General microbiome

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities – Wang et al. – Microbiome

Human oral microbiome

[PREPRINT]The prevalence of motility within the human oral microbiota – Rocha et al. – bioRxiv

Human gut microbiome

A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis – McGregor et al. – Parasites & Vectors

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer – Serrano-Villar et al. – Nature Medicine

[PREPRINT]Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer – Li et al. – bioRxiv

Diversity of plant DNA in stool is linked to dietary quality, age, and household income – Petrone et al. – PNAS

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

Alterations in fecal β-defensin-3 secretion as a marker of instability of the gut microbiota – Saqib et al. – Gut Microbes

The effect of prenatal stress on offspring depression susceptibility in relation to the gut microbiome and metabolome – Li et al. – Journal of Affective Disorders

[PROTOCOL]Gastrointestinal and Microbiome Profiling in Rodent Models of Neurological and Psychiatric Disorders – Kong et al. – Schizophrenia

Animal microbiome (for animals in the wild)

[PREPRINT]Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle – Vasco et al. – bioRxiv

Bioinformatics

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses – Elek et al. – Microbioal Genomics

[PREPRINT]Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data – Pope et al. – bioRxiv

MBECS: Microbiome Batch Effects Correction Suite – Olbrich, Künstner and Busch – BMC Bioinformatics

Techniques

[PREPRINT]High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific amplicons and long-read sequence – Stalder, Maurhofer and Croll – bioRxiv