Bile acid fitness determinants of aBacteroides fragilisisolate from a human pouchitis patient

Abstract

Bacteroides fragiliscomprises 1-5% of the gut microbiota in healthy individuals but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and that likely impact microbial growth and community structure. In UC colectomy patients with surgically created ileoanal pouches, levels of the bile acid deoxycholate (DC) are reduced in the pouch. We developed aB. fragilisstrain isolated from a UC patient with pouch inflammation (i.e. pouchitis) as a genetic model system and have used this strain to identify genes and pathways that impact fitness in DC and crude bile. Treatment ofB. fragiliswith a DC concentration congruent with a healthy human gut reduced cell growth and remodeled transcription of approximately one-quarter of all genes. DC strongly induced transcription of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. We further definedB. fragilisgenes that impacted fitness in media containing DC or crude bile using a barcoded collection of ≈50,000 unique mutants. Genes that contribute to cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. The correspondence between genes that were transcriptionally regulated and genes that impacted fitness in bile was limited. Our study provides a genome-scale view of aB. fragilisbile response and genetic determinants of fitness in DC and crude bile.