate with overall dissolved organic carbon (DOC) concentration on these reefs, co-occurrence networks identified thousands of statistically significant associations between free or cell-associated viruses and organic compounds. Cell-associated phages had significantly more positive associations with compounds that had a reduced nominal oxidative state of carbon (NOSC). Furthermore, temperate phages were more frequently correlated with metabolites exhibiting higher Gibbs energy than putatively lytic phages. Six of the ten viruses with the highest number of positive associations with metabolites were temperate (i.e., encoded an integrase or were identified as a prophage), despite this network consisting of approximately 90% lytic viruses. These temperate viruses were predicted to infect members of the genus Sphingobium. Together, these findings reveal a connection between phage replication strategies and DOM energy availability, with potential implications for coral reef biogeochemistry.IMPORTANCECoral reefs are highly dynamic ecosystems where microbial communities and organic matter cycles are intricately linked. This study provides new insights into how bacteriophages interact with dissolved organic matter (DOM) composition, revealing that cell-associated bacteriophages, particularly temperate phages, are associated with more energy-rich organic compounds. These findings suggest that DOM could affect the lysis-lysogeny decision of temperate phages or that lysogeny may play an underappreciated role in shaping the reef carbon cycle. Energy-rich organic compounds have generally been associated with increased algal abundances and coral decline. By demonstrating significant connections between viral infection strategies and the energy content of DOM, our results highlight the potential for phages to influence coral reef biogeochemistry and health.},
}

@article {pmid42390679,
year = {2026},
author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F},
title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {6},
pages = {},
pmid = {42390679},
issn = {1573-3017},
support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; },
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; },
abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
*Iron/chemistry
*Microbiota/drug effects
*Chromium
*Charcoal/chemistry
*Environmental Restoration and Remediation/methods
Bacteria/drug effects
*Metal Nanoparticles

@article {pmid42392820,
year = {2026},
author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY},
title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {9},
pages = {2652-2664},
doi = {10.19540/j.cnki.cjcmm.20260107.707},
pmid = {42392820},
issn = {1001-5302},
mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; },
abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.},
}

Animals
*Drugs, Chinese Herbal/administration & dosage
*Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics
Rats
Male
Metabolomics
Metagenomics
Rats, Sprague-Dawley
*Brain Ischemia/metabolism/drug therapy/genetics
Humans
Oxidative Stress/drug effects
Blood-Brain Barrier/drug effects/metabolism
Brain/metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Disease Models, Animal

@article {pmid42394335,
year = {2026},
author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X},
title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {55},
number = {3},
pages = {491-498},
doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019},
pmid = {42394335},
issn = {1000-8020},
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; },
abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.

METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1∶1∶1 ratio) and Mix-B group(same bacterial strains, in a 10∶1∶1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 × 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.

RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, β-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.

CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Mice
Mice, Inbred C57BL
Lactobacillus acidophilus/physiology
Tryptophan/metabolism
Indoles/metabolism
Bifidobacterium animalis/physiology
Lacticaseibacillus rhamnosus/physiology
Feces/microbiology
*Microbiota

@article {pmid42394341,
year = {2026},
author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V},
title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.},
journal = {Journal of environmental quality},
volume = {55},
number = {4},
pages = {e70215},
doi = {10.1002/jeq2.70215},
pmid = {42394341},
issn = {1537-2537},
support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; },
mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; },
abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.},
}

New Caledonia
Seasons
*Seawater/microbiology
*Microbiota
RNA, Ribosomal, 16S/analysis
Bacteria/classification
Tropical Climate
*Environmental Monitoring
Archaea
Ecosystem

@article {pmid42397430,
year = {2026},
author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H},
title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42397430},
issn = {1436-6215},
mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.

METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.

RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.

CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.},
}

Animals
Proto-Oncogene Protein c-ets-1/metabolism/genetics
*T-Lymphocytes, Regulatory/metabolism
Mice
*Crohn Disease/diet therapy/metabolism
*Colitis/diet therapy
Forkhead Transcription Factors/metabolism/genetics
*Interleukin-10/genetics/metabolism/deficiency
Disease Models, Animal
Cell Differentiation/drug effects
Core Binding Factor Alpha 2 Subunit/metabolism/genetics
Mice, Knockout
Mice, Inbred C57BL
Gastrointestinal Microbiome
Male

@article {pmid42397950,
year = {2026},
author = {Karthik, Y and Nanjareddy, K and Arthikala, MK},
title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2693436},
pmid = {42397950},
issn = {1559-2324},
mesh = {*Glycine max/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.},
}

*Glycine max/microbiology/growth & development/metabolism
*Rhizosphere
*Microbiota/physiology
Soil Microbiology
Plant Roots/microbiology

@article {pmid41313537,
year = {2026},
author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS},
title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {4},
pages = {5223-5245},
pmid = {41313537},
issn = {1867-1314},
mesh = {Humans ; *Obesity/microbiology/metabolism/therapy ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; Animals ; Prebiotics/administration & dosage ; Dysbiosis/microbiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.},
}

Humans
*Obesity/microbiology/metabolism/therapy
*Gastrointestinal Microbiome
Probiotics/administration & dosage
Animals
Prebiotics/administration & dosage
Dysbiosis/microbiology
Fatty Acids, Volatile/metabolism

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
mesh = {Animals ; *Anopheles/genetics/microbiology/classification ; *RNA, Ribosomal, 16S/genetics ; *Genetic Variation ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Gastrointestinal Microbiome/genetics ; *Electron Transport Complex IV/genetics ; Phylogeny ; India ; Bacteria/genetics/classification ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

Animals
*Anopheles/genetics/microbiology/classification
*RNA, Ribosomal, 16S/genetics
*Genetic Variation
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
*Gastrointestinal Microbiome/genetics
*Electron Transport Complex IV/genetics
Phylogeny
India
Bacteria/genetics/classification

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
mesh = {*Microbiota/genetics ; *Climate Change ; Metagenomics/methods ; Biocuration ; Metagenome ; *Databases, Factual ; Data Curation ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

*Microbiota/genetics
*Climate Change
Metagenomics/methods
Biocuration
Metagenome
*Databases, Factual
Data Curation

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {},
pmid = {42121077},
issn = {1471-2377},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; *Epilepsy, Temporal Lobe/microbiology/epidemiology ; *RNA, Ribosomal, 16S/genetics ; Adult ; Case-Control Studies ; Comorbidity ; Middle Aged ; Feces/microbiology ; *Mental Disorders/microbiology/epidemiology ; },
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

Humans
Female
Male
*Gastrointestinal Microbiome/genetics
*Epilepsy, Temporal Lobe/microbiology/epidemiology
*RNA, Ribosomal, 16S/genetics
Adult
Case-Control Studies
Comorbidity
Middle Aged
Feces/microbiology
*Mental Disorders/microbiology/epidemiology

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; R01 DK108366/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Zimbabwe ; *HIV Infections/immunology/microbiology/drug therapy ; Female ; Male ; Adult ; Rural Population ; *Gastrointestinal Microbiome ; *Diet ; Urban Population ; Middle Aged ; Inflammation ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

Humans
Zimbabwe
*HIV Infections/immunology/microbiology/drug therapy
Female
Male
Adult
Rural Population
*Gastrointestinal Microbiome
*Diet
Urban Population
Middle Aged
Inflammation

@article {pmid42129938,
year = {2026},
author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z},
title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42129938},
issn = {2049-2618},
support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology/physiology ; Female ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Reproduction/physiology ; Multiomics ; Pregnancy ; Metagenomics/methods ; Metabolomics ; Litter Size ; *Gastrointestinal Microbiome ; Lactation ; },
abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.},
}

Animals
*Rumen/microbiology
Sheep/microbiology/physiology
Female
*Bacteria/classification/genetics/isolation & purification/metabolism
*Reproduction/physiology
Multiomics
Pregnancy
Metagenomics/methods
Metabolomics
Litter Size
*Gastrointestinal Microbiome
Lactation

