Category Archives: Human oral

June 9 , 2026

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Human Microbiome

Remodelling of cystic fibrosis respiratory microbiota in response to extended elexacaftor–tezacaftor–ivacaftor therapy – Helen Gavillet – microbiome

Metabolic host-microbe crosstalk in stabilization of epithelial HIF – Alexander S. Dowdel – microbiome

Animal Microbiome

Reproductive aging drives deterministic microbiota assembly to mitigate uterine oxidative phosphorylation impairment via spermidine production in laying hens – Dong Dai – microbiome

Gut bacterial regulation of primate adaptive thermogenesis at high altitude -Xiaochen Wang – microbiome

Livestock Microbiome

Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen – Li Wang – microbiome

Plant Microbiome

Deterministic assembly of rhizosphere bacterial community enables predictable and stable suppression of Verticillium wilt via microbial homeostasis – jiamin Ai – microbiome

Steering root-associated microbiomes via direct and soil legacy effects of neighbors – Mireadili Kuerban – microbiome

Biosynthesized selenium nanoparticles increase soybean resistance to root rot by recruiting beneficial microbes and reprogramming host metabolism – Haixu Liu – microbiome

Environmental / Built Microbiome

Longitudinal analysis of stowaway microorganisms aboard modules and cargo spacecraft of the Chinese Space Station – Ying Zhang – microbiome

Marine Microbiome

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

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

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 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 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