April 29 , 2026

Gut microbiome

Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice – Jinhua Tang – Microbiome

Puerarin modulates the gut-liver-ovarian axis to ameliorate reproductive aging in breeder hens – Zhenwu Huang – microbiome

Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources – Yechan Zhao – microbiome

Environmental Microbiome

Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit – Lu Long – microbiome

Livestock Microbiome

Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis – Tongwei Liu – microbiome

Plant Microbiome

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot – Chuan You – microbiome

Microbiome & Cancer / Immunology

Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways – Kyungchan Min – microbiome

April 28 ,2026

Plant microbiome

What do we know about the seed microbiome? – Xiangning Qi – microbiome

Human gut microbiome

Porphyromonas gingivalis induces intestinal inflammation through gingipain-dependent gut microbiome dysbiosis – Ming Li – microbiome

Tryptophan metabolism mediated by the gut microbiota inhibits pyroptosis via the AhR signaling pathway to maintain intestinal epithelial homeostasis Mengqi Liu – microbiome

Marine microbiome

Coral color morphs exhibit distinct microbial and proteomic profiles linked to stress and immune mechanisms in a changing ocean – Nathalia Delgadillo-Ordoñez – microbiome

Environmental microbiome

Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake – Bao-Zhu Fang – microbiome

March 31,2026

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

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

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

Reproductive / Urogenital Microbiome & Host–Pathogen Interactions

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

 Gut Microbiome, Diet, and Host Health

Total and different types of olive oil consumption, gut microbiota, and cognitive function changes in older adultsJiaqi 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 aerobiomesRussell 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-lifeElena Fernández-Trapote – microbiome

Microbiome–Immune System Interactions

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

Animal microbiome

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

January 13 , 2026

Environmental & Wastewater Microbiomes

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

Correction: Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plantsHuifeng 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 lactationMoli Li – Springer nature

Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambsTianrong 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

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

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

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