@article {pmid42300757,
year = {2026},
author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y},
title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.},
journal = {Food & function},
volume = {17},
number = {13},
pages = {6062-6079},
doi = {10.1039/d6fo01565d},
pmid = {42300757},
issn = {2042-650X},
mesh = {Animals ; *Kefir/microbiology/analysis ; *Colitis/chemically induced ; Dextran Sulfate/adverse effects ; Intestinal Barrier Function ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Fermentation ; Tibet ; Mice, Inbred C57BL ; Inflammation ; RAW 264.7 Cells ; Bacteria/classification/genetics/isolation & purification ; Milk ; Cultured Milk Products ; },
abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.},
}

Animals
*Kefir/microbiology/analysis
*Colitis/chemically induced
Dextran Sulfate/adverse effects
Intestinal Barrier Function
Mice
*Gastrointestinal Microbiome/drug effects
Male
Fermentation
Tibet
Mice, Inbred C57BL
Inflammation
RAW 264.7 Cells
Bacteria/classification/genetics/isolation & purification
Milk
Cultured Milk Products

@article {pmid42316995,
year = {2026},
author = {Gu, Y and Li, L and Zhang, H and Ye, T and Zhu, Q and Zhao, X and Xie, K and Ge, R and Han, J and Qin, Y},
title = {Dietary purple sweet potato anthocyanin extracts attenuate intestinal barrier decline in naturally aged mice via the microbiota-autophagy-stem cell axis.},
journal = {Food & function},
volume = {17},
number = {13},
pages = {6227-6245},
doi = {10.1039/d6fo00039h},
pmid = {42316995},
issn = {2042-650X},
mesh = {Animals ; *Anthocyanins/pharmacology ; *Ipomoea batatas/chemistry ; Mice ; *Aging/drug effects ; *Stem Cells/drug effects/metabolism ; *Plant Extracts/pharmacology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Male ; Intestinal Mucosa/drug effects/metabolism ; Dietary Supplements ; },
abstract = {Age-related deterioration of the intestinal epithelial barrier exacerbates systemic metabolic and functional decline, highlighting the gut as a key target for dietary interventions in healthy aging. Here, using naturally aged mice and intestinal organoids, we demonstrate that supplementation with purple sweet potato anthocyanins (PSPAs) alleviates systemic aging phenotypes, including impaired motor coordination, hepatic lipid dysregulation, insulin resistance, and cellular senescence, while concurrently restoring intestinal barrier integrity. PSPAs enhanced tight junction protein expression and epithelial architecture, independently of inflammation resolution, and promoted the proliferative and differentiation capacity of intestinal stem cells (ISCs). Metagenomic profiling revealed that PSPAs remodeled aging-associated gut microbiota composition and functions. Fecal microbiota transplantation established the causal contribution of microbiota remodeling to ISC rejuvenation, while luminal content-organoid assays confirmed the role of microbial metabolites. Integrative metabolomics identified metabolic changes linked to autophagy-related processes, including altered SCFA profiles, while transcriptomic analysis highlighted PI3K-AKT signaling as a major pathway associated with microbial and metabolic remodeling. Collectively, this multi-omics study establishes a mechanistic framework in which PSPAs alleviate aging-associated barrier decline through a "microbiota-autophagy-stem cell" axis, providing important insights into polyphenol-based strategies for gut-centered healthy aging.},
}

Animals
*Anthocyanins/pharmacology
*Ipomoea batatas/chemistry
Mice
*Aging/drug effects
*Stem Cells/drug effects/metabolism
*Plant Extracts/pharmacology
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Intestinal Barrier Function/drug effects
Male
Intestinal Mucosa/drug effects/metabolism
Dietary Supplements

@article {pmid42384916,
year = {2026},
author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA},
title = {Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/bioinformatics/btag422},
pmid = {42384916},
issn = {1367-4811},
support = {//Lawrence Livermore National Laboratory/ ; },
mesh = {*Metadata ; *Metagenomics/methods ; Humans ; *Databases, Genetic ; *Metagenome ; *Microbiota/genetics ; Biocuration ; Software ; },
abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.},
}

*Metadata
*Metagenomics/methods
Humans
*Databases, Genetic
*Metagenome
*Microbiota/genetics
Biocuration
Software

@article {pmid42386249,
year = {2026},
author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J},
title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {1},
pages = {101323},
doi = {10.1016/j.ajcnut.2026.101323},
pmid = {42386249},
issn = {1938-3207},
mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; },
abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).

OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.

METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.

RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.

CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.},
}

Humans
*Endotoxemia/complications/blood
Male
Female
*Postprandial Period
*Coronary Disease/complications/blood
Middle Aged
Lipopolysaccharides/blood
Diet, Fat-Restricted
Recurrence
Diet, Mediterranean
Aged
Gastrointestinal Microbiome
*Cardiovascular Diseases/etiology

@article {pmid42153646,
year = {2026},
author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV},
title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.},
journal = {mSphere},
volume = {11},
number = {6},
pages = {e0013926},
pmid = {42153646},
issn = {2379-5042},
support = {075-15-2025-475//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; *COVID-19/microbiology ; *Metagenome ; *Lung/microbiology ; *Gastrointestinal Microbiome/genetics ; SARS-CoV-2 ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics/methods ; Plasmids/genetics ; Feces/microbiology ; Male ; Klebsiella pneumoniae/genetics ; Female ; Middle Aged ; Aged ; Candida/genetics/drug effects/isolation & purification ; Pandemics ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.},
}

Humans
*COVID-19/microbiology
*Metagenome
*Lung/microbiology
*Gastrointestinal Microbiome/genetics
SARS-CoV-2
*Bacteria/genetics/classification/isolation & purification/drug effects
Metagenomics/methods
Plasmids/genetics
Feces/microbiology
Male
Klebsiella pneumoniae/genetics
Female
Middle Aged
Aged
Candida/genetics/drug effects/isolation & purification
Pandemics

@article {pmid42381379,
year = {2026},
author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA},
title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690687},
doi = {10.1080/19490976.2026.2690687},
pmid = {42381379},
issn = {1949-0984},
mesh = {Animals ; *Probiotics/administration & dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.},
}

Animals
*Probiotics/administration & dosage
Multiomics
*Saccharomyces boulardii/physiology
Receptors, Aryl Hydrocarbon/metabolism/agonists
Signal Transduction
*Gastrointestinal Microbiome
*Colorectal Neoplasms/immunology/microbiology/metabolism/therapy
Mice
Bacteria/classification/genetics/isolation & purification

@article {pmid42385223,
year = {2026},
author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A},
title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70359},
pmid = {42385223},
issn = {2045-8827},
mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; },
abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.},
}

*Rivers/microbiology/chemistry
*Metagenomics
Seasons
Bangladesh
*Bacteria/genetics/classification/drug effects/isolation & purification
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
Water Quality
Shotgun Sequencing

@article {pmid41738567,
year = {2026},
author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D},
title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.},
journal = {Journal of fish diseases},
volume = {49},
number = {8},
pages = {e70143},
doi = {10.1111/jfd.70143},
pmid = {41738567},
issn = {1365-2761},
support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; },
abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
*Unionidae/virology
RNA-Dependent RNA Polymerase/genetics
Metagenomics
Transcriptome
Epidemics/veterinary
*Virome
Hepatopancreas/virology

@article {pmid42071059,
year = {2026},
author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D},
title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42071059},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; },
mesh = {Multiomics ; Animals ; Metabolomics/methods ; *Agriculture/methods ; Cattle ; Metagenomics/methods ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; Chromatography, Liquid ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Soil Microbiology ; },
abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.},
}

Multiomics
Animals
Metabolomics/methods
*Agriculture/methods
Cattle
Metagenomics/methods
Gas Chromatography-Mass Spectrometry
*Metabolome
Chromatography, Liquid
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
*Microbiota
Soil Microbiology

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42103925},
issn = {2045-2322},
mesh = {Animals ; Larva/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

Animals
Larva/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
*Gastrointestinal Microbiome
Metagenomics
Phylogeny
Nitrogen/metabolism
RNA, Ribosomal, 16S/genetics
Gastrointestinal Tract/microbiology

@article {pmid42371206,
year = {2026},
author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T},
title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42371206},
issn = {1573-0972},
support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; },
mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth & development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; China ; Microbiota/genetics ; },
abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.},
}

*Phosphorus/metabolism
*Soil Microbiology
*Soil/chemistry
*Nitrogen/metabolism
Oryza/growth & development
*Nitrogen Cycle
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenome
China
Microbiota/genetics

@article {pmid42374590,
year = {2026},
author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB},
title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42374590},
issn = {2049-2618},
support = {Heritage_2020-005_RESTOROMIC//Österreichischen Akademie der Wissenschaften/ ; },
mesh = {Austria ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Sodium Chloride ; Transcriptome ; Salinity ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.

RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.

CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.},
}

Austria
*Microbiota/genetics
Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
Sodium Chloride
Transcriptome
Salinity
Adaptation, Physiological

@article {pmid42376319,
year = {2026},
author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S},
title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828012},
pmid = {42376319},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; },
abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.

METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.

RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p = 0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p = 0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p < 0.05).

CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.},
}

Humans
*Colorectal Neoplasms/microbiology
*Feces/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Multiomics
High-Throughput Nucleotide Sequencing
Adult
Metagenome

@article {pmid42377624,
year = {2026},
author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C},
title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42377624},
issn = {1573-0972},
mesh = {*Wastewater/microbiology ; *Microalgae/growth & development/microbiology ; Phylogeny ; *Bacteria/isolation & purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; },
abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.},
}

*Wastewater/microbiology
*Microalgae/growth & development/microbiology
Phylogeny
*Bacteria/isolation & purification/classification/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Biomass
Microbial Consortia
Coculture Techniques
Biofuels
DNA, Bacterial/genetics
Metagenomics
Water Purification

@article {pmid42378712,
year = {2026},
author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M},
title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {6},
pages = {},
pmid = {42378712},
issn = {1876-4479},
support = {//Takeda Pharmaceutical Company Ltd/ ; },
mesh = {Humans ; *Crohn Disease/complications/genetics/microbiology ; *Rectal Fistula/genetics/microbiology/etiology/pathology/metabolism ; Multiomics ; Female ; Male ; Adult ; Epithelial-Mesenchymal Transition/genetics ; Transcriptome ; Middle Aged ; Intestinal Mucosa/pathology/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; Metabolomics ; },
abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.

DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n = 23) or CgF (n = 17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.

RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.

CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.},
}

Humans
*Crohn Disease/complications/genetics/microbiology
*Rectal Fistula/genetics/microbiology/etiology/pathology/metabolism
Multiomics
Female
Male
Adult
Epithelial-Mesenchymal Transition/genetics
Transcriptome
Middle Aged
Intestinal Mucosa/pathology/metabolism
Gastrointestinal Microbiome/genetics
Gene Expression Profiling
Metabolomics

@article {pmid42104260,
year = {2026},
author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R},
title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42104260},
issn = {1471-2180},
mesh = {*Hydrothermal Vents/microbiology ; *Antimicrobial Peptides/pharmacology/genetics/chemistry ; Arctic Regions ; *Microbiota ; Biofilms ; *Bacteria/genetics/classification/drug effects ; *Seawater/microbiology ; Archaea/genetics/classification/metabolism ; Metagenomics ; *Antimicrobial Cationic Peptides/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.

RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.

CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.},
}

*Hydrothermal Vents/microbiology
*Antimicrobial Peptides/pharmacology/genetics/chemistry
Arctic Regions
*Microbiota
Biofilms
*Bacteria/genetics/classification/drug effects
*Seawater/microbiology
Archaea/genetics/classification/metabolism
Metagenomics
*Antimicrobial Cationic Peptides/pharmacology
Microbial Sensitivity Tests

@article {pmid42115187,
year = {2026},
author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X},
title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42115187},
issn = {2158-3188},
mesh = {Animals ; *Autophagy/physiology ; Rats ; *TOR Serine-Threonine Kinases/metabolism ; *Major Depressive Disorder/microbiology/metabolism ; Male ; *Dysbiosis/metabolism/complications ; *Gastrointestinal Microbiome/physiology ; *Lysine/metabolism/blood ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Prefrontal Cortex/metabolism ; Behavior, Animal ; Humans ; Adolescent ; Sirolimus/pharmacology ; Depression ; },
abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.},
}

