Human gut microbiome

[REVIEW]Crosstalk between gut microbiome and neuroinflammation in pathogenesis of HIV-associated neurocognitive disorder – Chen et al. – Journal of the Neurological Sciences

Purified diet affects intestinal epithelial proliferation and barrier functions through gut microbial alterations – Shiratori et al. – International Immunology

[PREPRINT]Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults – Prochazkova et al. – bioRxiv

Causal relationship between gut microbiota and gastrointestinal diseases: a mendelian randomization study – Wu et al. – Journal of Translational Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

[PREPRINT]Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland – Zalewska et al. – bioRxiv

Assessing the microbiota of the snail intermediate host of trematodes, Galba truncatula – McCann et al. – Parasites & Vectors

Plant, root, and soil microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Tabassum et al. – Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Zhang et al. – Microbiome

Built environment (subways, indoor surfaces)

[PREPRINT]Identification and classification of the genomes of novel Microviruses in a poultry slaughterhouse – Xie et al. – bioRxiv

Bioinformatics

[PREPRINT]iVirP: An integrative, efficient, and user-friendly pipeline to annotate viral contigs from raw reads of metagenome or VLP sequencing – Li, Jiao and liang – bioRxiv

[PREPRINT]Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments – Wang et al. – bioRxiv

Techniques

[PREPRINT]MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers – Wang et al. – bioRxiv

Microbes in the news

How does chronic stress harm the gut? New clues emerge – Kozlov – Nature