David Berry

Prevalent glutamyl-endopeptidases in the commensal skin microbiome have itch-relevant activity

The paper identifies Esp and Csp as functional glutamyl endopeptidases from commensal staphylococci that activate itch signaling and disrupt skin barrier function in atopic dermatitis.

Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans

This study shows that sulfoquinovose is not metabolized by mice or humans but is degraded by gut microbiota, with differences in degradation pathways between mice and humans.

Gut microbial diversity and inferred capacity to produce short-chain fatty acids are tied to acute stress reactivity in healthy adults

Nutrient landscape shapes the genetic diversification of the human gut commensal Bacteroides thetaiotaomicron

This study shows that complex nutrient environments drive genetic diversification in Bacteroides thetaiotaomicron through increased SNPs and DNA inversions, leading to adaptive traits like faster glucose depletion and amylopectin degradation.

Rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice revealed through deep population-level sequencing

This study tracks rapid genetic diversification of Bacteroides thetaiotaomicron in mono-associated mice over 28 days, identifying polymorphisms, phase-variable loci, and spatial variation in the gut.

Broad diversity of human gut bacteria accessible via a traceable strain deposition system

The paper establishes a publicly available collection of 340 human gut bacterial strains, including 29 newly described species, and identifies plasmids and megaplasmids within these isolates.

Benchmarking of shotgun sequencing depth highlights limitations of strain-level analysis and shallow metagenomics

This study benchmarks shotgun sequencing depth in metagenomics, showing that strain-level analysis and functional insights require deep sequencing, while shallow sequencing has significant limitations.

Edited Filamin A in myeloid cells reduces intestinal inflammation and protects from colitis

This study shows that RNA editing of FLNA in myeloid cells reduces intestinal inflammation and protects against colitis in mice and humans.

Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in a prominent gut symbiont

This study shows that human-derived miR-21 interacts with gut microbiota and regulates bacterial transcripts involved in indole and L-tryptophan biosynthesis, potentially influencing intestinal function and disease.

Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida

This study identifies Shewanella as a potential producer of polyunsaturated fatty acids (PUFAs) in the gut of Eisenia fetida earthworms, revealing distinct microbial and fatty acid profiles in gut and soil environments.