@article {pmid42189287,
year = {2026},
author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M},
title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {8},
pages = {},
pmid = {42189287},
issn = {1432-0851},
support = {PE00000019//NextGenerationEU/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/immunology/genetics ; *Neoplasms/drug therapy/microbiology/immunology ; *Immunotherapy/methods ; *Biomarkers, Tumor ; Machine Learning ; Feces/microbiology ; Biomarkers ; },
abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.},
}

Humans
*Metagenomics/methods
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/immunology/genetics
*Neoplasms/drug therapy/microbiology/immunology
*Immunotherapy/methods
*Biomarkers, Tumor
Machine Learning
Feces/microbiology
Biomarkers

@article {pmid42203770,
year = {2026},
author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M},
title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42203770},
issn = {2041-1723},
support = {1026-00386B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; },
mesh = {Humans ; *Oligosaccharides/metabolism ; *Weaning ; *Milk, Human/metabolism/chemistry ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/physiology/genetics ; *Dietary Fiber/metabolism ; Infant ; Metagenomics ; Metagenome ; Clostridium/metabolism/genetics/isolation & purification ; Bifidobacterium/metabolism/genetics ; Adult ; },
abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.},
}

Humans
*Oligosaccharides/metabolism
*Weaning
*Milk, Human/metabolism/chemistry
Feces/microbiology
Female
*Gastrointestinal Microbiome/physiology/genetics
*Dietary Fiber/metabolism
Infant
Metagenomics
Metagenome
Clostridium/metabolism/genetics/isolation & purification
Bifidobacterium/metabolism/genetics
Adult

@article {pmid42204574,
year = {2026},
author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N},
title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.},
journal = {Annals of neurology},
volume = {100},
number = {2},
pages = {334-340},
doi = {10.1002/ana.78243},
pmid = {42204574},
issn = {1531-8249},
support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; },
mesh = {Humans ; *Parkinson Disease/virology/diagnosis/genetics ; Female ; Male ; Case-Control Studies ; *Metagenomics/methods ; *Prodromal Symptoms ; Middle Aged ; Aged ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; },
abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026;100:334-340.},
}

Humans
*Parkinson Disease/virology/diagnosis/genetics
Female
Male
Case-Control Studies
*Metagenomics/methods
*Prodromal Symptoms
Middle Aged
Aged
*Virome/genetics
*Gastrointestinal Microbiome/genetics

@article {pmid42209465,
year = {2026},
author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L},
title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42209465},
issn = {2041-1723},
mesh = {*Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Carbon Dioxide/metabolism ; Genome, Viral ; *Polymorphism, Single Nucleotide ; Evolution, Molecular ; Anaerobiosis ; CRISPR-Cas Systems/genetics ; },
abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.},
}

*Bacteriophages/genetics/physiology
*Microbiota/genetics
*Carbon Dioxide/metabolism
Genome, Viral
*Polymorphism, Single Nucleotide
Evolution, Molecular
Anaerobiosis
CRISPR-Cas Systems/genetics

@article {pmid42361932,
year = {2026},
author = {Ying, Y and Zheng, X and Yang, J and Ye, H and Dong, Z and Ji, Y and Li, S and Tan, X and Zhang, W},
title = {Tong-Xie-Yao-Fang ameliorates IBS-D: Potential role of Alistipes finegoldii-associated gut tryptophan indole metabolism.},
journal = {Journal of ethnopharmacology},
volume = {371},
number = {},
pages = {122061},
doi = {10.1016/j.jep.2026.122061},
pmid = {42361932},
issn = {1872-7573},
mesh = {Animals ; *Irritable Bowel Syndrome/drug therapy/metabolism/microbiology ; *Tryptophan/metabolism ; Mice, Inbred C57BL ; Male ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Indoles/metabolism ; *Gastrointestinal Microbiome/drug effects ; Colon/metabolism/drug effects/microbiology ; Mice ; Receptors, Aryl Hydrocarbon/metabolism ; Disease Models, Animal ; Indoleacetic Acids/metabolism ; Basic Helix-Loop-Helix Proteins/metabolism ; *Diarrhea/drug therapy/metabolism/microbiology ; Humans ; },
abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent chronic gastrointestinal condition characterized by visceral hypersensitivity, low-grade mucosal inflammation, and impaired epithelial barrier integrity. Current therapies remain limited, highlighting the need for more alternative strategies. Tong-Xie-Yao-Fang (TXYF), a classical Chinese herbal formula, has shown clinical efficacy in IBS-D, however, the mechanisms underlying its therapeutic effects remain unclear.

AIM OF THE STUDY: This study aimed to investigate whether and how TXYF exerts therapeutic effects by modulating colonic tryptophan metabolism, with a particular focus on the gut microbiota.

MATERIALS AND METHODS: IBS-D model was induced by combining chemical irritation and wrap restraint stress in C57BL/6J mice, and multi-omics approaches were employed to identify specific microbiota and metabolites modulated by TXYF. The multi-omics findings were further verified in vivo and in vitro.

RESULTS: TXYF treatment significantly alleviated IBS-D symptoms in our model. Non-targeted metabolomics identified the tryptophan-indole pathway as a key axis modulated by TXYF, with indole-3-acetic acid (IAA) emerging as a prominent differential metabolite in colonic tissue. Western blot analysis showed that TXYF activated the aryl hydrocarbon receptor (AhR) in the colon. Integrative metagenomic and metabolomic analyses revealed a strong association between Alistipes finegoldii and colonic indole and IAA levels. Consistent with these findings, transplantation of A. finegoldii combined with tryptophan supplementation, or administration of IAA alone, recapitulated the therapeutic effects of TXYF against IBS-D. In vitro, both IAA and faecal supernatant from TXYF-treated mice protected against tumour necrosis factor-induced epithelial barrier disruption in an AhR-dependent manner.

CONCLUSION: Collectively, the present study suggests that the therapeutic efficiency of TXYF against IBS-D is closely associated with its ability to modify microbiota-derived colonic IAA production, with gut microbiota member Alistipes finegoldii playing a key role in this effect.},
}

Animals
*Irritable Bowel Syndrome/drug therapy/metabolism/microbiology
*Tryptophan/metabolism
Mice, Inbred C57BL
Male
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Indoles/metabolism
*Gastrointestinal Microbiome/drug effects
Colon/metabolism/drug effects/microbiology
Mice
Receptors, Aryl Hydrocarbon/metabolism
Disease Models, Animal
Indoleacetic Acids/metabolism
Basic Helix-Loop-Helix Proteins/metabolism
*Diarrhea/drug therapy/metabolism/microbiology
Humans

@article {pmid42383698,
year = {2026},
author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO},
title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {32},
number = {9},
pages = {972-984},
pmid = {42383698},
issn = {1477-0970},
mesh = {Humans ; *Tryptophan/metabolism/blood ; *Bile Acids and Salts/metabolism/blood ; Male ; *Multiple Sclerosis/metabolism/blood ; Female ; Adult ; Middle Aged ; *Tobacco Smoking/adverse effects/metabolism ; *Gastrointestinal Microbiome/physiology ; Indoles/metabolism/blood ; },
abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.

OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.

METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N = 266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.

RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).

CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.},
}

Humans
*Tryptophan/metabolism/blood
*Bile Acids and Salts/metabolism/blood
Male
*Multiple Sclerosis/metabolism/blood
Female
Adult
Middle Aged
*Tobacco Smoking/adverse effects/metabolism
*Gastrointestinal Microbiome/physiology
Indoles/metabolism/blood

@article {pmid42417706,
year = {2026},
author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY},
title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {28},
pages = {22337-22347},
doi = {10.1021/acs.jafc.6c02819},
pmid = {42417706},
issn = {1520-5118},
mesh = {*Oryza/microbiology/growth & development/chemistry/classification ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; Germination ; Fungi/genetics/classification/isolation & purification ; *Seeds/microbiology/growth & development/chemistry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.},
}

*Oryza/microbiology/growth & development/chemistry/classification
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota
Germination
Fungi/genetics/classification/isolation & purification
*Seeds/microbiology/growth & development/chemistry
RNA, Ribosomal, 16S/genetics

@article {pmid42449941,
year = {2026},
author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S},
title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
pmid = {42449941},
issn = {1422-0067},
support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; },
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Soil Microbiology
Bacteria/genetics/classification
Metagenome

@article {pmid42450074,
year = {2026},
author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S},
title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
pmid = {42450074},
issn = {1422-0067},
support = {CARS-12//China Agriculture Research System/ ; },
mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; },
abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.},
}

*Seeds/microbiology/genetics
*Transcriptome
*Microbiota/genetics
*Brassica rapa/microbiology/genetics
Gene Expression Profiling
Stress, Physiological
*Brassica napus/microbiology/genetics

@article {pmid42450138,
year = {2026},
author = {Getsina, M and Tsyba, N and Chernevskaya, E},
title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
pmid = {42450138},
issn = {1422-0067},
mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; },
abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.},
}

*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism
Humans
Prognosis
*Biomarkers, Tumor/metabolism
Microbiota
Metabolomics/methods
Circulating Tumor DNA/blood
Early Detection of Cancer

@article {pmid42451140,
year = {2026},
author = {Ibor-Miguel, M and Pérez-Sánchez, D and Marques-Martínez, L and Aura-Tormos, JI and Guinot-Barona, C and Miralles, EG},
title = {Influence of Early Feeding Practices on Oral Microbiota Composition During Infancy and Potential Implications for Early Childhood Caries: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
pmid = {42451140},
issn = {2072-6643},
mesh = {Humans ; Infant ; *Dental Caries/microbiology/epidemiology ; *Microbiota ; *Mouth/microbiology ; Breast Feeding ; Child, Preschool ; Infant, Newborn ; Female ; *Feeding Behavior ; Child ; Infant Nutritional Physiological Phenomena ; Milk, Human ; Infant Formula ; },
abstract = {BACKGROUND: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components-immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria-that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk.

OBJECTIVES: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes.

METHODS: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity.

RESULTS: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12-448 participants; age range at microbiota assessment: 2 days-14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (≥12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated.

