General microbiome
[Review]Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Liu et al. Microbiome
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter – Hoarfost et al. – Nature Communications
Covid19 and Metabolome
Sex differences in global metabolomic profiles of COVID-19 patients – Escarcega et al. – Cell Death & Disease
Pregnancy and early life
Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures? – Keburiya et al. – BMC Women’s Health
Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies – Lebeaux et al. – Pediatric Research
Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome
Human respiratory microbiome
The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Shimizu et al. – Thoacic Cancer
Human skin microbiome
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata – Agostinetto et al. – Databases
Human gut microbiome
Dynamic microbiome and metabolome analyses reveal the interaction between gut microbiota and anti-PD-1 based immunotherapy in hepatocellular carcinoma – Wu et al. – International Journal of Cancer
[Review]Exploring the multifactorial aspects of Gut Microbiome in Parkinson’s Disease – Pavan et al. – Folia Microbiologica
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
[Preprint]Gut microbiota of homing pigeons shows summer-winter variation under constant diet indicating a substantial effect of temperature – Dietz et al. – bioRxiv
Animal microbiome (for animals in the wild)
[Review]Bumblebees with the socially transmitted microbiome: A novel model organism for gut microbiota research – Zhang & Zheng – Insect Science
Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats – Xiao et al. – The ISME Journal
Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses – Li et al. – Front. Vet. Sci.
Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates – Microbiology Spectrum
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats – Liu et al. – Microbiome
Bioinformatics
CBEA: Competitive balances for taxonomic enrichment analysis – Nguyen, Hoen & Frost – PLOS Computational Biology
Clustering compositional data using Dirichlet mixture model – Pal & Heumann – PLOS One
Techniques
Generation and application of pseudo–long reads for metagenome assembly – Sim et al. – Giga Science
[Preprint]A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities – Shaffer et al. – bioRxiv
[Preprint]Estimating Microbial Population Data from Optical Density – Mira, Yeh & Hall – bioRxiv