June 9 , 2026

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

13 July, 2019

Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy