M. S. Donia

A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules

This study identifies disease-associated small molecules from the gut microbiome of IBD patients using metagenomic analysis and synthetic biology.

Bacterial DNA on the skin surface overrepresents the viable skin microbiome

This study shows that viable bacteria in the skin microbiome are mainly in hair follicles, not on the skin surface, and that surface DNA mostly comes from dead cells.

Pseudomonas aeruginosa detachment from surfaces via a self-made small molecule

This study identifies a Pseudomonas aeruginosa-produced small molecule, MHQ, that disperses surface-attached bacteria by inhibiting Type IV Pili activity.

Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products

The paper introduces decRiPPter, a machine learning and pan-genomic approach to discover novel RiPP classes, identifying 42 new candidate families from Streptomyces genomes.

Cutibacterium acnes antibiotic production shapes niche competition in the human skin microbiome

The paper identifies cutimycin, an antibiotic produced by Cutibacterium acnes, which reduces Staphylococcus colonization in human skin follicles.

Systematic mapping of drug metabolism by the human gut microbiome

The paper systematically maps drug metabolism by the human gut microbiome, showing 13% of 575 drugs are metabolized by a single microbiome sample.