Category Archives: Metabolomics

March 31,2026

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Human Microbiome

The interplay between Peptostreptococcus and Fusobacterium as novel signatures in colorectal cancer recurrence – Yunhui Zhang – microbime

Dysbiosis of the nasal microbiome is associated with prospective acute exacerbation of COPD – Cristian Roca – microbiome

Water–vapor treatment of shower systems in healthcare facilities: reshaping built-environment microbiomes to improve Legionella control and protect at-risk patients – Tian You – microbiome

Animal Microbiome

Limosilactobacillus reuteri enhances production performance and ovarian function via modulation of the gut-ovary axis in laying hens – Yanchao Geng – microbiome

Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles – Qi Huang – microbiome

Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance – Le Xu – microbiome

plant microbiome

Differential contributions of an antimicrobial effector from Verticillium dahliae to virulence and tomato microbiota assembly across natural soils – Wilko Punt – microbiome

Environmental & Data Microbiome

Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets – Hiroshi Mori – mi9crobiome

March 3rd ,2026

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Human Microbiome

Early risperidone exposure impairs cognitive function by perturbation of the gut microbiome and bile acids/tyrosine-PTP1B axis – Huaiyu Ye – microbiome

Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum -Chiara Mazzoni – microbiome

Animal Microbiome

Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets – Wangyuan Yao – microbiome

Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities – Jiayi Zhang – microbiome

Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost – Ming Geng – microbiome

Plant Microbiome

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae – Guanjing Cai – microbiome

Ecology-guided Bacillus SynCom from a rice–duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression – Yingjie Song – microbiome

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation – Ruonan Wang – microbiome

Marine and Aquatic Environmental Microbiome

Reconstruction of coral holobionts and elucidation of the causal relationships among symbiodiniaceae, bacteria, and coral through single-cell raman spectroscopy metabolomics – Yang Shu – microbiome

Unlocking the unexplored AMPSphere in marine rare species – Shen Fan – microbiome

Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate – Shohei Yasuda – microbiome

Stress-induced enrichment of Pseudomonas sp. stimulates the adaptive response of Auxenochlorella pyrenoidosa and antibiotic-resistant proliferation -Qian Liu – microbiome

Built Environment and Cultural Heritage Microbiome

Unraveling the microbiomes contributing to biodeterioration dynamics of limestone heritage at the Longmen Grottoes archeological site – Xiaoying Zhang – microbiome

February 26 , 2026

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Gut Microbiome

Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep – Luoyang Ding – microbiome

Cross-kingdom genomic variation in chicken gut microbiomes: insights from China’s diverse local breeds – Jiayu Zhang – microbiome

Microbiota-derived propionate suppresses Salmonella virulence gene expression via LuxS quorum sensing – Qianyun Zhang – microbiome

rumen microbiome

Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle – Youyoung Choi – microbiome

January 28, 2026

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Reproductive / Urogenital Microbiome & Host–Pathogen Interactions

The interactive relationship between Fusobacterium necrophorum, Bacteroides pyogenes, and Porphyromonas levii in driving inflammatory uterine disease – Dianjun Cao – microbiome

 Gut Microbiome, Diet, and Host Health

Total and different types of olive oil consumption, gut microbiota, and cognitive function changes in older adults –Jiaqi Ni – microbiome

Environmental Microbiome & Antimicrobial Resistance (Resistome)

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems

– Wanli He – microbiome

Spatial and temporal patterns of public transit aerobiomes – Russell J. S. Or – microbiome

Food Chain, Meat Microbiome & Resistome Dynamics

Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life – Elena Fernández-Trapote – microbiome

Microbiome–Immune System Interactions

Commensal microbe-derived butyrate enhances T follicular helper cell function to boost mucosal vaccine efficacy – Haeun Ko – microbiome

Animal microbiome

A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate – Lena-Sophie Paul – microbiome

January 13 , 2026

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Environmental & Wastewater Microbiomes

Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes – Antonia Weiss – Springer nature

Correction: Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Springer nature

Ruminant & Livestock Gut Microbiomes

The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows – Jianhao Yang – Springer nature

Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation – Moli Li – Springer nature

Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs – Tianrong Chen – Springer nature

Host-Associated Gut Microbiomes (Non-Human Models)

Ningxiang pig-derived Enterococcus hirae protects against E. coli-induced gut dysbiosis and inflammation via acetate/propionate-MyD88-NF-κB axis in piglets – Longlin Zhang – Springer nature

Insect & Evolutionary Microbiomes

Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera Pentatomidae) –Jingjing Sun – Springer nature

December 05, 2025

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See you at MVIF next week!

