General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv

Bioinformatics

Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment