David Berry

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.

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.

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.

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.

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.

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.

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

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.

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.

This study shows that the Parkinson's drug entacapone disrupts gut microbiome homeostasis by sequestering iron, affecting microbial metabolism and promoting iron-scavenging organisms with resistance genes.

This study identifies putative keystone taxa in the human gut microbiome using correlation network analysis and evaluates the impact of taxonomic resolution on their detection.

This study identifies and correlates xenobiotics in breast milk and infant stool from Nigerian mother-infant pairs, showing links between chemical exposure and gut microbiome composition.