CONCLUSIONS: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies.},
}

Humans
Infant
*Dental Caries/microbiology/epidemiology
*Microbiota
*Mouth/microbiology
Breast Feeding
Child, Preschool
Infant, Newborn
Female
*Feeding Behavior
Child
Infant Nutritional Physiological Phenomena
Milk, Human
Infant Formula

@article {pmid42451600,
year = {2026},
author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I},
title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
pmid = {42451600},
issn = {1420-3049},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; },
abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.},
}

Humans
*Wound Healing/drug effects
*Microbiota
Chronic Disease
*Host Microbial Interactions
Animals
Probiotics/therapeutic use
Skin Microbiome
Biofilms
Translational Research, Biomedical

@article {pmid42185318,
year = {2026},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR},
title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42185318},
issn = {2041-1723},
support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Skin Microbiome ; Humans ; Metagenome ; *Skin/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Anti-Infective Agents/pharmacology/metabolism ; *Microbiota ; Multigene Family ; Phylogeny ; },
abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.},
}

*Skin Microbiome
Humans
Metagenome
*Skin/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Anti-Infective Agents/pharmacology/metabolism
*Microbiota
Multigene Family
Phylogeny

@article {pmid42229598,
year = {2026},
author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y},
title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.},
journal = {Bioresource technology},
volume = {458},
number = {},
pages = {135043},
doi = {10.1016/j.biortech.2026.135043},
pmid = {42229598},
issn = {1873-2976},
mesh = {*Lignin/metabolism ; *Methane/biosynthesis/metabolism ; Electron Transport ; *Microbial Consortia/physiology ; *Metabolic Networks and Pathways ; Hydrogen-Ion Concentration ; Animals ; Cattle ; Manure/microbiology ; },
abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.},
}

*Lignin/metabolism
*Methane/biosynthesis/metabolism
Electron Transport
*Microbial Consortia/physiology
*Metabolic Networks and Pathways
Hydrogen-Ion Concentration
Animals
Cattle
Manure/microbiology

@article {pmid42243631,
year = {2026},
author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW},
title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {33},
number = {8},
pages = {1446-1456},
doi = {10.1093/jamia/ocag088},
pmid = {42243631},
issn = {1527-974X},
support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; U19 AI44297/NH/NIH HHS/United States ; },
mesh = {*Dashboard Systems ; *Wastewater/virology ; *Genomics ; Humans ; *Virome ; User-Computer Interface ; },
abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.

MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.

RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.

DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.

CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.},
}

*Dashboard Systems
*Wastewater/virology
*Genomics
Humans
*Virome
User-Computer Interface

@article {pmid42262118,
year = {2026},
author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P},
title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0050126},
doi = {10.1128/msystems.00501-26},
pmid = {42262118},
issn = {2379-5077},
mesh = {Animals ; Cattle ; Third Generation Cephalosporins ; *Feces/microbiology ; *Escherichia coli/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cephalosporins/pharmacology ; Escherichia coli Infections/microbiology/veterinary ; },
abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.},
}

Animals
Cattle
Third Generation Cephalosporins
*Feces/microbiology
*Escherichia coli/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Cephalosporins/pharmacology
Escherichia coli Infections/microbiology/veterinary

@article {pmid42262136,
year = {2026},
author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G},
title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0028426},
doi = {10.1128/msystems.00284-26},
pmid = {42262136},
issn = {2379-5077},
support = {ID 2721017//Fondazione Regionale Ricerca Biomedica/ ; MFAG-2024 ID 31114//AIRC/ ; ZIA BC 010793/NH/NIH HHS/United States ; ZIA BC 011152/NH/NIH HHS/United States ; ZIA BC 011153/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Bacteria/genetics/classification ; },
abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.

IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.},
}

Humans
*Microbiota
*Metagenomics/methods
*Gastrointestinal Microbiome
Bacteria/genetics/classification

@article {pmid42264042,
year = {2026},
author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H},
title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.},
journal = {Bioresource technology},
volume = {458},
number = {},
pages = {135134},
doi = {10.1016/j.biortech.2026.135134},
pmid = {42264042},
issn = {1873-2976},
mesh = {*Metagenomics ; *Geologic Sediments/microbiology ; *Sewage/microbiology/chemistry ; *Carbon/metabolism ; Biological Oxygen Demand Analysis ; *Organic Chemicals/metabolism ; *Bacteria/metabolism/genetics ; *Cities ; Extracellular Polymeric Substance Matrix ; *Microbiota/genetics ; Biodegradation, Environmental ; },
abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.},
}

*Metagenomics
*Geologic Sediments/microbiology
*Sewage/microbiology/chemistry
*Carbon/metabolism
Biological Oxygen Demand Analysis
*Organic Chemicals/metabolism
*Bacteria/metabolism/genetics
*Cities
Extracellular Polymeric Substance Matrix
*Microbiota/genetics
Biodegradation, Environmental

@article {pmid42300737,
year = {2026},
author = {Bueno de Mesquita, CP and Stallard-Olivera, E and Fierer, N},
title = {Predicting oxygen levels in microbial habitats using a metagenome-based approach.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0054526},
doi = {10.1128/msystems.00545-26},
pmid = {42300737},
issn = {2379-5077},
support = {NNF24SA0092560//Novo Nordisk Fonden/ ; 313162/Z/24/Z/WT_/Wellcome Trust/United Kingdom ; #W911-NF-23-1-0311//Army Research Office/ ; },
mesh = {*Oxygen/analysis/metabolism ; *Metagenome ; Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/metabolism ; *Microbiota ; Humans ; Ecosystem ; },
abstract = {Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats.IMPORTANCEOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.},
}

*Oxygen/analysis/metabolism
*Metagenome
Soil Microbiology
*Metagenomics/methods
*Bacteria/genetics/metabolism
*Microbiota
Humans
Ecosystem

@article {pmid42308920,
year = {2026},
author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC},
title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {201},
number = {},
pages = {119656},
doi = {10.1016/j.biopha.2026.119656},
pmid = {42308920},
issn = {1950-6007},
mesh = {*Synbiotics/administration & dosage ; Animals ; *Antioxidants/pharmacology/therapeutic use/administration & dosage ; Male ; Humans ; Disease Progression ; Mice, Inbred C57BL ; Pilot Projects ; Liver/metabolism/drug effects/pathology ; Diet, High-Fat ; Mice ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; Gastrointestinal Microbiome/drug effects ; *Fatty Liver/drug therapy/metabolism ; Drug Synergism ; Middle Aged ; Feces/microbiology ; },
abstract = {BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.

METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n = 27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.

RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p < 0.05), and increased the respiratory exchange ratio (p < 0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p < 0.05), while antioxidants primarily reduced adipose tissue (p < 0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p < 0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p < 0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.

CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.},
}

*Synbiotics/administration & dosage
Animals
*Antioxidants/pharmacology/therapeutic use/administration & dosage
Male
Humans
Disease Progression
Mice, Inbred C57BL
Pilot Projects
Liver/metabolism/drug effects/pathology
Diet, High-Fat
Mice
*Non-alcoholic Fatty Liver Disease/metabolism/drug therapy
Gastrointestinal Microbiome/drug effects
*Fatty Liver/drug therapy/metabolism
Drug Synergism
Middle Aged
Feces/microbiology

@article {pmid42328867,
year = {2026},
author = {Wang, Y and Sheng, P and Wang, S and Zhong, X and Cao, H and Li, D and Yan, J and Yang, J and Wang, Y and Peng, J and Sun, F and Wang, S and Feng, Y and Sun, J and Zhang, F},
title = {Gut microbiota translocation contributes to early islet apoptosis in streptozotocin-induced diabetes.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0017226},
doi = {10.1128/msystems.00172-26},
pmid = {42328867},
issn = {2379-5077},
support = {2022YFF1100601//National Key Research and Development Program of China/ ; LCYJ202347//Wuxi Translational Medicine Research Institute/ ; 2023YFF1104305//National Key Research and Development Program of China/ ; 82370809//National Natural Science Foundation of China/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; BK20221204//Funding for Leading Talents in Medical and Health Profession in Wuxi Taihu Lake Talent Plan/ ; CXTD2021003//Key Discipline Construction Program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; HB2023063//Medical Key Discipline Program of Wuxi Health Commission/ ; },
mesh = {Animals ; *Apoptosis ; *Diabetes Mellitus, Experimental/pathology/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Mice ; *Islets of Langerhans/pathology/metabolism ; Male ; Fecal Microbiota Transplantation ; Streptozocin ; Intestinal Barrier Function ; *Bacterial Translocation ; Dysbiosis ; Mice, Inbred C57BL ; },
abstract = {Dysbiosis of the gut microbiota and impaired intestinal barrier are associated with diabetes development. The translocation of gut microbiota induced by streptozotocin (STZ) has been confirmed to damage pancreatic islets. However, it remains uncertain whether dysregulated gut microbiota plays an essential role in the translocation leading to pancreatic injury. In specific pathogen-free (SPF) and germ-free (GF) mice treated with STZ, we measured glucose metabolism levels, pancreatic islet damage, intestinal barrier integrity, and bacterial content in the pancreas to investigate the role of gut microbiota translocation in diabetes development. Shotgun metagenomic sequencing was used to analyze the impact of STZ on gut microbiota structure and function. Fecal microbiota transplantation was performed to explore if gut microbiota translocation depends on STZ-induced structural dysregulation. STZ induced intestinal damage in SPF mice, resulting in gut microbiota translocation to the pancreas, pancreatic apoptosis, and dysregulated glucose metabolism. Despite inherent intestinal barrier damage, absence of pancreatic apoptosis in GF mice further indicates that gut microbiota translocation is an essential prerequisite for STZ-induced pancreatic islet apoptosis. STZ significantly altered mouse gut microbiota composition and function. Transplantation of fecal microbiota from STZ-treated or saline-treated mice into STZ-induced GF mice also resulted in microbial translocation and pancreas apoptosis. Apoptosis of β cells in STZ-treated mice results from gut microbiota translocating to the pancreas through impaired intestinal barrier caused by STZ treatment independent of alterations in the gut microbial community.IMPORTANCEIn our study, the apoptosis of β cells in STZ-treated mice is the result of the translocation of gut microbiota to the pancreas through the impaired intestinal barrier induced by STZ, independent of alterations in the gut microbiota. These findings proposed the potential role of compounds in impairing the intestinal barrier integrity, promoting microbiota migration and finally damaging pancreatic islets.},
}

Animals
*Apoptosis
*Diabetes Mellitus, Experimental/pathology/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Mice
*Islets of Langerhans/pathology/metabolism
Male
Fecal Microbiota Transplantation
Streptozocin
Intestinal Barrier Function
*Bacterial Translocation
Dysbiosis
Mice, Inbred C57BL

@article {pmid42370706,
year = {2026},
author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, MØ},
title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0057726},
doi = {10.1128/msystems.00577-26},
pmid = {42370706},
issn = {2379-5077},
support = {NNF20OC0061313//Novo Nordisk Fonden/ ; NOD-AOL 101125376/ERC_/European Research Council/International ; 295910//Norges Forskningsråd/ ; NNF20OC0061165//Novo Nordisk Fonden/ ; },
mesh = {*Lignin/metabolism ; *Lakes/microbiology ; *Denitrification ; *Geologic Sediments/microbiology ; *Microbial Consortia ; Bacteria/metabolism/genetics/classification ; Nitrates/metabolism ; Eutrophication ; Metagenome ; },
abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.},
}

