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 20, 2026

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See you next week at MVIF!

See you next week at #MVIF 47! Heads up ⏰ due to daylight saving time, start times shift by 1 hour in some regions:1 hour earlier for Atlantic, 1 hour later for Pacific!

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-03-16T09:09:52.170Z

Gut microbiome

Gut microbiota modulation via repeated donor fecal transplantation improves motor and gastrointestinal symptoms in drug-naïve Parkinson’s disease: a randomized phase 2 trial – Rui Zhang – Signal Transduction and Targeted Therapy 

Clinical Review: Advances in the pathophysiology, diagnosis, and management of celiac disease – John B Doyle – BMJ

Circulating gut microbial metabolites and risk of coronary heart disease: A prospective multi-stage metabolomics study – Yulu Zheng – Plos Medicine

Nasal microbiome

Composition and dynamics of the adult nasal microbiome – Cindy M. Liu – Microbiome

Respiratory tract microbiome

Mass azithromycin distribution and antibiotic resistance in the gut and nasopharynx: a cluster-randomized trial – Thuy Doan – Nature Medicine 

Animal microbiome

Microbial communities associated with two populations of the sponge Chondrilla nucula under present and projected climate conditions in the Aegean Sea – Gioti Anastasia – ARPHA Preprints

Comparative analysis of stress markers, metabolic health, and gut microbiota in healthy and disabled dogs in long-term shelters in Thailand – Adul Saengthong – Plos One

Priority effects drive strain-level community composition of honeybee gut microbiota – Aiswarya Prasad – The ISME Journal

Animal experiments

Estropausal gut microbiota transplant improves measures of ovarian function in adult mice – Minhoo Kim – Nature Aging 

Plant, root, soil microbiome

Breeding effects on the root-associated microbiome of Zea mays L. are linked to plant-induced variation in soil water potentials – Nicolas Tyborski – ISME Communications

🤩 Now out in @isme-microbes.bsky.social Comms!#NicolasTyborski and our wonderful #Rhizotraits team unravel how old landraces and modern varieties of maize distinctly modulate their #rhizosphere #microbiomes under drought via soil water potentials!🌽🥵🦠Thanks to #BayCEER #Rhizo4Bio #bmftr_bund

— Tillmann Lueders (@luederslab.bsky.social) 2026-03-19T14:42:21.506Z

Food microbiome

Leveraging publicly available datasets and machine learning approaches for predicting the health benefits of fermented foods – Elizabeth A. McDaniel – bioRxiv

Bioinformatics

MATRIX: Rapid Quantification of Total and Active Microbial Cells with Single Cell Phenotypes for Environmental Microbiomes – Milena Gonzalo – bioRxiv

So thrilled to share episode 2 of #MVIFconversations with you all!Getting to sit down with @bykriscampbell.bsky.social was such a privilege! If you're curious about where microbiome science is headed and why rigorous science communication matters more than ever, this one's for you.1/2

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2026-02-24T09:48:59.589Z

March 19, 2026

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Gut microbiome

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals – Gabriel Baldanzi – Nature Medicine

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution – Ioannis Ntekas – Nature Microbiology

Respiratory Microbiome

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19 – Abigail Glascock – Nature Microbiology

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

Animal Microbiome

Towards standardization in pig microbiome research based on a comprehensive twenty-year review – Samuel Onyilokwu Enokela – Animal Microbiome

Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks – Peter Fauszt –  Animal Microbiome

Oral Microbiome

Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities – Muhammed Manzoor – Journal of Oral Microbiology

Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia – Jun Hyung Cha – Journal of Oral Microbiology

Water Microbiome

Water mass specific genes dominate the Southern Ocean microbiome – Emile Faure – Nature Communications

Plant Microbiome

Impacts of climate extremes on plant pathogens, microbiomes and plant health – Chao Xiong – Nature Reviews Microbiology

Heritability of the Pinus radiata root microbiome – Natalie Graham – Frontiers in Plant Science

Bioinformatics

DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models – Awais Qureshi – BMC Bioinformatics

RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli – Evgeny Tankhilevich – Bioinformatics

MetaFX: feature extraction from whole-genome metagenomic sequencing data – Artem Ivanov – Bioinformatics

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

February 13, 2026

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Gut microbiome

Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function – H. Krukowski – Nature Microbiology

Baby-to-baby strain transmission shapes the developing gut microbiome – Liviana Ricci – Nature

