Category Archives: Animal microbiome

June 4 , 2026

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Gut Microbiome

Associations between body composition and gut microbiota in female college students with and without dance training – Caifang Qiu – PLOS ONE

Imaging the impact of rotifer consumption on bacterial behaviors in the zebrafish gut – Susana Marquez Rosales – PLOS ONE

Environmental Microbiome

The livestock drinking water system as an active reservoir for antimicrobial resistance: A systematic review and one health gap analysis – Sujan Adhikar – PLOS ONE

Viral Microbiome

ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance – FuGuo Liu – PLOS ONE

Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus) – Jack W Wheelahan – PLOS ONE

Expanding diversity of tick-borne phleboviruses (Phlebovirus mukawaense, Mudanjiang phlebovirus, Gomselga Virus, and Onega tick phlebovirus) in Russia – Mikhail Y Kartasho – PLOS ONE

Phage / Mobile Genetic Elements

Phage-plasmid-like elements are found throughout diverse environments and encode niche-specific functional traits – James I Mulle – PLOS ONE

Microbiological quality assessment of potential pathogenic bacteria and multidrug resistance patterns in commercial electrolyte drinks in Dhaka, Bangladesh – Sananda Saha – PLOS ONE

Pathogen & Disease-related Microbiology

Leishmania major virulence attenuation in vitro: An old conundrum revisited in the omics era – Evgeny S Gerasimov – PLOS ONE

Microbiological quality assessment of potential pathogenic bacteria and multidrug resistance patterns in commercial electrolyte drinks in Dhaka, Bangladesh – Sananda Saha – PLOS ONE

Microbiome Tools / Bioinformatics / Methods

TIPP-SD: A new method for species detection in microbiomes – Chengze Shen – PLOS ONE

AgrOmicSo: A client-server interface for accessible large-scale analysis of next-generation sequencing data – Dong-Jun Lee – PLOS ONE

Antimicrobial Resistance (AMR Microbiome)

The livestock drinking water system as an active reservoir for antimicrobial resistance: A systematic review and one health gap analysis
Sujan Adhikar

May 29, 2026

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See you next week at MVIF!

June is right around the corner and the #MVIF 50 program is officially out! 🤩Highlights:🇧🇩 Dipto Kundu🇸🇪 @joseecologist.bsky.social Keynote:🇺🇸 @julesdeep.bsky.social Talks:🇺🇸 Samuel Degregori🇺🇸 Anna Samarra🇨🇳 Dehan Cai

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-05-20T19:52:38.426Z

Global microbiome

Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISME Journal

Gut microbiome

Divergent Resilience of Bacterial and Fungal Gut Microbiota After Colorectal Surgery: Insights From a Prospective Longitudinal Cohort Study – Simon Wetzel – MedComm

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation – Mi Ni – Cell Host & Microbe

Glad that our paper is out today in @cp-cellhostmicrobe.bsky.social A baby received a routine course of amoxicillin. In that infant's #gut 💩, we could see something remarkable, already present **before** the antibiotic arriveda single strain 🦠 of #Akkermansia muciniphila was already running 1/n

— Gang Fang (@gangfang.bsky.social) 2026-05-19T16:28:37.915Z

Dietary transition to an Indigenous Greenlandic diet induces instant shifts in gut microbiota composition – a pilot intervention study – Mads B. W. Bjørnsen – Frontiers in Microbiomes

Review: Next-generation probiotics: an outlook into current applications and future developments – Lara Kern – Nature Reviews Microbiology

Oral microbiome

Machine learning reveals microbiome differences by periodontitis severity – Soo Hyun Seo – PlosOne
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0349686

Animal microbiome

Integrated Responses: Multi-dimensional Evidence of Diet-Microbiome Coupling of Fish across a River Continuum in a Dry-Hot Valley – Yaqiu Liu – Global Ecology and Conservation