*Lignin/metabolism
*Lakes/microbiology
*Denitrification
*Geologic Sediments/microbiology
*Microbial Consortia
Bacteria/metabolism/genetics/classification
Nitrates/metabolism
Eutrophication
Metagenome

@article {pmid42370713,
year = {2026},
author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ},
title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0113625},
doi = {10.1128/msystems.01136-25},
pmid = {42370713},
issn = {2379-5077},
support = {18-ERD-041//Lawrence Livermore National Laboratory/ ; SCW1632//U.S. Department of Energy/ ; },
mesh = {*Virion/genetics/isolation & purification ; *Grassland ; *Soil Microbiology ; *Virome/genetics ; *Metagenomics/methods ; Genome, Viral ; Soil/chemistry ; },
abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.},
}

*Virion/genetics/isolation & purification
*Grassland
*Soil Microbiology
*Virome/genetics
*Metagenomics/methods
Genome, Viral
Soil/chemistry

@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
support = {R56AG079586//National Institute of Health/ ; },
mesh = {*Microbiota ; *Machine Learning ; Humans ; Multivariate Analysis ; },
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

*Microbiota
*Machine Learning
Humans
Multivariate Analysis

@article {pmid42377028,
year = {2026},
author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K},
title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.},
journal = {mSystems},
volume = {11},
number = {7},
pages = {e0048926},
doi = {10.1128/msystems.00489-26},
pmid = {42377028},
issn = {2379-5077},
support = {081901/21-25//Bundesinstitut für Sportwissenschaft (BISp)/ ; 01EA1707 & 01EA1708//Bundesministerium für Bildung und Forschung (BMBF)/ ; EXC2151-390873048//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {Humans ; *Athletes ; Female ; Germany ; Adult ; *Gastrointestinal Microbiome/genetics ; Male ; Young Adult ; Adolescent ; *Bacteria/classification/genetics ; Metagenomics ; },
abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.},
}

Humans
*Athletes
Female
Germany
Adult
*Gastrointestinal Microbiome/genetics
Male
Young Adult
Adolescent
*Bacteria/classification/genetics
Metagenomics

@article {pmid42449467,
year = {2026},
author = {Gan, L and Yang, Z and Zhang, Y and Wang, S and Meng, F and Liu, Y and Dorji, T},
title = {Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00928-1},
pmid = {42449467},
issn = {2524-6372},
support = {QYXTZX-AL2022-05//Regional Science and Technology Collaborative Innovation Special Project of Ngari in Tibetan Autonomous Region of China/ ; 2019QZKK0600//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U20A2005//the Joint Key Research Fund under cooperative agreement between the National Natural Science Foundation of China (NSFC) and Tibet Autonomous Region (TAR)/ ; 42122005//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear.

RESULTS: A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway.

CONCLUSIONS: Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.},
}

@article {pmid42262316,
year = {2026},
author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J},
title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.},
journal = {Chemical research in toxicology},
volume = {39},
number = {7},
pages = {1302-1310},
doi = {10.1021/acs.chemrestox.5c00556},
pmid = {42262316},
issn = {1520-5010},
mesh = {Animals ; *Polyesters/chemistry/toxicity/pharmacology ; *Microplastics/chemistry/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polylactic Acid-Polyglycolic Acid Copolymer/chemistry/toxicity ; Male ; Liver/metabolism/drug effects ; },
abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.},
}

Animals
*Polyesters/chemistry/toxicity/pharmacology
*Microplastics/chemistry/toxicity
*Gastrointestinal Microbiome/drug effects
*Polylactic Acid-Polyglycolic Acid Copolymer/chemistry/toxicity
Male
Liver/metabolism/drug effects

@article {pmid42300931,
year = {2026},
author = {Medouni-Haroune, L and Medouni-Adrar, S and Messaoudene, L and Negrichi, S and Bouiche, C and Sahraoui-Remini, Y and Allam, A and Meghlaoui, Z and Mouhoubi, K and Abbou, A and Brahimi, N and Mellal, MK and Sari, Z and Madani, K},
title = {Animal-based diets and the human gut microbiota: an integrative review combining metagenomic profiling and graphical synthesis of diet-microbiota associations.},
journal = {Food & function},
volume = {17},
number = {14},
pages = {6294-6314},
doi = {10.1039/d6fo00371k},
pmid = {42300931},
issn = {2042-650X},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; *Diet ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Animal Feed/analysis ; },
abstract = {This review examines the relationships between animal-based diets, gut microbiota architecture, and human health by integrating insights from metagenomic studies and literature-based graphical representations. The gut microbiota is a complex microbial ecosystem, whose organization is closely linked to intestinal homeostasis and host health. Drawing on published metagenomic datasets, the review synthesizes patterns of dominant microbial groups and their organization within the gut, providing a framework for interpreting diet-related microbial variations across different geographic and cultural contexts. Evidence from the literature on animal-derived foods is integrated through graphical visualization to illustrate associations between specific foods and gut microbial taxa. These visualizations highlight distinct association patterns and microbial responses to various animal-based dietary components. The review discusses these patterns in relation to intestinal health, disease susceptibility, and potential dietary interventions. Overall, this work provides a structured, integrative perspective on the impact of animal-based diets on gut microbiota architecture, emphasizing the relevance of combining metagenomic insights with literature-based synthesis to inform nutritional science and public health strategies.},
}

Humans
Animals
*Gastrointestinal Microbiome
*Diet
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
*Animal Feed/analysis

@article {pmid42390352,
year = {2026},
author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Jingjing, X and Lianyi, H and Wang, B and Li, Y and Roeselers, G and Gong, S},
title = {Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.},
journal = {Food & function},
volume = {17},
number = {14},
pages = {6596-6607},
doi = {10.1039/d6fo02082h},
pmid = {42390352},
issn = {2042-650X},
mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; China ; Infant, Newborn ; Female ; Feces/microbiology ; *Metabolome ; Male ; Bacteria/classification/genetics/isolation & purification ; Child, Preschool ; Bifidobacterium ; Prebiotics ; Breast Feeding ; Infant Formula ; East Asian People ; },
abstract = {The neonatal period is a critical stage of development during which the gut microbiome profoundly influences both short- and long-term health and nutrition. Its maturation from infancy to childhood is shaped by interacting environmental factors, including feeding mode, birth mode, and geographic location. A clinical study of 445 infants and toddlers (aged 0-24 months) from six socioeconomically diverse regions in China investigated age-related trajectories of gut microbiome and metabolomic development, with a particular focus on feeding mode. The study included a breastfed reference group and a formula-fed group that received an open-label formula containing a prebiotic mixture of short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS, 9 : 1). Longitudinal fecal samples were analyzed using shotgun metagenomic and metabolomic approaches. Feeding mode was strongly associated with variations in gut microbiome structure and function, along with birth mode and geographic location. Bifidobacterium and Bacteroides were the dominant taxa in both groups and exhibited dynamic abundance trajectories over time. Increased Bifidobacterium abundance was correlated with gene functions involved in starch and fatty acid metabolism as well as the fructose-6-phosphoketolase pathway (Bifid shunt). Comparative metabolomic analyses of amino acids and bile acids revealed highly similar metabolic profiles between the two groups. These findings highlight the association between feeding mode with the developing gut microbiome and describe age-dependent trajectories in Chinese children.},
}

Humans
Infant
*Gastrointestinal Microbiome
China
Infant, Newborn
Female
Feces/microbiology
*Metabolome
Male
Bacteria/classification/genetics/isolation & purification
Child, Preschool
Bifidobacterium
Prebiotics
Breast Feeding
Infant Formula
East Asian People

@article {pmid42446470,
year = {2026},
author = {Almulhim, F and Narayanasamy, S and Wang, C and Mandal, P and Bensaddek, D and Amad, M and Hong, PY},
title = {Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70372},
pmid = {42446470},
issn = {1462-2920},
support = {BAS/1/1033-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Wastewater/microbiology/chemistry ; Proteomics ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Biofilms ; Metagenomics ; Nitrogen/metabolism ; Denitrification ; },
abstract = {Reclaimed wastewater is increasingly reused for irrigation and other non-potable applications; however, inadequately treated effluent has raised concerns regarding environmental and public health impacts. Water quality in reclaimed distribution systems is shaped by multiple factors, particularly hydraulic stagnation in pipes and storage reservoirs. Stagnation can alter microbial community stability and facilitate persistence of pathogenic taxa. To investigate how prolonged stagnation affects microbial community structure and function, we integrated metagenomics and metaproteomics analyses of biofilms under flow and stagnant conditions over 3, 5 and 7 months. Prolonged stagnation caused pronounced compositional shifts, including strong reductions in nitrogen-removing taxa such as Nitrospira and Nitrosomonas. Correspondingly, key nitrification and denitrification proteins were depleted ≥ twofold under stagnation, indicating impaired nitrogen conversion processes. Stagnation also enriched motility- and transport-related functions and promoted Acidovorax persistence, a genus including phytopathogenic species. In contrast, flow conditions sustained nitrogen-cycling activity, contaminant-degrading enzymes, and quorum-quenching proteins, supporting greater biostability. Overall, our findings show that prolonged stagnation disrupts microbial community balance, suppresses essential nitrogen-cycling and detoxification pathways, and reduces the functional robustness of treated wastewater. Maintaining hydraulic flow within reclaimed water systems is therefore critical for preserving microbial functionality and ensuring safe and reliable reuse in irrigation and other non-potable applications.},
}

*Wastewater/microbiology/chemistry
Proteomics
*Microbiota
*Bacteria/genetics/classification/metabolism/isolation & purification
Biofilms
Metagenomics
Nitrogen/metabolism
Denitrification