Join us in December for #MVIF 44!We will discuss diverse #microbiome topics:human urinary, gut, oral and nasal microbiomes, extreme environments, anda new sequence alignment tool.

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-11-24T10:34:26.363Z

General microbiome

Consensus Statement: STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies – Julia M. Kelliher – Nature Microbiology

Urinary microbiome

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection – Michael L. Neugent – NPJ Biofilms and Microbiomes

Thrilled to share that our recent work is out in npj Biofilms and Microbiomes. 🧵 (1/4)www.nature.com/articles/s41…

— Mike Neugent PhD (@mikeneugent.bsky.social) 2025-11-24T17:49:26.272Z

Vaginal microbiome

Microbial and seminal traces of sexual intercourse and forensic implications – Sarah Ahannach – Microbiome

Ambient temperature affects the composition of the vaginal microbiome, and temperature-sensitive vaginal microbes influence assisted reproductive technology outcomes – Zheng Liu –  – Microbiome

Gut microbiome

HGMT: a database of human gut microbiota for tumors and immunotherapy response – Jinxin Liu – Genome Biology

Review: Circadian rhythms as a modulator of gut microbiota-tumor microenvironment crosstalk – Qinglong Xu – Cellular and Molecular Life Sciences

Dynamics of gut metabolome and microbiota maturation during early life – Anna-Katariina Aatsinki – iScience

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk – Pamela Ferretti – Nature Communications

Animal microbiome

Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function – Omar E. Tovar-Herrera – Nature Ecology & Evolution

Longitudinal changes in gut microbiota across reproductive states in wild baboons – Chelsea A. Southworth – bioRxiv

Probiotic effect of B. subtilis PS-216 in broiler chickens: modulation of weight, feed conversion, short chain fatty acids, microbiota and meat quality – Katarina Šimunović – Animal Microbiome

Animal experiments

The microbial metabolite imidazole propionate modulates hypothalamic activity and stress-induced behaviors – Gulistan Agirman – Cell Host & Microbe

Excited to share new work by Guli Agirman + co that identifies a direct mechanism linking gut microbial imidazole propionate to stress! 🧠🦠 Btw this image was made by Nano Banana Pro 🍌. First time I've gotten a model to accurately generate a science graphic 🤯 authors.elsevier.com/a/1mA5M6t8JE…

— Elaine Hsiao (@pipethero.bsky.social) 2025-11-25T17:45:03.571Z

Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function – Yi Wang – PNAS

Selection and transmission of the gut microbiome alone can shift mammalian behavior – Taichi A. Suzuki – Nature Communications

Postbiotics

Review: Postbiotics as microbial-derived therapeutics for wound healing disorders: from molecular mechanisms to future application – Miroslav Dinić – Home  Cell Communication and Signaling

Phages and viruses

Unveiling the global urban virome through wastewater metagenomics – Nathalie Worp – Nature Communications 

Soil, root and plant microbiome

Rare taxa modulate the emergence of dominants in microbial communities – Jianing Wang – mBio

Integrated effects of anaerobic soil disinfestation and beneficial microbes in strawberry production – Baker D. Aljawasim – PlosOne

Food microbiome

Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams – Giulia Longhi – Current Research in Microbial Sciences

Environmental microbiome

The Microflora Danica atlas of Danish environmental microbiomes – C. M. Singleton – Nature

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬www.nature.com/articles/s41…

— Morten Kam Dahl Dueholm (@mkddueholm.bsky.social) 2025-12-03T20:50:16.284Z

Bioinformatics

TAGINE: Fast Taxonomy-based Feature Engineering for Microbiome Analysis – Shiri Baum – bioRxiv

Creating unity: linking 16S rRNA gene sequence information to the core taxonomy of genomes – Hilde Vinje – Environmental Microbiome

LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation – Wei Xue – Nature Communications

cFMD v1.3.0 is here! 🚀We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMDWhile we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.1/4