Our new study on how altitudinal gradients in river systems affect the #diet – #microbiome coupling in the #benthic stone #loach (#Schistura fasciolata) across the Yuanjiang-Red River Basin, #China [1/3]#SymbioSky #MicroSky #microbiomesky @hostmicrobelit.bsky.socialdoi.org/10.1016/j.ge…

— Kostas Kormas 🐟🦞🐚🦭💩🔬🧪🧬📝 ✈️ 🏳️‍🌈 (@kkormas.bsky.social) 2026-05-26T09:39:52.164Z

Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge – Alessandro N. Garritano – Microbiome

Plant, root, soil microbiome

Low intra-microbiota antagonism underlies stable and protective barley root microbiota – Lisa Katharina Mahdi – bioRxiv

Here we show that low intra-microbiota antagonism underlies stable, protective barley root microbiota. Microbiota function cannot be predicted from beneficial traits of individual strains alone, but depends on compatibility among community members. #Microbiome #Plantwww.biorxiv.org/content/10.6…

— Team_Zuccaro (@algazuccaro.bsky.social) 2026-05-24T14:31:30.515Z

Bioinformatics

Microbe Decoder uncovers functional traits of microbes in microbiome datasets – Timothy J Hackmann – Nucleic Acids Research

ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics – Parsa Ghadermaz – bioRxiv

The elusive resistome: a global comparison reveals large discrepancies among detection pipelines – Juan S. Inda-Díaz – bioRxiv 

We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project?That question sent us down a rabbit hole.Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles.1/3

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2026-05-15T10:52:09.330Z

April 29 , 2026

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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

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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

April 17,2026

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See you next week at MVIF!

#MVIF 48 starts next week! Free registration: cassyni.com/s/mvif-48⭐️ Highlights:🇺🇸 Rachel R. Rock🇺🇸 @pamferretti.bsky.social ⭐️ Keynote:🇦🇺 @pam-engelberts.bsky.social and @jamesvolmer.bsky.social ⭐️ Talks: 🇨🇳 Linxing Chen🇨🇳 Zhemin Zhou🇦🇺 Hoai-An Nguyen

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-04-13T11:02:11.436Z


Gut microbiome

Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study – Jennifer L. Arzu – BMC Medical Genomics 

Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review – Aswin Viswan – Microbial Ecology

Respiratory Microbiome

The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation – Jiale Yu – Journal of Advanced Research

Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis – Lucia Grassi – npj Biofilms Microbiomes

Animal Microbiome

Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows – Guangfu Tang – Microbiome

Spiroplasma Display an Intricate Continuum of Infection Heterogeneity and Persistence in Myrmica Ants – Diego Castillo Franco – Molecular Ecology

Oral Microbiome

Loss of salivary agglutinin induces changes in the salivary microbiome and accelerates development of oral cancer – Marcell Costa de Medeiros – Microbiome

Water Microbiome

Ecological water replenishment reshapes the river microbiome along an urban-rural gradient: Enhanced diversity but compromised stability – Hongyuan Tian – Journal of Hydrology: Regional Studies

Soil Microbiome

Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland – Linnea K. Hernandez – Microbiome

Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials – Nils Kleinbölting – Scientific Reports

Plant Microbiome

Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits – Denis Kiplimo – Environmental Microbiome

Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress – Caryn Kgokonyane Lenonyane – Scientific Reports

Bioinformatics

Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials – Tom Eilers – Scientific Reports

Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies – Bianca-Maria Cosma – PLOS One

Genomic characterization of Comamonas kerstersii isolated from diarrheal patients in Bangladesh – Noshin Ibnat Rib – PLOS One

I had the joy of giving a kindergarten workshop: “Bacteria in and around us!” 🦠✨To spark their imagination and start our discussion, I showed them the beautiful @contamclub.bsky.social 2026 calendar, full of vividly colored and uniquely shaped bacterial colonies.1/3

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2026-04-16T10:46:01.481Z

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