@article {pmid42447082,
year = {2026},
author = {Rodríguez, JA and Santos-Bay, L and Narechania, A and Carøe, C and Sirén, K and Mak, SST and Broman Nielsen, I and Ramsøe, M and Pontén, TS and Lillevang, S and Andersen, LT and Gilbert, MTP},
title = {The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0350187},
pmid = {42447082},
issn = {1932-6203},
mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota/genetics ; Metagenome ; Food Microbiology ; Pasteurization ; Lactococcus lactis/genetics/isolation & purification ; Clostridium tyrobutyricum/genetics/isolation & purification ; },
abstract = {One of the biggest challenges for dairy producers is the substantial variability in final product properties caused by changes in the production environment. In cheese production, this variation is influenced by several factors, particularly the milk base and its pretreatment, which shape the microbiome throughout the process and ultimately affect the cheese's organoleptic characteristics. To examine the impact of three different pretreatments for pasteurised milk- microfiltration, protein fortification, and pasteurisation only (control)- on microbiome dynamics, we generated metagenome sequencing data from 14 cheese production steps across these three production trials at a Danish dairy factory. We constructed three metagenomic co-assemblies, identifying nine high-quality metagenome-assembled genomes. Our analysis revealed that a specific strain of Lactococcus lactis dominates the process, while other minor bacterial species persist at very low abundances (<1%), contributing non-negligibly to product properties. Notably, we detected DNA from Clostridium tyrobutyricum, a known bacterium whose heat-resistant spores may cause dairy spoilage, in pasteurised only and protein-fortified milk trials but was nearly absent in microfiltered milk. To enhance our analyses, we implemented KHILL, a novel k-mer based method, which facilitates metagenomic co-assembly and enables early detection of unwanted microorganisms. Our findings provide industrial dairy producers with a comprehensive view of microbial dynamics during cheese production, offering insights to improve process consistency and product quality.},
}

*Cheese/microbiology
Animals
*Milk/microbiology
*Microbiota/genetics
Metagenome
Food Microbiology
Pasteurization
Lactococcus lactis/genetics/isolation & purification
Clostridium tyrobutyricum/genetics/isolation & purification

@article {pmid42106361,
year = {2026},
author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X},
title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42106361},
issn = {2055-5008},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&D Programme/ ; },
mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Early Detection of Cancer/methods ; *Gastrointestinal Microbiome ; Metagenome ; Cohort Studies ; Computational Biology/methods ; Adenoma/diagnosis/microbiology ; },
abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.},
}

*Colorectal Neoplasms/diagnosis/microbiology
Humans
*Early Detection of Cancer/methods
*Gastrointestinal Microbiome
Metagenome
Cohort Studies
Computational Biology/methods
Adenoma/diagnosis/microbiology

@article {pmid42151282,
year = {2026},
author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G},
title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42151282},
issn = {2045-2322},
support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Università e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Università e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; },
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Shotgun Sequencing ; *Metagenome ; Nanopore Sequencing/methods ; Benchmarking ; Bacteria/genetics/classification ; },
abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.},
}

*Metagenomics/methods
*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Shotgun Sequencing
*Metagenome
Nanopore Sequencing/methods
Benchmarking
Bacteria/genetics/classification

@article {pmid42156772,
year = {2026},
author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and , and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E},
title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42156772},
issn = {2041-1723},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
mesh = {Animals ; Dogs/microbiology ; *Aging/physiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Metagenomics ; Diet/veterinary ; Cohort Studies ; Humans ; Pets/microbiology ; },
abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.},
}

Animals
Dogs/microbiology
*Aging/physiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Metagenomics
Diet/veterinary
Cohort Studies
Humans
Pets/microbiology

@article {pmid42185948,
year = {2026},
author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P},
title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42185948},
issn = {1471-2164},
support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Hemiptera/microbiology/genetics/classification ; *Symbiosis ; Phylogeny ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Genetic Variation ; Microbiota ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.

RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.

CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.},
}

Animals
*Hemiptera/microbiology/genetics/classification
*Symbiosis
Phylogeny
Metagenomics
RNA, Ribosomal, 16S/genetics
Genetic Variation
Microbiota
Bacteria/genetics/classification

@article {pmid42349523,
year = {2026},
author = {Muqaddas, K and Mahnoor, and Hayat, O and Islam, A and Khan, R and Naz, S},
title = {Cutaneous leishmaniasis promotes skin microbial dysbiosis and exacerbation of local inflammatory responses.},
journal = {Microbial pathogenesis},
volume = {218},
number = {},
pages = {108655},
doi = {10.1016/j.micpath.2026.108655},
pmid = {42349523},
issn = {1096-1208},
mesh = {Humans ; *Leishmaniasis, Cutaneous/pathology/microbiology/parasitology ; Skin Microbiome ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Female ; *Skin/microbiology/pathology/parasitology ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Leishmania tropica/isolation & purification/genetics ; DNA, Bacterial/genetics/chemistry ; *Inflammation/pathology ; Microbiota ; Adult ; DNA, Ribosomal Spacer/genetics/chemistry ; Phylogeny ; },
abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.},
}

Humans
*Leishmaniasis, Cutaneous/pathology/microbiology/parasitology
Skin Microbiome
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Female
*Skin/microbiology/pathology/parasitology
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
Leishmania tropica/isolation & purification/genetics
DNA, Bacterial/genetics/chemistry
*Inflammation/pathology
Microbiota
Adult
DNA, Ribosomal Spacer/genetics/chemistry
Phylogeny

@article {pmid42440035,
year = {2026},
author = {Mathiyazhagan, S and Balu, B and Gunaseelan, RJ and Piliyan, R and Perumal, S and Natesan, M},
title = {Discovery of novel bio-resources from the hidden biodiversity of marine mangrove ecosystems.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {10},
pages = {},
pmid = {42440035},
issn = {1573-2983},
mesh = {*Wetlands ; *Biodiversity ; Animals ; Biological Products ; Fungi/metabolism ; Bacteria/metabolism ; Biotechnology ; Invertebrates/metabolism ; },
abstract = {Marine mangrove wetlands are ecologically complex ecosystems that serve as rich reservoirs of biologically active compounds with significant biotechnological potential. This review synthesizes current knowledge on mangrove-associated microorganisms and biota, including bacteria, fungi, algae, and invertebrates, with emphasis on their bioassay activities and derived bioactive metabolites. Various analytical approaches, including chromatographic techniques, LC-MS/NMR analysis, and in silico tools, have been employed to identify and characterize compounds such as enzymes, polysaccharides, biosurfactants, and antimicrobial peptides. These biomolecules exhibit diverse functional applications in medicine, environmental management, and industrial processes, including nitrogen fixation, bioremediation, and hydrocarbon degradation. The review highlights that mangrove-derived bioactive compounds are influenced by both ecological interactions and environmental conditions. Furthermore, recent advances indicate a shift toward genome-guided discovery using multi-omics and metagenomic approaches, enabling the identification of novel biosynthetic pathways, particularly from unculturable microorganisms. This integrated approach enhances the efficiency of bioactive compound discovery and supports scalable production through synthetic biology. Overall, mangrove ecosystems represent promising platforms for sustainable biotechnological innovation, underscoring the need for their conservation and the development of integrated validation strategies.},
}

*Wetlands
*Biodiversity
Animals
Biological Products
Fungi/metabolism
Bacteria/metabolism
Biotechnology
Invertebrates/metabolism

@article {pmid42034975,
year = {2026},
author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K},
title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42034975},
issn = {1471-2180},
support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; },
mesh = {Wetlands ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; *Poa/microbiology ; Lakes/microbiology ; Soil/chemistry ; Phylogeny ; Tibet ; Metagenome ; RNA, Ribosomal, 16S/genetics ; China ; Biodiversity ; },
abstract = {The Qinghai Lake alpine wetland, a critical ecological barrier on the northeastern Qinghai-Tibet Plateau, relies heavily on its rhizosphere microbial communities to sustain regional ecosystem stability. This study investigated the dominant forage grass Poa alpigena across sites subjected to varying anthropogenic disturbance intensities-high-intensity grazing (Haergai, HE), moderate grazing (Sanjiaocheng, SJ), and an undisturbed control (Haixinshan, X)-using metagenomic sequencing to compare rhizosphere and non-rhizosphere soil microbiomes. Results identified Proteobacteria, Actinobacteria, and Planctomycetes as the dominant phyla, collectively representing > 55% of microbial composition. At the genus level, Streptomyces, Pseudomonas, and Sphingomonas exhibited significant enrichment. α-Diversity (Chao1 and Shannon indices) was markedly higher in rhizosphere than non-rhizosphere soils, while β-diversity (PCoA) revealed distinct spatial clustering. Mantel tests identified soil moisture, pH, and conductivity as key drivers of microbial community assembly. Functional profiling showed non-rhizosphere microbes were enriched in environmental stress-response pathways (e.g., quorum sensing, lipopolysaccharide biosynthesis), whereas rhizosphere microbes dominated metabolic processes like valine/leucine degradation and arginine biosynthesis. LEfSe analysis further highlighted site-specific taxa: Streptomyces and Sphingopyxis in Haergai, Nocardioides in Sanjiaocheng, and Pseudomonas with Azospirillum in Haixinshan. These findings deepen our understanding of microbial responses to anthropogenic pressures and offer actionable insights for restoring degraded alpine grasslands.},
}

Wetlands
*Soil Microbiology
*Rhizosphere
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
*Poa/microbiology
Lakes/microbiology
Soil/chemistry
Phylogeny
Tibet
Metagenome
RNA, Ribosomal, 16S/genetics
China
Biodiversity

@article {pmid42103726,
year = {2026},
author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G},
title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42103726},
issn = {2041-1723},
support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; Reproducibility of Results ; *DNA Contamination ; *Metagenome/genetics ; Microbiota/genetics ; *Software ; Animals ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.},
}

*Metagenomics/methods
Computational Biology/methods
Reproducibility of Results
*DNA Contamination
*Metagenome/genetics
Microbiota/genetics
*Software
Animals
High-Throughput Nucleotide Sequencing

@article {pmid42106331,
year = {2026},
author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P},
title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42106331},
issn = {2041-1723},
support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; },
mesh = {Humans ; Multiomics ; *Open Reading Frames/genetics ; Proteomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Micropeptides ; Proteome/genetics ; Metagenomics/methods ; Mass Spectrometry ; },
abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.},
}

Humans
Multiomics
*Open Reading Frames/genetics
Proteomics/methods
*Bacterial Proteins/genetics/metabolism
*Gastrointestinal Microbiome/genetics
Micropeptides
Proteome/genetics
Metagenomics/methods
Mass Spectrometry

@article {pmid42106335,
year = {2026},
author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I},
title = {Population-scale characterization of the oral microbiome and associations with metabolic health.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42106335},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/genetics ; Female ; *Mouth/microbiology ; Male ; Phenotype ; Metagenome ; Liver/metabolism/diagnostic imaging ; Adult ; Continuous Glucose Monitoring ; Middle Aged ; *Metabolic Diseases/microbiology/metabolism ; Adiposity ; Absorptiometry, Photon ; },
abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.},
}

Humans
*Microbiota/genetics
Female
*Mouth/microbiology
Male
Phenotype
Metagenome
Liver/metabolism/diagnostic imaging
Adult
Continuous Glucose Monitoring
Middle Aged
*Metabolic Diseases/microbiology/metabolism
Adiposity
Absorptiometry, Photon