Animals
*Autophagy/physiology
Rats
*TOR Serine-Threonine Kinases/metabolism
*Major Depressive Disorder/microbiology/metabolism
Male
*Dysbiosis/metabolism/complications
*Gastrointestinal Microbiome/physiology
*Lysine/metabolism/blood
Rats, Sprague-Dawley
Fecal Microbiota Transplantation
Disease Models, Animal
Prefrontal Cortex/metabolism
Behavior, Animal
Humans
Adolescent
Sirolimus/pharmacology
Depression

@article {pmid42127418,
year = {2026},
author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC},
title = {Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42127418},
issn = {1751-7370},
support = {IN219624//Dirección General de Asuntos del Personal Académico (DGAPA)/Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT)/ ; IN217821//Dirección General de Asuntos del Personal Académico (DGAPA)/Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT)/ ; //Universidad Nacional Autónoma de Mexico/ ; //Calgary Foundation/ ; //Office of the Associate Dean Research of the University of Calgary's Cumming School of Medicine/ ; //Alberta Children's Hospital Research Institute/ ; //internal University of Calgary start-up funds/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Bacteria/classification/genetics/isolation & purification ; Eukaryota/classification/genetics/isolation & purification ; *Family Characteristics ; Feces/microbiology ; Longitudinal Studies ; Metagenomics ; Mexico ; RNA, Ribosomal, 18S/genetics ; Rural Population ; Sequence Analysis, DNA ; *Gastrointestinal Microbiome ; },
abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S ribosomal RNA gene sequencing, we characterized bacterial and eukaryotic gut microbiomes in an intensively sampled longitudinal cohort of 10 infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing a detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, and bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and birth mode also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.},
}

Female
Humans
Infant
Infant, Newborn
Bacteria/classification/genetics/isolation & purification
Eukaryota/classification/genetics/isolation & purification
*Family Characteristics
Feces/microbiology
Longitudinal Studies
Metagenomics
Mexico
RNA, Ribosomal, 18S/genetics
Rural Population
Sequence Analysis, DNA
*Gastrointestinal Microbiome

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {41},
number = {7},
pages = {2062-2072},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
mesh = {Humans ; *Gallbladder Neoplasms/etiology/metabolism/microbiology ; Multiomics ; *Metabolomics ; *Carcinogenesis/metabolism/genetics ; Dysbiosis/complications ; *Microbiota ; Animals ; Proteomics ; Helicobacter ; Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

Humans
*Gallbladder Neoplasms/etiology/metabolism/microbiology
Multiomics
*Metabolomics
*Carcinogenesis/metabolism/genetics
Dysbiosis/complications
*Microbiota
Animals
Proteomics
Helicobacter
Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome

@article {pmid42362550,
year = {2026},
author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R},
title = {Remodelling of the gut virome after long-term fasting.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42362550},
issn = {2055-5008},
mesh = {*Fasting ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/genetics/classification/isolation & purification ; Humans ; Metagenomics/methods ; Bacteria/virology/classification ; Feces/virology/microbiology ; Bacteroides/virology ; Faecalibacterium/virology ; },
abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.},
}

*Fasting
*Virome
*Gastrointestinal Microbiome
Bacteriophages/genetics/classification/isolation & purification
Humans
Metagenomics/methods
Bacteria/virology/classification
Feces/virology/microbiology
Bacteroides/virology
Faecalibacterium/virology

@article {pmid42362787,
year = {2026},
author = {Sinha, B and Khandeparker, L},
title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42362787},
issn = {1573-2959},
mesh = {*Plastics/analysis ; Seasons ; *Biofilms ; *Environmental Monitoring ; *Microbiota ; Estuaries ; Bacteria/classification ; },
abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.},
}

*Plastics/analysis
Seasons
*Biofilms
*Environmental Monitoring
*Microbiota
Estuaries
Bacteria/classification

@article {pmid42366019,
year = {2026},
author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J},
title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70367},
doi = {10.1111/1462-2920.70367},
pmid = {42366019},
issn = {1462-2920},
support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation & purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; },
abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.},
}

*Soil Microbiology
*Caves/microbiology
*Ascomycota/isolation & purification/genetics/physiology
Seasons
*Bacteria/metabolism/genetics/classification/isolation & purification
Soil/chemistry
China
Microbiota
Nitrogen Cycle