Category Archives: General 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 22, 2026

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Gut microbiome

Network topology of the gut microbiome associates with metabolic health in obesity – Blanca Lacruz-Pleguezuelos – Nature Communications

High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome – Purnika Damindi Ranasinghe – Scientific Reports 

Animal Microbiome

Host Filtering Shapes the Soil–gut Microbiome Linkages in Pastoral Systems – Upulika Jayaneththi – Microbial Ecology

Oral Microbiome

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors – Jesse R. Willis – npj Biofilms and Microbiomes

Water Microbiome

Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers – Susanna R. Grigson – Nature Communications

Soil Microbiome

Soil microbes are the tiny bioengineers running Earth’s underground factory – Suzanne Hassan-Dalléac – Communications Earth & Environment

Plant Microbiome

Nitrogen Application Under Integrated Water–Fertilizer Management Regulates Rhizosphere Nitrogen Dynamics, Microbial Communities, and Maize Productivity – Mengqi Huang – Microbial Ecology

Bioinformatics

Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires – Quinten R. Ducarmon – Nature Microbiology

Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health – John Demby Sandi – PLoS Neglected Tropical Disease

May 8, 2026

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See you next week at MVIF!

#MVIF 49 program is out! 🤩 Free registration: cassyni.com/s/mvif-49Highlights: 🇮🇱 Netta Barak 🇳🇬 Gandonu Selome Ruth⭐️ Sponsor spotlight by Dagmara Lewandowska #IntegraBiosciencesKeynote:🇩🇪 Georg ZellerTalks:🇲🇦 Suleiman Aminu🇨🇳 Hongbin Liu🇳🇱 Jiyang Chan

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-04-30T09:34:17.767Z

Gut microbiome

Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults – Thomas Karner – Neurobiology of Stress

In our new study at @univie.ac.at , gut microbiome composition was linked to stress reactivity. Higher microbial diversity and inferred butyrate-producing capacity were associated with stronger cortisol reactivity, which may reflect a more adaptive response. 🧠🦠

— Thomas Karner (@thomaskarner.bsky.social) 2026-04-22T15:08:33.422Z

Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition – Zachary J. Pelland – PlosOne

Gut microbiome is associated with recurrence-free survival in patients with resected high-risk melanoma receiving adjuvant immune checkpoint blockade – Mykhaylo Usyk – Cell

Genome-wide sweeps create ecological units in the human gut microbiome – Xiaoqian Annie Yu – Nature

Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns – Tarini Shankar Ghosh – Nature Communications

Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri – Youssef El Mouali – Cell Host & Microbe 

Review: The impact of artificial sweeteners on bacterial physiology and the microbiome – Ciaram Staber – Trends in Microbiology 

Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition – Serena Boscaini – Nature Communications

If you missed it earlier this week check out the video on new research led by APC's @jfcryan.bsky.social & @moloneyger.bsky.social where they reveal for the first time how #coffee influences communication between the gut and the brain. buff.ly/x884r4f #GutBrainAxis #Microbiome #CoffeeScience

— APC Microbiome Ireland (@apcmicrobiomeirel.bsky.social) 2026-04-24T12:54:33.975Z

Urinary microbiome

Fatty acid auxotrophy as driver of Lactobacillus symbiosis in the female urinary tract – Michael L. Neugent – BioRxiv

Oral microbiome

Integrative host–microbiome modeling uncovers the implication of oral–gut translocation in advanced cirrhosis – Yi Jin – iMeta

Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children – Simon Yersin – Gut Microbes

📢 new paper alert! 📢Do we find the same #bacteria in the mouth and in the gut of stunded children?Go find out: doi.org/10.1080/1949…#microbiome #gut #gutmicrobes #metagenomicWith @vonaeschlab.bsky.social at @dmf-unil.bsky.social

— Simon Yersin (@yersim.bsky.social) 2026-04-07T12:42:09.651Z

Plant microbiome

The Anna Karenina principle in the assembly of plant microbiome under pathogen stress – Da Li – npj Biofilms and Microbiomes

Bioinformatics

Evaluating Reference-Independent Pipelines for the Detection of Spreading Organisms in Metagenomic Datasets – Nikolay Sergeevich Popov – BioRxiv

Learning the Language of the Microbiome with Transformers – Neythen J Treloar – BioRxiv

Holobiont

Viewing ourselves as nature: Holobiont literacy influences nature connectedness – Jake M. Robinson – Ambio

What happens when people learn that humans are not standalone organisms, but walking ecosystems?Our new paper explored whether learning about the #holobiont concept – humans are symbiotic assemblages of a host & trillions of microbes – influences nature connectedness.1/

— Jake Robinson (@jake1.bsky.social) 2026-05-06T22:07:54.693Z

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

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

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

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