@article {pmid42176229,
year = {2026},
author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB},
title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42176229},
issn = {1751-7370},
support = {//National Science Foundation/ ; #2025250//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; #2025337//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; #2025262//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; LS-ECIAMEE-00001638//Simons Foundation/ ; DEB 2236782//NSF CAREER award/ ; },
mesh = {*Carbon/metabolism ; *Bacteria/genetics/metabolism/classification ; *Microbiota/genetics ; rRNA Operon ; Genome Size ; Metagenomics ; Heterotrophic Processes ; },
abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.},
}

*Carbon/metabolism
*Bacteria/genetics/metabolism/classification
*Microbiota/genetics
rRNA Operon
Genome Size
Metagenomics
Heterotrophic Processes

@article {pmid42191017,
year = {2026},
author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Barra Caracciolo, A and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V},
title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.},
journal = {New biotechnology},
volume = {94},
number = {},
pages = {121-135},
doi = {10.1016/j.nbt.2026.05.013},
pmid = {42191017},
issn = {1876-4347},
mesh = {*Metals, Heavy/isolation & purification/metabolism ; *Soil Pollutants/metabolism/isolation & purification ; Biodegradation, Environmental ; *Soil Microbiology ; *Microbiota ; *Rhizosphere ; Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - such as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.},
}

*Metals, Heavy/isolation & purification/metabolism
*Soil Pollutants/metabolism/isolation & purification
Biodegradation, Environmental
*Soil Microbiology
*Microbiota
*Rhizosphere
Bacteria/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42377908,
year = {2026},
author = {Deng, Y and Borton, MA and Nesbø, CL and Forster, MD and Konhauser, KO and Gingras, MK and Goss, GG and Wrighton, KC and Lanoil, BD and Zhong, C and Alessi, DS},
title = {Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {8},
pages = {},
doi = {10.1093/femsec/fiag070},
pmid = {42377908},
issn = {1574-6941},
support = {SQ2024AAA120010//National Major Science and Technology Projects of China/ ; //National Natural Science Foundation of China/ ; CRDPJ-469308-14//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; China ; Biodiversity ; *Water Microbiology ; *Archaea/genetics/classification/isolation & purification ; *Microbiota ; Hydraulic Fracking ; Salinity ; Oil and Gas Fields/microbiology ; Metagenome ; *Groundwater/microbiology/chemistry ; },
abstract = {Microbial communities inhabiting hydraulically fractured subsurface waters are increasingly recognized as important components of unconventional oil and gas systems because they can influence water quality, infrastructure integrity, and biogeochemical processes during flowback and production. However, a quantitative cross-basin understanding of their taxonomic diversity, ecological organization, and potential functional variation remains limited. In this study, we analyzed 16S rRNA gene amplicons, metagenomes, and geochemical data from flowback and produced water from the Sichuan Basin, China, and conducted a quantitative comparison to data previously reported from the same basin and hydraulic fracturing regions in North America. Our findings revealed strong co-occurrence patterns among fermentative, sulfidogenic, and methanogenic micro-organisms, which emerged as core members of microbial communities across all fractured subsurface environments. Notably, microbial diversity and selected metabolic traits differed across basins in the low-salinity systems of China, whereas high-salinity basins in North America exhibited reduced diversity and more constrained metabolic capabilities. These differences are consistent with salinity acting as an important ecological filter across the analyzed basins. Our results indicate that basin-specific geochemical context, particularly salinity, is closely associated with cross-basin differences in microbial diversity, community composition, and selected metabolic traits in fractured subsurface waters. These findings support the value of integrating geological, geochemical, and microbiological information when interpreting microbial risks and water-management strategies in hydraulic fracturing systems.},
}

RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
China
Biodiversity
*Water Microbiology
*Archaea/genetics/classification/isolation & purification
*Microbiota
Hydraulic Fracking
Salinity
Oil and Gas Fields/microbiology
Metagenome
*Groundwater/microbiology/chemistry

@article {pmid42398246,
year = {2026},
author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X},
title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.},
journal = {Journal of environmental management},
volume = {413},
number = {},
pages = {130396},
doi = {10.1016/j.jenvman.2026.130396},
pmid = {42398246},
issn = {1095-8630},
mesh = {Animals ; Parks, Recreational ; *Snails/microbiology ; Dogs ; *Introduced Species ; *Drug Resistance, Microbial/genetics ; China ; Feces/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.},
}

Animals
Parks, Recreational
*Snails/microbiology
Dogs
*Introduced Species
*Drug Resistance, Microbial/genetics
China
Feces/microbiology
Drug Resistance, Bacterial

@article {pmid42434559,
year = {2026},
author = {Saraiva, M and Gerilovych, A and Ay, H},
title = {Editorial: Harnessing aquatic microbial symbioses for sustainable aquaculture: unveiling biodiversity and ecosystem dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1897215},
doi = {10.3389/fmicb.2026.1897215},
pmid = {42434559},
issn = {1664-302X},
}

@article {pmid42436177,
year = {2026},
author = {Eriksson, D and Righetti, D and Benedetti, F and Gruber, N and Paoli, L and Salazar, G and Sunagawa, S and Vogt, M},
title = {Nitrogen fixation rates increase with diazotroph richness in the global ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61132-2},
pmid = {42436177},
issn = {2045-2322},
abstract = {Marine nitrogen fixation is a key process to support and maintain the ocean's primary production, yet our knowledge of the distribution and diversity of the diazotrophic microbes that are capable of fixing nitrogen is very limited. Here, integrating microscopic and metagenomic data, we determine the biogeography and richness of the main diazotrophic taxa across the global ocean. Analyzing 22,000 records and 15 species, we deduce a latitudinal gradient in diazotroph richness, with higher richness to the tropics driven by temperature and nutrient levels. Cyanobacteria dominate in nutrient-poor gyres, while non-cyanobacterial diazotrophs thrive in nutrient-rich zones. Across the global ocean, diazotroph richness is found to correlate positively with nitrogen fixation rates, suggesting a positive biodiversity-ecosystem function relationship. While this relationship is robust to spatial autocorrelation and confounding environmental drivers, spatial dependence in the global datasets and potential unmeasured covariates may influence local-scale inferences. The findings suggest that positive biodiversity-ecosystem functioning relationships with implications for global biogeochemical cycling exist in marine plankton.},
}

@article {pmid42437978,
year = {2026},
author = {Xia, J and Meng, L and Fang, Y and Ban, H and Okazaki, Y and Yoshida, T and Endo, H and Nagasaki, K and Ogata, H},
title = {Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom.},
journal = {Microbes and environments},
volume = {41},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME26018},
pmid = {42437978},
issn = {1347-4405},
mesh = {Japan ; *Genetic Variation ; *Giant Viruses/genetics/classification/isolation & purification ; *Eutrophication ; Phylogeny ; Genome, Viral ; Metagenomics ; Seawater/virology ; Biodiversity ; },
abstract = {Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Knowledge on their population genetic dynamics is mostly derived from a small number of laboratory-based experiments, while patterns in nature are rarely observed. To overcome this limitation, we traced the genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan by integrating cell counting, metabarcoding, and metagenomic and metatranscriptomic sequencing. The results obtained revealed that HaV dominated the giant virus community in most samples, with relative abundance up to 56%. Despite its high abundance, the HaV population exhibited a low level of microdiversity, but had a higher pN/pS ratio than other giant viruses in the study site. Microdiversity increased during the early sampling period, peaked mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, which may be driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Collectively, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variations.},
}

Japan
*Genetic Variation
*Giant Viruses/genetics/classification/isolation & purification
*Eutrophication
Phylogeny
Genome, Viral
Metagenomics
Seawater/virology
Biodiversity

@article {pmid42430137,
year = {2026},
author = {Allen, L and Sheneman, A and Morrow, MA},
title = {Post-wildfire soil bacterial MAGs and metagenome analysis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0044426},
doi = {10.1128/mra.00444-26},
pmid = {42430137},
issn = {2576-098X},
abstract = {We compare the differences between bacteria in soil affected by a wildfire to an unaffected area from Minnewaska State Park, NY, located in the biodiverse northern Shawangunk Ridge. We detail our metagenomic sequencing data, relative abundance of bacterial phyla, and the taxonomic classification of three MAGs.},
}

@article {pmid42430408,
year = {2026},
author = {Khan, N and Nasir, MM and Aziz, U and Manzoor, H and Raziq, MF and Hussain, Z and Jabeen, I and Kayani, MUR},
title = {Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0340748},
pmid = {42430408},
issn = {1932-6203},
mesh = {*Crohn Disease/microbiology/genetics ; Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; Molecular Dynamics Simulation ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/chemistry/metabolism ; Colitis, Ulcerative/microbiology/genetics ; },
abstract = {Metagenomics has revealed disease-associated shifts in microbial taxa and functions in inflammatory bowel disease (IBD) patients. However, the role of genomic variation in gut commensals remains poorly understood. Here, we integrated metagenomic profiling, variant calling, and structural bioinformatics to identify disease-associated variants in the gut microbes. Crohn's disease (CD) and ulcerative colitis (UC) showed significant negative associations with Bacteroides uniformis, Bacteroides vulgatus, and Eubacterium rectale. These bacteria exhibited 190,712 single-nucleotide polymorphisms, including 479 CD-specific and 235 UC-specific variants. Variant prioritization identified a CD-specific Val170Leu substitution in the conserved starch-binding domain of the Starch Utilization System D (SusD) protein in B. uniformis. Structural modeling and cyclodextrin docking indicated reduced binding affinity in the mutant, while 200-ns molecular dynamics simulations showed stable ligand retention only in the wild type. These findings suggest that impaired starch metabolism driven by SusD variation may contribute to B. uniformis depletion in CD and demonstrate the value of integrating metagenomics with structural analyses to identify functionally relevant microbial variants.},
}

*Crohn Disease/microbiology/genetics
Humans
*Metagenomics/methods
*Computational Biology/methods
Polymorphism, Single Nucleotide
Molecular Dynamics Simulation
Bacteroides/genetics
*Gastrointestinal Microbiome/genetics
Bacterial Proteins/genetics/chemistry/metabolism
Colitis, Ulcerative/microbiology/genetics