Animal Microbiome

Microbiome by transcriptome interactions triggered by a switch to an alternative diet in Nellore cattle – Anna Carolina Fernandes – Scientific Reports

Maternal supplementation with rumen-protected arginine reshapes the ileal microbiome and enhances neonatal lamb growth – Xiangjian Peng –  Animal Microbiome

Oral Microbiome

Stimuli-responsive, antimicrobial-loaded nanocarriers for oral biofilm control and microbiome restoration – Ding Chen – International Journal of Oral Science

Modulating the oral microbiome with dental biomaterials: A review of challenges, advances, and future perspectives – Woojin Choi – Biomaterials

Plant Microbiome

Large-scale multi-omics unveils host–microbiome interactions driving root development and nitrogen acquisition – Nannan Li – Nature Plants

Ecological composite fertilizer application enhances wheat yield and optimizes rhizosphere microbial community under reduced fertilization – Yu Wang – Frontiers in Plant Science

Bioinformatics

argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) – Svetlana Ugarcina Perovic – Bioinformatics

A negative binomial latent factor model for paired microbiome sequencing data – Hyotae Kim – BMC Bioinformatics

January 29, 2026

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Animal microbiome

Host genetic background and environment have different effects on the establishment and structure of the adult worker honey bee gut microbiota – Breven Stark – PLOS ONE

Microbiota discovered in scorpion venom – Barbara Murdoch – PLOS ONE

Animal experiments / Disease models

Intestinal decontamination with rifaximin attenuates LSEC dysfunction and liver fibrosis in mice – Tingting Su – PLOS ONE

Periplaneta americana extract ameliorates recurrent oral ulcers in rats by enhancing the intestinal epithelial barrier and regulating gut microbiota – Kailing Li – PLOS ONE

Formononetin ameliorates SP-induced urticaria in mice via suppressing TAK1/MAK signaling pathway -Yan Wu –PLOS ONE

Lipopolysaccharide induced mouse depression model can better simulate changes in peripheral blood FFAs in alMDD -Jincai Pan –PLOS ONE

Human microbiome (gut & reproductive)

Stool and vaginal microbiome profiles patterns among Black and White endometrial cancer survivors: A pilot study in North Carolina – Mu Jin – PLOS ONE

Infection, immunity & host–microbe interactions

Examining the role of IgA in a persistent model of Staphylococcus aureus colonization – Yunys Perez-Betancourt – PLOS Pathogens

Diversify and conquer: How effector diversity is shaped by host–microbe co-evolution -Marion C Müller – PLOS Pathogens

Oo-No: Ophidiomyces ophidiicola–bacterial interactions and the role of skin lipids in development of ophidiomycosis – Jason W Dallas – PLOS Pathogens

Probiotics & food microbiology

In-vitro evaluation of probiotic potential of gut microbes isolated from retail chicken – Sangram Biswas – PLOS ONE

Antimicrobial resistance & clinical microbiology

Extended-spectrum β-lactamase and carbapenemase-producing Enterobacterales among adult patients and their family members at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia – Dessie Abera – PLOS ONE

Microbiome methods & bioinformatics

PCR bias impacts microbiome ecological analyses – Dharmik R Rathod – PLOS Computational Biology

CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches – Maor Knafo – PLOS ONE

Environmental & applied microbiology

Developing a simple, cost-effective proof-of-concept vaccine candidate against EHEC for cattle – Cecilia M Duarte – PLOS ONE

Preventive effect of bentonite against pyoderma via direct binding capability of staphylococci – Mao Kaneki – PLOS ONE

Ultraviolet light and polyethylene glycol as environmental cleaning agents to reduce contamination of Pseudogymnoascus destructans in bat hibernacula – Alyssa J Stulberg – PLOS ONE

Water, pollution & human exposure

Micro- and nanoplastics in biological samples following a drinking water intervention in Barcelona, Spain – Emma Calikanzaros – PLOS Water

Human disease & biomarkers

Evidence of an allostatic response by intestinal tissues following induction of joint inflammation – Meghan M Moran – PLOS ONE

Multi-modal data to identify key factors influencing lung injury in ARDS patients undergoing invasive mechanical ventilation: A prospective multi-center observational study protocol – Zhimei Duan – PLOS ONE

Integrative genomic analysis reveals DHX58 as a key player in gastric cancer – Yan Li – PLOS ONE