— Segata Lab (@cibiocm.bsky.social) 2025-11-26T13:09:52.484Z

November 14, 2025

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Gut Microbiome & Host Health

Sleep deprivation disrupts diurnal rhythmicity of gut microbiota and blood inflammatory cytokines in mice — Weiran Shan et al. (PLOS ONE)

Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts — Guo Hu et al. (PLOS Biology)

The role of hypothyroidism in cirrhosis pathogenesis: A retrospective cohort study and multi-omics integration analysis — Ziyang Yang et al. (PLOS Genetics)

Multi-omics analysis reveals metabolic regulation of phosphatidylcholine, triglycerides, phosphatidylethanolamine, and cardiolipin metabolism in mouse liver with MASLD — Hong Liang & Kang Song (PLOS ONE)

Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study — Ulrika Andersson-Hall et al. (PLOS ONE)

Microbial Pathogens, Immunity & Infection

Exploring the gut microbiota of Pacific white shrimp suffering pale shrimp disease — Lalitphan Kitsanayanyong et al. (PLOS ONE)

Dominance of Zygosaccharomyces and shifts in bacterial pathways under antimicrobial pressure — Maria Cecilia Rasuk et al. (PLOS ONE)

How transcriptional networks control Verticillium plant infection — Ying-Yu Chen et al. (PLOS Pathogens)

Integrative machine learning and multi-omics framework identifies shared biomarkers for rheumatoid arthritis and ulcerative colitis — Meili Liu et al. (PLOS ONE)

The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the ectocervical epithelium — Vilde Kaldhusdal et al. (PLOS Pathogens)

Characterization of ORF19.7608 (PPP1), a biofilm-induced gene of Candida albicans — Nmerichukwu C. Iwuchukwu et al. (PLOS ONE)

Differential regulation of the eicosanoid biosynthesis pathway during Enterocytozoon hepatopenaei infection in shrimp — Wananit Wimuttisuk et al. (PLOS ONE)

Animal, Environmental & Soil Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and fiber fractions in Asiatic lions — Mengmeng Sun et al. (PLOS ONE)

From pre-oral secretions to gut digestion: How Lucilia sericata larvae handle Leishmania major — Azam Malekian et al. (PLOS ONE)

Targeted pathogen profiling of ancient feces reveals common enteric infections (725–920 CE) — Drew Capone et al. (PLOS ONE)

Starve or share? Phosphate availability shapes plant–microbe interactions — Maja Schmidt et al. (PLOS Pathogens)

Pathogenicity and transmission of Morganella morganii in honey bees — Yijun Chen & Qiang Huang (PLOS Pathogens)

Mitogenomics of the tropical bont tick reveals vertical and horizontal transmission of Rickettsia africae — Elisha Chatanga et al. (PLOS NTDs)

Differentiation of bacterial communities in the coral Orbicella faveolata across life-cycle stages — Amanda Pérez-Trejo et al. (PLOS ONE)

Insect-derived polymer hydrogel based on fibroin matrix from whole silkworm larvae — Maki Yamazaki et al. (PLOS ONE)

Thermophilic microbiome acclimation improves anaerobic digestion of food waste — Hengxuan Shao et al. (PLOS ONE)

Epidemiology, Public Health & Clinical Microbiology

Assessing piperacillin/tazobactam vs. ceftriaxone + metronidazole for children with perforated appendicitis — Daniel Briatico et al. (PLOS ONE)

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis in raw milk — Inamullah et al. (PLOS ONE)

Hematological ratios, immune-related adverse events, and mortality in patients receiving immune checkpoint inhibitors — Sophie Lekkerkerker et al. (PLOS ONE)

Geographical and climatic risk factors for COVID-19 in southwest Iran — Koorosh Nikaein et al. (PLOS ONE)

Anthropometric and neurocognitive consequences of Campylobacter, ETEC, and norovirus infections: A systematic review — Patricia B. Pavlinac et al. (PLOS NTDs)

Neuroscience, Immunology & Molecular Networks

Skin melanin is associated with body temperature regulation in humans and mice — Kale S. Bongers et al. (PLOS ONE)

Oxytocin neurons drive melanocortin circuit maturation via vesicle release — Pierre-Yves Barelle et al. (PLOS Biology)