@article {pmid42430921,
year = {2026},
author = {Li, Z and Xie, R and Zhang, W and Cheng, J and Jia, P and Liu, C and Guo, X and Zhuang, L and Chen, T},
title = {Lead fraction transformation drives microbial functional recovery and coupled nutrient cycling-metal resistance networks in Pb-Zn tailings.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142947},
doi = {10.1016/j.jhazmat.2026.142947},
pmid = {42430921},
issn = {1873-3336},
abstract = {Ecological remediation of lead-zinc (Pb-Zn) mine tailings, characterized by nutrient deficiency and high concentrations of toxic metals, represents a significant environmental challenge. While revegetation is a promising strategy, the underlying microbial functional responses, particularly the coupling between nutrient cycling and heavy metal detoxification, remain insufficiently understood. This study investigated the geochemical evolution and microbial functional succession of a Pb-Zn tailings pond, encompassing fresh tailings, weathering, and revegetation areas. Geochemical analysis, metagenomic sequencing, and the cultivation of the dominant bacterial strain were employed. Results demonstrated that revegetation significantly enhanced microbial α-diversity and shifted community assembly toward stochasticity. Metagenomic analysis revealed a substantial increase in the abundance and diversity of functional genes related to carbon, nitrogen, phosphorus, and sulfur (C/N/P/S) cycling, concurrent with the enrichment of metal resistance genes. The transformation of Pb fraction, specifically a decrease in bioavailable (exchangeable) fractions and an increase in stable (organic-bound, residual) fractions, was identified as the key driver of microbial functional recovery. Co-occurrence network analysis demonstrated a strong synergy between the Pb resistance gene zntA/yhhO and core nutrient-cycling genes. Furthermore, the dominant isolated strain, Pseudomonas aeruginosa QPBII-1, exhibited high Pb(Ⅱ) removal efficiency (98.5%). Multi-faceted characterization indicated its removal mechanism involves extracellular immobilization and intracellular reduction of Pb(Ⅱ) to less toxic Pb(0)/PbO, supported by genomic evidence (e.g., pbrA, narB). This study demonstrates that revegetation fosters an integrated microbial network that couples biogeochemical cycling with metal resistance, providing a mechanistic basis for developing sustainable bioremediation strategies for metalliferous tailings.},
}

@article {pmid40877570,
year = {2026},
author = {Chia, M and Ng, AHQ and Ravikrishnan, A and Mohamed Naim, AN and Wearne, S and Common, J and Nagarajan, N},
title = {Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body.},
journal = {Nature biotechnology},
volume = {44},
number = {7},
pages = {1178-1189},
pmid = {40877570},
issn = {1546-1696},
mesh = {Humans ; Skin Microbiome/genetics ; *Metagenomics/methods ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; *Skin/microbiology ; *Metagenome/genetics ; Staphylococcus/genetics ; Microbiota/genetics ; },
abstract = {Metatranscriptomics methods for the skin are hampered by low microbial biomass, contamination with host cells and low RNA stability. In this study, we developed a robust, clinically tractable skin metatranscriptomics workflow that provides high technical reproducibility of profiles, uniform coverage across gene bodies and strong enrichment of microbial mRNAs. Paired application of this protocol with metagenomics to five skin sites in a cohort of 27 healthy adults identifies a notable divergence between transcriptomic and genomic abundances. Specifically, Staphylococcus species and the fungi Malassezia had an outsized contribution to metatranscriptomes at most sites, despite their modest representation in metagenomes. Species-level analysis shows signatures of microbial adaptation to their niches. Gene-level analysis identifies diverse antimicrobial genes transcribed by skin commensals in situ, including several uncharacterized bacteriocins. Correlation of microbial gene expression with organismal abundances uncovers more than 20 genes that putatively mediate interactions between microbes. This work highlights how skin metatranscriptomics identifies active species and microbial functions in situ.},
}

Humans
Skin Microbiome/genetics
*Metagenomics/methods
*Transcriptome/genetics
*Gene Expression Profiling/methods
*Skin/microbiology
*Metagenome/genetics
Staphylococcus/genetics
Microbiota/genetics

@article {pmid41094150,
year = {2026},
author = {Zhang, Y and Bhosle, A and Bae, S and Eckenrode, K and Huang, X and Tang, J and Lavrentovich, D and Awad, L and Hua, J and Wang, Y and Morgan, XC and Li, B and Krueger, A and Garrett, WS and Franzosa, EA and Huttenhower, C},
title = {Predicting functions of uncharacterized gene products from microbial communities.},
journal = {Nature biotechnology},
volume = {44},
number = {7},
pages = {1126-1141},
pmid = {41094150},
issn = {1546-1696},
support = {R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U19AI110820//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Bacterial Proteins/genetics/metabolism ; Multiomics ; },
abstract = {The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions for >443,000 protein families (~82.3% previously uncharacterized), including >27,000 protein families with weak homology to known proteins and >6,000 protein families without homology. These were drawn from 1,595 gut metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2/iHMP). Integrating additional information such as sequence similarity, genomic proximity and domain-domain interactions improves performance of the method. Our method's implementation, FUGAsseM, is generalizable and predicts protein function in both well-studied and undercharacterized communities. FUGAsseM achieves similar levels of accuracy in the context of microbial communities when compared to state-of-the-art approaches designed for application to single organisms while simultaneously providing much greater breadth of coverage. This initial study expands the functional landscape of the human gut microbiome and allows for exploration of microbial proteins in undercharacterized communities.},
}

Humans
*Microbiota/genetics
Metagenome/genetics
*Bacterial Proteins/genetics/metabolism
Multiomics

@article {pmid41766220,
year = {2026},
author = {Schwedhelm, C and Pinart, M and Forslund-Startceva, SK and Oluwagbemigun, K and Dötsch, A and Schlicht, K and Schwarz, F and Siampani, SM and Avraam, D and De Angelis, M and Bouwman, J and Brigidi, P and Caderni, G and Calabrese, FM and Cuadrat, RRC and De Filippo, C and De Filippis, F and Ercolini, D and Fabbrini, M and Laudes, M and Nöthlings, U and Özsezen, S and Sharon, I and Schulze, MB and Turroni, S and Vitali, F and Pischon, T and Nimptsch, K},
title = {Associations of Adiposity With Gut Microbiota Composition Among Adults-Results From a Federated Analysis of Individual Participant Data From Eight European Observational Studies.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {27},
number = {8},
pages = {e70106},
doi = {10.1111/obr.70106},
pmid = {41766220},
issn = {1467-789X},
support = {FKZ 01EA1906A//Bundesministerium für Bildung und Forschung/ ; 01EA1906B//Bundesministerium für Bildung und Forschung/ ; 01EA1906F//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; //Fund for Scientific Research (FRS-FNRS, Belgium)/ ; //Research Foundation-Flanders (FWO, Belgium)/ ; //Institut National de la Santé et de la Recherche Médicale/ ; //Bundesministerium für Ernährung und Landwirtschaft/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; //National Institute of Health Carlos III/ ; //the Netherlands Organization for Health Research and Development (ZonMw, the Netherlands)/ ; //Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie/ ; //Ministry of Science and Technology (Israel)/ ; //Formas (Sweden) and HDHL-Intimic Era-Net (EarlyFOOD)/ ; JTC-2017-7//Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"/ ; //European Union/ ; DZD Grant 82DZD00302//Ministerium für Ländliche Entwicklung, Umwelt und Landwirtschaft des Landes Brandenburg/ ; 442326535//National Research Data Infrastructure for Personal Health Data (NFDI4Health) by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; },
mesh = {Humans ; *Adiposity/physiology ; *Gastrointestinal Microbiome/physiology ; Europe ; Adult ; Body Mass Index ; *Obesity/microbiology ; Observational Studies as Topic ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S ; },
abstract = {Gut microbiota may contribute to the adiposity-associated disease risk, but human studies reported inconsistent associations of adiposity with gut microbiota composition. We examined associations of body mass index (BMI) with alpha diversity and relative microbial abundance at the phylum and genus taxonomic levels (based on 16S rRNA amplicon sequencing or metagenomics) among 7415 adults from eight European observational studies in a joint federated analysis of harmonized data using DataSHIELD. Higher BMI (per 5 kg/m[2]) was associated with lower alpha diversity (β: -0.05; 95% CI: -0.07, -0.03) and, on the phylum level, positively associated with Proteobacteria, but neither with Firmicutes nor Bacteroidetes nor their ratio, where high between-study heterogeneity was observed. On the genus level, BMI was inversely associated with the relative abundance of Faecalibacterium of the Firmicutes phylum (β: -0.11; 95% CI: -0.14, -0.07) but positively with the odds of detection of Dorea, Streptococcus, and Clostridium (all three Firmicutes) as well as Collinsella (Actinobacteria). This federated analysis of multiple studies found lower alpha diversity, alongside depleted Faecalibacterium, as well as higher odds of detection of Dorea, Streptococcus, Clostridium, and Collinsella with higher adiposity. By combining data from diverse study populations using harmonized data and statistical methods, our analysis partly overcomes sources of heterogeneity that may explain previously observed inconsistencies.},
}

Humans
*Adiposity/physiology
*Gastrointestinal Microbiome/physiology
Europe
Adult
Body Mass Index
*Obesity/microbiology
Observational Studies as Topic
Male
Female
Middle Aged
RNA, Ribosomal, 16S

@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Proteomics/methods ; Bacteria/genetics/metabolism/classification ; Metagenome ; Archaea/genetics/metabolism/classification ; *Proteome ; Tandem Mass Spectrometry ; },
abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.},
}

*Soil Microbiology
*Microbiota
*Proteomics/methods
Bacteria/genetics/metabolism/classification
Metagenome
Archaea/genetics/metabolism/classification
*Proteome
Tandem Mass Spectrometry

@article {pmid42098310,
year = {2026},
author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C},
title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42098310},
issn = {2399-3642},
support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Virome/genetics ; Humans ; *HIV Infections/virology/blood/drug therapy ; *Dysbiosis/virology ; Metagenomics ; *Respiratory System/virology ; },
abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.},
}

*Virome/genetics
Humans
*HIV Infections/virology/blood/drug therapy
*Dysbiosis/virology
Metagenomics
*Respiratory System/virology

@article {pmid42424147,
year = {2026},
author = {Ebel, ER and Kulkarni, AS and Mongad, DS and Olm, MR and Devi, SI and Mir, BA and Ozarkar, S and Sonnenburg, ED and Shouche, YS and Sonnenburg, JL and Dhotre, DP},
title = {Gut microbiomes of tribal communities in India vary with dairy and grain consumption.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694242},
pmid = {42424147},
issn = {1949-0984},
mesh = {Humans ; India ; Feces/microbiology ; *Diet ; *Edible Grain/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Dairy Products ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Tract/microbiology ; },
abstract = {Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%-47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.},
}

Humans
India
Feces/microbiology
*Diet
*Edible Grain/metabolism
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
*Dairy Products
Male
Adult
RNA, Ribosomal, 16S/genetics
Female
Gastrointestinal Tract/microbiology