Identifying biomarkers for diagnosis and disease activity monitoring in PSC-IBD and UC through proteomic profiling: A prospective study protocol – Ondrej Fabian – PLOS ONE

S100-alarmins, antenatal corticosteroids and the risk of late-onset sepsis in preterm infants – Gloria Kessler – PLOS ONE

Exploring the role of the key gene TNFAIP3 between periodontitis and influenza A through bioinformatic analysis and molecular docking – Mingxiang Xu – PLOS ONE

GC-MS based bioactive profiling of Phyllanthus niruri and its antibacterial potential – Zubair Khalid Labu – PLOS ONE

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 23, 2026

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Animal microbiome

Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes -Jian-Ping Ying –PLOS ONE

Bacterial community associated with the surface and inside of centipede forcipules: Identification and characterization -Yasutaka Tanaka – PLOS ONE

Human reproductive & urinary microbiome

Vaginal chlorhexidine gluconate versus fluconazole for recurrent vulvovaginal candidiasis: A randomized noninferiority trial – Cathrin Alvendal – PLOS ONE

Infection and transplantation / Host–microbe interactions

DnaK supports intracellular persistence of Staphylococcus xylosus and confers mechanical resilience to a human breast cancer cell line – Lei Ye – PLOS ONE

Investigation of a viable but non-culturable state in Porphyromonas gingivalis and host cell invasion – Adenrele Oludiran – PLOS ONE

Microbial ecology & symbiosis

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis – Sunnyjoy Dupuis – PLOS ONE

Oral microbiome & animal experiments

Effects of glycyrrhizin on healing and prevention of recurrent aphthous stomatitis in hamster models – Fumie Shiba – PLOS ONE

Plant, soil & ecological microbiome

Tree species-specific strategies of soil aggregation driven by SOC–GRSP coupling under nitrogen addition and precipitation reduction -Mingxin Zhou – PLOS ONE

Microbial genomics & bioremediation

Genomic analysis of Acinetobacter baumannii DUEMBL6 reveals diesel bioremediation potential and biosafety concerns – Nizam Uddin – PLOS ONE

Human gut & inflammatory disease

Identification of hypoxia- and mitophagy-related diagnostic biomarkers for ulcerative colitis based on bioinformatic analysis and machine learning – Zewei Sheng – PLOS ONE

Oral & dental archaeology / Ancient microbiome

Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy – Jaruschka Pecnik – PLOS ONE

Cancer & clinical oncology

Radiomics profiling combined with clinical risk factors for preoperative lymphatic metastasis prediction in colorectal cancer: A multicenter study – Fangda Guo – PLOS ONE

Toxicology & respiratory health

Potential mechanisms and effects of AFB1-induced asthma: A comprehensive analysis based on network toxicology and molecular docking – Zhiyue Yu – PLOS ONE

Human development & diet (archaeology / isotopes)

Fed the same way? Exploring the influence of breastfeeding, weaning, and childhood diet on adult sex ratios through stable isotope analysis of incremental dentine in Medieval Tuscany – Alessio Amaro – PLOS ONE

January 16, 2026

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Human Microbiome

The testobolome in microbial testosterone metabolism and human health – Liisa Veerus –  
npj biofilms and microbiomes 

Multi-omic definition of metabolic obesity through adipose tissue–microbiome interactions – Rima M. Chakaroun – Nature Medicine

Gut microbiome

The microbiome at the centre of NAD+ supplementation – Youngjae Jo – Nature Metabolism

Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes – Xiongjian Wu – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

High microbial diversity in glacial habitats uncoupled from the specialized microbiomes of resident chironomid fauna – Valeria Lencioni – PLOS One

Bacterial communities show distinctive spatial diversity patterns in productive truffle orchards amended with peat-based substrate – Pedro Marco –  Environmental Microbiome

Plant Microbiome

Root Triterpenoid Metabolites Drive the Assembly and Feedback Regulation of the Rhizosphere Microbiome During Flowering to Senescence in Rhododendron hybridum – Fei Shan – Frontiers in Microbiology

Drought-Tolerant Rhizobacterial Consortia Enhance Grapevine Growth and Tolerance to Water Deficit – Ginevra Canavera – Frontiers in Plant Science

Bioinformatics

Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study – Tanya T. Karagiannis – PLOS Computational Biology

Novel artificial selection method improves function of simulated microbial communities – Bjorn Vessman – PLOS Computational Biology