Today’s digest features some excellent human and mouse microbiome research, a highly detailed study of human associated Bifidobacterium longum, as well as a non microbiome picks on the history of rhinoceros in Cell and how to write a lab protocol in Nature.

General microbiome

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory – Bittleston et al. mSystems

Human gut microbiome

Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial – Leo et al. EBioMedicine

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals  – Tarallo et al. Gut

Associations between the gut microbiome and metabolome in early life – Nguyen et al. BMC Microbiology

Animal Experiments

The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Lynn et al. Cell Reports

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model – Xiao et al. Microbiome

Water Microbiome

Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage–bacteria interplay in deep-sea snail holobionts – Zhou et al. Microbiome

Soil microbiome

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil – Starr et al. mSphere

Bioinformatics

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Ling et al. Microbiome

Non-microbiome picks

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family – Lie et al. Cell

Five keys to writing a reproducible lab protocol – Nature