@article {pmid42424326,
year = {2026},
author = {Brown, CR and Yacoub, MN and Bogan, JE and Buehler, MD and Hoffman, ML and Krumbeck, JA and Loughman, ZJ},
title = {Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0350824},
pmid = {42424326},
issn = {1932-6203},
mesh = {Animals ; *Cloaca/microbiology/parasitology ; *Cryptosporidium/isolation & purification ; *Snakes/microbiology/parasitology ; *Microbiota ; *Cryptosporidiosis/microbiology/parasitology ; Animals, Wild/microbiology ; },
abstract = {The Eastern Indigo Snake (EIS; Drymarchon couperi), a federally threatened species native to the southeastern United States, serves as a valuable model for examining the effects of captivity and infection on gastrointestinal microbial composition in reptiles. As an alternative to direct gut sampling, we examined the cloacal microbiomes of EISs to evaluate changes in microbial community structure across our study groups. This study assessed the cloacal microbiome of wild and captive EISs using shotgun metagenomic sequencing. Samples were divided into three groups for comparative microbiome analysis: captive snakes positive for Cryptosporidium serpentis (C. serpentis), captive snakes negative for C. serpentis, and wild snakes. Alpha (Shannon index, paired Wilcoxon test) and beta diversity (Bray-Curtis dissimilarity, PERMANOVA, CAP) metrics were used to assess microbial diversity and community composition across groups. Furthermore, a linear discriminant analysis effect size (LEfSe) was used to identify microbial taxa significantly enriched in C. serpentis-positive versus C. serpentis-negative captive snakes. Bacterial, fungal, bacteriophage, nematode, and protozoan taxa were significantly enriched in C. serpentis-positive snakes compared with C. serpentis-negative captive snakes, based on a linear discriminant analysis (LDA) score ≥ 2.5 and p ≤ 0.05. Total taxa species Shannon diversity was consistent between C. serpentis-positive and negative captive snakes (p = 0.55) while wild snake samples were significantly more diverse (p = 0.026). Wild snakes also exhibited a significantly increased Shannon diversity of fungi (p = 0.044), protozoa (p = 0.012), and nematodes (p = 0.008) compared to their captive counterparts. This study offers the first in-depth characterization of the cloacal microbiome in reptiles, specifically in EISs, using shotgun metagenomic sequencing. The findings establish a foundation for exploring microbiota-host interactions with implications for reptile health, disease ecology, and conservation management.},
}

Animals
*Cloaca/microbiology/parasitology
*Cryptosporidium/isolation & purification
*Snakes/microbiology/parasitology
*Microbiota
*Cryptosporidiosis/microbiology/parasitology
Animals, Wild/microbiology

@article {pmid42425637,
year = {2026},
author = {Elsheshtawy, A and Clokie, BGJ and Saugh, S and Adler, KD and Michniewski, SM and MacKenzie, S and Clokie, MRJ and Sicheritz-Pontén, T and Albalat, A},
title = {Microbial succession and spoilage dynamics revealed by multi-omics in Norway lobster (Nephrops norvegicus) during ice storage.},
journal = {Food microbiology},
volume = {140},
number = {},
pages = {105151},
doi = {10.1016/j.fm.2026.105151},
pmid = {42425637},
issn = {1095-9998},
mesh = {Animals ; *Nephropidae/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Seafood/microbiology/analysis ; Food Storage ; Multiomics ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Shellfish/microbiology ; *Microbiota ; Ice ; Food Microbiology ; },
abstract = {The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.},
}

Animals
*Nephropidae/microbiology
*Bacteria/genetics/classification/isolation & purification
*Seafood/microbiology/analysis
Food Storage
Multiomics
RNA, Ribosomal, 16S/genetics
Metagenomics
*Shellfish/microbiology
*Microbiota
Ice
Food Microbiology

@article {pmid42426126,
year = {2026},
author = {Barcaccia, G and Rambaldi Migliore, N and Gabelli, G and Agostini, V and Palumbo, F and Moroni, E and Nicolini, V and Gao, L and Mattutino, G and Porter, A and Palmowski, P and Procopio, N and Perego, UA and Iorizzo, M and Sharbel, TF and Baima Bollone, P and Torroni, A and Squartini, A and Achilli, A},
title = {DNA signatures preserved in the official 1978 sample collection of the Shroud of Turin.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42426126},
issn = {2045-2322},
support = {rif: 2023-1373//Fondazione Cariplo/ ; DAFNAE1-DOR-00719//University of Padova/ ; MR/Y019989/1//UKRI FLF/ ; 2022Y8BSAL//Ministero dell'Università e della Ricerca/ ; },
mesh = {Humans ; Animals ; *DNA, Mitochondrial/genetics ; Microbiota/genetics ; Phylogeny ; Metagenomics ; Genetic Variation ; Sequence Analysis, DNA ; },
abstract = {This research provides novel insights into the diversity of DNA extracted from samples collected from the Turin Shroud in 1978, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. We identified several human mitochondrial DNA (mtDNA) lineages, including K1a1b1a, which matches the 1978 official collector's mitogenome, H2a2 (i.e., the lineage of the mtDNA reference sequence rCRS), H1b, which is common in Western Eurasia, and the rare H33, which is also present in the Near East. Additionally, the reconstructed microbiome of the Shroud reveals a rich tapestry of multiple microbes commonly found on the human epidermis, as well as archaeal communities adapted to high salinity and fungi including molds. These findings are consistent with the preservation conditions experienced by the Shroud over the centuries. The presence of abundant Mediterranean endemic red coral, various cultivated plants (e.g., carrot, wheat, corn, bananas, and peanuts) and domesticated animals (e.g., cattle, pigs, chickens, dogs, and cats) provide a fascinating glimpse into the diverse biological sources of the contaminants that have accumulated on the Turin Shroud over time. Finally, radiocarbon dating of two distinct threads collected from the reliquary is consistent with their use in repair interventions of the Shroud carried out in 1534 and 1694 CE.},
}

Humans
Animals
*DNA, Mitochondrial/genetics
Microbiota/genetics
Phylogeny
Metagenomics
Genetic Variation
Sequence Analysis, DNA

@article {pmid42426176,
year = {2026},
author = {Latorre, F and Jaillon, O and Sieracki, ME and Cruaud, C and Massana, R and Logares, R},
title = {Global population structure in MAST-4 unicellular marine predators.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10607-z},
pmid = {42426176},
issn = {2399-3642},
support = {CTM2015-69936-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; PID2022-137508NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RYC-2013-12554//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; CEX2019-000928-S//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; 240904//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Marine heterotrophic flagellates (HFs) are key unicellular predators in marine food webs. Understanding their diversity and distributions is crucial for comprehending ocean ecosystems. MAST-4, an uncultured clade of Marine Stramenopiles, comprises a key group of bacterivorous heterotrophic flagellates (HFs) in the ocean microbiome. While we know that temperature is a major driver of MAST-4's biogeography, the population structure of MAST-4 species remains poorly known, limiting our ability to understand their ecology and adaptations. Here, we investigate the global population diversity and structure of MAST-4 species A, B, C, and E using metagenomics and single-cell genomics data from the Tara Oceans expedition. We find substantial population divergence in MAST-4A and C, with lower divergence in species B and E. Temperature and salinity are the primary factors structuring these populations. Analyses of positively selected genes reveal genomic regions likely involved in population adaptation to different environments. Our findings enhance the understanding of the population diversity and structure of these critical unicellular predators, providing insights into their ecological roles and adaptations in the global ocean. They also contribute to our general understanding of microbial populations, a largely unexplored dimension of biodiversity that plays a crucial role in grasping the impacts of global change.},
}

@article {pmid42426489,
year = {2026},
author = {Dimri, A and Sharma, P and Vishvakarma, R and Sharma, S},
title = {Effect of Probiotics on the Gut-Mammary Pathway: Implications on Infant Microbiota Transfer and Development.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {42426489},
issn = {2161-3311},
mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; Female ; *Gastrointestinal Microbiome ; Infant, Newborn ; Milk, Human/microbiology ; Lactobacillus ; Bifidobacterium ; Pregnancy ; Infant ; *Gastrointestinal Tract/microbiology ; Lactation ; *Mammary Glands, Human/microbiology ; },
abstract = {PURPOSE OF REVIEW: Transfer of microbiota from the maternal gut, during lactation, takes place via breastmilk, which establishes an intricate beneficial microbial ecosystem in the gut of the newborn. A healthy gut microbiota influences and enhances the neonatal health, and aids in multidimensional development-metabolically, immunologically, neurologically, and hormonally. Several microorganisms like Lactobacillus and Bifidobacterium get transferred to the infant gut and play a key role in its colonization and programming. Administration of such microbes, or probiotics, to the mother can assist in improving the benefits imparted by breastmilk to the infant, and can also provide health benefits to the mother. In recent years, there has been a focus on related metagenomic studies and the immunological effects of individual genera have also been studied in detail. In this review, we observe the gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios. We also analyze the level of evidence of potential of some promising probiotic strains in the transfer, establishment, and development of infant gut microbiota based on recently conducted studies.

RECENT FINDINGS: The analysis of recent metagenomic studies proved that strains like Bifidobacterium infantis, Lactobacillus rhamnosus, and Limosilactobacillus reuteri exibit a high level of evidence in benefitting the microbiota transfer as well as establishment, diversification, and development of the infant gut ecosystem. Hence, these strains in particular, can be given as supplements to mothers during pregnancy and lactation, in order to improve their inherent immunity and the overall health of the mother-infant dyad. With the advent of metagenomics, the roles, functions and effects of microbes in the gut-mammary pathway have been re-examined. This review, critically evaluates the recent studies related to gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios with particular emphasis on the strength and quality of their evidence.},
}

Humans
*Probiotics/administration & dosage/pharmacology
Female
*Gastrointestinal Microbiome
Infant, Newborn
Milk, Human/microbiology
Lactobacillus
Bifidobacterium
Pregnancy
Infant
*Gastrointestinal Tract/microbiology
Lactation
*Mammary Glands, Human/microbiology

@article {pmid42428252,
year = {2026},
author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y},
title = {The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.},
journal = {Environmental health perspectives},
volume = {134},
number = {3},
pages = {335-350},
pmid = {42428252},
issn = {1552-9924},
mesh = {Humans ; *Air Pollution/adverse effects/statistics & numerical data ; *Gastrointestinal Microbiome/drug effects ; Aged ; Particulate Matter/adverse effects ; Ozone ; Male ; Female ; *Cognition/drug effects ; *Cognitive Dysfunction/epidemiology ; *Air Pollutants ; *Environmental Exposure/statistics & numerical data ; },
abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway given their crucial role in the gut-brain axis. OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circulating metabolites in the association of residential PM2.5 and O3 exposure with cognitive dysfunction. METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated by using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-Mental State Examination and Hasegawa Dementia Scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes. RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and l-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase. CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation.},
}

Humans
*Air Pollution/adverse effects/statistics & numerical data
*Gastrointestinal Microbiome/drug effects
Aged
Particulate Matter/adverse effects
Ozone
Male
Female
*Cognition/drug effects
*Cognitive Dysfunction/epidemiology
*Air Pollutants
*Environmental Exposure/statistics & numerical data

@article {pmid40165002,
year = {2026},
author = {Wang, H and Su, Q and Sun, H and Meng, Y and Xing, X and Zheng, H and Li, Y},
title = {Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander.},
journal = {Integrative zoology},
volume = {21},
number = {4},
pages = {850-863},
pmid = {40165002},
issn = {1749-4877},
mesh = {Animals ; *Caudata/microbiology ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics/analysis ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; China ; Metagenome ; },
abstract = {The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.},
}

Animals
*Caudata/microbiology
*Genetic Variation
RNA, Ribosomal, 16S/genetics/analysis
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification
China
Metagenome

@article {pmid41579151,
year = {2026},
author = {Gan, T and Zhang, N and Liu, L and Li, W and Ding, M and Chen, J and Zhou, T and Mao, A},
title = {Lactobacillus plantarum CCFM639 Alleviates Hypertension by Reshaping Gut Microbiota and Regulating Key Metabolites.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {5},
pages = {6878-6892},
pmid = {41579151},
issn = {1867-1314},
support = {82400481//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Hypertension/microbiology/metabolism/drug therapy ; *Lactiplantibacillus plantarum/physiology ; *Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; Metabolome ; Male ; Feces/microbiology ; Female ; Middle Aged ; Bacteria/classification/isolation & purification/genetics ; Blood Pressure ; Adult ; },
abstract = {A strong association between the gut microbiome and hypertension has emerged. Our previous work demonstrated that supplementation with L. plantarum CCFM639 (CCFM639) reduced blood pressure (BP) in hypertensive mice involving inhibiting the growth of S. aureofaciens Tü117 and conducted an exploratory randomized trial in adults with prehypertension or stage 1 hypertension. Here, we evaluate the effects of CCFM639 supplementation (10[9] CFU/day for 8 weeks) on the gut microbiome and serum metabolome in a subset of these participants (n = 20). Untargeted metabolomic analysis was performed on serum samples, and stool microbiome composition was assessed via metagenomic sequencing. Mono-CCFM639 supplementation altered the metabolomic profile without affecting gut microbiota diversity but reshaped microbial composition. CCFM639 supplementation modulated both the gut microbiome and serum metabolome. Circulating gut-derived metabolites are likely to account for the improvements in BP, suggesting that CCFM639 supplementation could be a key component of nutritional interventions targeting the gut microbiota for hypertension management.},
}

Humans
*Hypertension/microbiology/metabolism/drug therapy
*Lactiplantibacillus plantarum/physiology
*Gastrointestinal Microbiome
*Probiotics/administration & dosage
Metabolome
Male
Feces/microbiology
Female
Middle Aged
Bacteria/classification/isolation & purification/genetics
Blood Pressure
Adult

@article {pmid41896698,
year = {2026},
author = {Jung, S and Militsi, E and Huck, O},
title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.},
journal = {Oral diseases},
volume = {32},
number = {5},
pages = {1237-1272},
doi = {10.1111/odi.70215},
pmid = {41896698},
issn = {1601-0825},
mesh = {Humans ; *Microbiota ; *Autoimmune Diseases/microbiology/immunology ; *Mouth/microbiology ; Dysbiosis/microbiology ; Sjogren's Syndrome/microbiology ; Saliva/microbiology ; Arthritis, Rheumatoid/microbiology ; },
abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.

METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).

RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sjögren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct β-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.

CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.},
}

Humans
*Microbiota
*Autoimmune Diseases/microbiology/immunology
*Mouth/microbiology
Dysbiosis/microbiology
Sjogren's Syndrome/microbiology
Saliva/microbiology
Arthritis, Rheumatoid/microbiology

@article {pmid42098386,
year = {2026},
author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y},
title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42098386},
issn = {2399-3642},
support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Polyesters/metabolism ; *Lead/metabolism/toxicity ; Biodegradation, Environmental ; *Microbiota/drug effects/genetics ; Soil Microbiology ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/genetics/metabolism ; *Genes, Viral ; Rhizosphere ; },
abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.},
}

*Polyesters/metabolism
*Lead/metabolism/toxicity
Biodegradation, Environmental
*Microbiota/drug effects/genetics
Soil Microbiology
*Soil Pollutants/metabolism/toxicity
*Bacteria/genetics/metabolism
*Genes, Viral
Rhizosphere

@article {pmid42140051,
year = {2026},
author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M},
title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.},
journal = {Marine pollution bulletin},
volume = {230},
number = {},
pages = {119879},
doi = {10.1016/j.marpolbul.2026.119879},
pmid = {42140051},
issn = {1879-3363},
mesh = {Animals ; *Bass/metabolism ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Multiomics ; *Dysbiosis/chemically induced ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.},
}

Animals
*Bass/metabolism
*Microplastics/toxicity
*Water Pollutants, Chemical/toxicity
Multiomics
*Dysbiosis/chemically induced
Metabolomics
Gastrointestinal Microbiome/drug effects

@article {pmid42163161,
year = {2026},
author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM},
title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42163161},
issn = {1471-244X},
mesh = {Humans ; *Major Depressive Disorder/genetics/microbiology ; *DNA, Mitochondrial/genetics ; Genome-Wide Association Study ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Adult ; Polymorphism, Single Nucleotide ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; },
abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.

METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.

RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p < 0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.

CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.

CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).},
}

Humans
*Major Depressive Disorder/genetics/microbiology
*DNA, Mitochondrial/genetics
Genome-Wide Association Study
Female
Male
*Gastrointestinal Microbiome/genetics
Adult
Polymorphism, Single Nucleotide
Middle Aged
Feces/microbiology
Case-Control Studies

@article {pmid42277260,
year = {2026},
author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C},
title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.},
journal = {Nature genetics},
volume = {58},
number = {7},
pages = {1595-1609},
pmid = {42277260},
issn = {1546-1718},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenome/genetics ; Genome-Wide Association Study ; Bacteria/genetics/classification ; Host-Pathogen Interactions/genetics ; },
abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.},
}

Humans
Female
*Vagina/microbiology
*Microbiota/genetics
*Metagenome/genetics
Genome-Wide Association Study
Bacteria/genetics/classification
Host-Pathogen Interactions/genetics

@article {pmid42295167,
year = {2026},
author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P},
title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.},
journal = {Infection and immunity},
volume = {94},
number = {7},
pages = {e0054225},
doi = {10.1128/iai.00542-25},
pmid = {42295167},
issn = {1098-5522},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; *Metagenomics/methods ; Vaginosis, Bacterial/microbiology ; Pregnancy Outcome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Microbiota
*Metagenomics/methods
Vaginosis, Bacterial/microbiology
Pregnancy Outcome
RNA, Ribosomal, 16S/genetics

@article {pmid42397535,
year = {2026},
author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK},
title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {21},
pages = {10626-10639},
pmid = {42397535},
issn = {1614-7499},
mesh = {*Feces/microbiology ; Humans ; Anaerobiosis ; Fatty Acids, Volatile ; Methane ; Microbiota ; Bacteria ; Archaea ; Hydrolysis ; },
abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.},
}

*Feces/microbiology
Humans
Anaerobiosis
Fatty Acids, Volatile
Methane
Microbiota
Bacteria
Archaea
Hydrolysis

@article {pmid42421950,
year = {2026},
author = {Lu, W and Wang, Y and Zhang, J and Li, Y and Huang, L and Yang, W and Zhou, S and Zhou, M and Chen, Y and Wu, R and Wang, Y and Zhang, H and Wan, J and Xia, F and Zhang, Z and Shen, L},
title = {Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1871586},
pmid = {42421950},
issn = {1664-3224},
mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immunotherapy/adverse effects/methods ; *Metabolome ; Metabolomics ; Multiomics ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/metabolism/microbiology/immunology ; Treatment Outcome ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; },
abstract = {BACKGROUND: Immunotherapy-based total neoadjuvant therapy (iTNT) is a promising strategy for microsatellite-stable locally advanced rectal cancer (LARC), yet therapeutic response and treatment-related toxicity remain heterogeneous. Integrated fecal microbiome and metabolome profiling may provide non-invasive biomarkers and functional clues for optimizing iTNT.

METHODS: We conducted a longitudinal fecal multi-omics study using samples from patients with microsatellite-stable LARC enrolled in the TORCH trial (NCT04518280). A total of 102 fecal samples were collected before treatment, during treatment, and after completion of iTNT. Metagenomic sequencing and untargeted metabolomics were integrated to characterize longitudinal microbial and metabolic changes. We also examined baseline features associated with therapeutic response, and multi-omics signatures linked to hematologic and gastrointestinal toxicities. A murine tumor model treated with radiotherapy plus immunotherapy, with or without GABA supplementation, was used for functional testing of the response-associated metabolite.

RESULTS: iTNT induced longitudinal gut microbiome remodeling. This remodeling was characterized by altered community structure, increased alpha diversity, enhanced microbial network connectivity, enrichment of Firmicutes-associated taxa, and depletion of Bacteroidetes and Proteobacteria. Fecal metabolomic profiles also shifted during treatment, with prominent changes in amino acid-related pathways and significant concordance between microbial and metabolic profiles. Responders were enriched in several Firmicutes-associated genera, including Ruminococcus, Anaerostipes, and Coprobacillus. In contrast, non-responders showed enrichment of Klebsiella and response-associated metabolites including gamma-aminobutyric acid (GABA). Microbial functional and metabolomic pathway analyses showed convergent enrichment of arginine and proline metabolism, which includes an alternative GABA-related metabolic route. Functionally, GABA supplementation weakened the antitumor efficacy of radiotherapy plus immunotherapy and was accompanied by systemic T cell dysfunction. In addition, specific microbial taxa and fecal metabolic features were associated with hematologic toxicity and diarrhea severity, with baseline metabolites showing exploratory potential for toxicity stratification.

CONCLUSION: This study provides a longitudinal fecal microbiome-metabolome resource for iTNT in LARC and identifies candidate microbial and metabolic features associated with treatment response and toxicity. GABA was functionally supported as a response-associated immunomodulatory metabolite, while candidate microbial functional signals warrant further mechanistic validation.},
}

Animals
Female
Humans
Male
Mice
*Feces/microbiology
*Gastrointestinal Microbiome/drug effects
*Immunotherapy/adverse effects/methods
*Metabolome
Metabolomics
Multiomics
*Neoadjuvant Therapy/adverse effects/methods
*Rectal Neoplasms/therapy/metabolism/microbiology/immunology
Treatment Outcome
Clinical Trials, Phase II as Topic
Randomized Controlled Trials as Topic
Multicenter Studies as Topic

@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.},
}