Elucidation and application of the neuroimmune axis between depression and autoimmune diseases — Fu Sun et al. (PLOS ONE)

Quantifying microbial interactions using an iterative generalized Lotka–Volterra approach — Yue Huang et al. (PLOS Computational Biology)

November 7, 2025

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General Microbiome

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes – Ricardo Leon-Sampedro – Nature

Gut microbiome

Pushing the frontier of gut microbiome health cross-kingdom and cross-organ – Tao Zuo  (左涛) – Nature

The early-life gut microbiome in common pediatric diseases: roles and therapeutic implications – Taiwo Bankole – Frontiers in Nutrition

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals – Christophe Boetto – Communications Biology

Respiratory Microbiome

Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort – Baolin Jia – Frontiers in Public Health

Distinguishing tuberculosis from non-tuberculous mycobacteria and other respiratory conditions by microbiome patterns – Jee Youn Oh –  Scientific Reports

Animal microbiome

Effects of avian Plasmodium exposure on the microbiota of Culex pipiens – Marta Garrigos – Nature

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P. Schmartz – Nature Communications

Animal Experiments

Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition – Leigh A. Frame – mSystems

Water Microbiome

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals – Ganiyu Oladunjoye Oyetibo – Scientific Reports

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems – Congmin Zhu – Nature Communications

Bringing the uncultivated microbial majority of freshwater ecosystems into culture – Michaela M. Salcher – Nature Communications

Bioinformatics

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand– Watchaporn Chuchaona – Scientific Reports

Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing – Shirin Ashraf – Nature Communications

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well – Eli K. Moore – Communications Earth & Environment 

October 17, 2025

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Gut Microbiome & Health

Lactic acid produced by optimal vaginal Lactobacillus spp. potently and specifically inactivates HIV-1 in vitro by targeting the viral RNA genome and reverse transcriptase
– Muriel Aldunate – PLOS Pathogens

Differential composition of the pulmonary microbiome in HIV-positive versus HIV-negative patients with Pneumocystis jirovecii
– Chang-Run Zhang – PLOS ONE

Risk of atopic dermatitis in periodontitis patients with and without dental scaling: A retrospective cohort study
– Ming-Che Chiang – PLOS ONE

Fecal carriage and associated factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae in children under five years old with diarrhea at a tertiary hospital in Tanzania
– Emily M. Jackson – PLOS ONE

Pathogens, Immunity & Host Interactions

Dietary tannic acid promotes intestinal clearance of Candida albicans by cross-linking hyphal chitosan
– Jia Feng – PLOS Pathogens

Trends in Clostridioides difficile infection prevalence among pediatric cancer patients: A systematic review and meta-analysis
– Muluneh Assefa – PLOS ONE

Multiplex serology for Streptobacillus moniliformis and other ‘rat bite fever-like’ microorganisms for seroprevalence studies in rodents
– Katja Schmidt – PLOS ONE

Animal & Environmental Microbiomes

Effects of rumen-protected or unprotected Clostridium butyricum on growth performance, rumen fermentation, immunity and antioxidation in fattening goats
– Caixia Zhang – PLOS ONE

The intracellular symbiont Wolbachia alters Drosophila development and metabolism to buffer against nutritional stress
– Amelia R. I. Lindsey – PLOS Genetics

Interactive effects of developmental and adult nutrition on lifespan and fecundity in a genetically diverse Drosophila population
– Andrew Jones – PLOS ONE

Metabolism, Health & Disease

Alterations in the serum metabolome in patients with the COVID-19 Omicron variant and in recovered cases
– Feng Gao – PLOS ONE

Humanized monoacylglycerol acyltransferase 2 mice on a high-fat diet exhibit impaired liver detoxification during metabolic dysfunction-associated steatotic liver disease
– J. Jose Corbalan – PLOS ONE

Current and future burden of gynecological cancers attributable to high body-mass index: A comprehensive global analysis and projection study
– Xuanyu Zhao – PLOS ONE

Developing and experimentally validating a glucocorticoid signaling-related gene signature to evaluate the prognosis and immunotherapeutic response in kidney renal clear cell carcinoma
– Yu Zhang – PLOS ONE

Computational & Bioinformatics Advances

ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug–food interactions
– Mogan Gim – PLOS Computational Biology

Advanced deep learning-based brain tumor classification using a novel customized CNN and optimized residual network
– Mehwish Rasheed – PLOS ONE

September 5, 2025

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See you next week at #GloMiNe2025!

Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT:cassyni.com/s/mvif-glomi…1/3

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-08-22T11:42:37.937Z

Gut microbiome

Gut fungi are associated with human genetic variation and disease risk – Emily P. Van Syoc – Plos Biology

The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients – Lin Zhang – npj Biofilms and Microbiomes

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research – Matija Tričković – Cell Host & Microbe

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

— Silas Kieser (@silask.bsky.social) 2025-08-29T10:06:18.408Z

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants – Raymond Kiu – Nature Communications

A defined microbial community reproduces attributes of fine flavour chocolate fermentation – David Gopaulchan – Nature Microbiology

Gut microbiome alterations precede graft rejection in kidney transplantation patients – Johannes Holle – American Journal of Transplantation

Adolescent girls at familial risk for depression with more advanced adrenarche have altered gut microbiota – A. Kolobaric – bioRxiv

Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial – Russell G. Davies – The Journal of Physiology

Resistome

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort – Katariina Pärnänen – Nature Communications

Oral microbiome

Complementary Predictors for Asthma Attack Prediction in Children: Salivary Microbiome, Serum Inflammatory Mediators, and Past Attack History – Shahriyar Shahbazi Khamas – Allergy

Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study – Cong Zhu – Microbiology Spectrum

SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania – Sterling L. Wright – Healthcare 

🧬🪥 Just published! Our new paper introduces the SANA-biome, a biocultural study exploring how diet, lifestyle, and the oral microbiome shape periodontal health in Romania.📰 Read the open-access protocol in Healthcare: 👉 http://www.mdpi.com/2227-9032/13…

— Sterling L. Wright (@anthbyte.bsky.social) 2025-08-27T16:01:43.887Z

Animal microbiome

Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota – Anum Ali Ahmad – BMC Microbiology

Thrilled that our new paper on the Red Grouse microbiota has now been published in BMC Microbiology: doi.org/10.1186/s128…! A really rewarding collaboration between our team and Nick Hesford and Kathy Fletcher from the Game & Wildlife Conservation Trust @gwct.org.uk.

— Laura Glendinning (@microbes4ever.bsky.social) 2025-08-19T14:12:37.569Z

Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota – Haishan Xie – Microbiology Spectrum

Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota – Anum Ali Ahmad – bioRxiv

Vaginal microbiome

Degradation of Resistant α-1,4-glucan by Vaginal Gardnerella Species is Associated with Bacterial Vaginosis – Rosanne Hertzberger – Current Microbiology 

Animal experiments

The microbiome is associated with obesity-related metabolome signature in the process of aging – Dana Binyamin – npj Biofilms and Microbiomes

Evidence for an indigenous female mouse urobiome – Sidra Sohail – bioRxiv 

Food microbiome 

Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities – Vincenzo Valentino – npj Biofilms and Microbiomes

Metabolomics

Microbes release lower-value metabolites at higher rates – Snorre Sulheim – bioRxiv

So excited to share this new paper by @sulheim.bsky.social and others! It's rare that you find a pattern, propose a hypothesis and the more you look, the more data you find that fits! Snorre's intuition, hard work and rigour to put it all together have been inspiring! Let us know what you think…

— Sara Mitri (@saramitri.bsky.social) 2025-08-22T14:05:47.584Z

Soil microbiome

236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient – Xiang Xiong – Scientific Data 

Bioinformatics

StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples – Johnathan Shih – bioRxiv

Comparison of iSeq and Miseq in 16S rRNA sequencing-based human gut microbiome analysis – Yanling Wang – bioRxiv 

Podcast

Biopolis – into the microbiome A young scientist is looking for answers in the human microbiome.

Food systems are teeming with complex microbial networks, carried from soil and water to crops, animals, and humans. Can we better track and steer these networks to enhance ecosystem health and food security? Find out more at this #FrontiersForum webinar ➡️ fro.ntiers.in/NfcCnmIEkWb

— Paul Cotter (@pauldcotter.bsky.social) 2025-09-05T13:25:35.039Z