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

Abstract

AbstractBacteroides fragiliscomprises 1-5% of the gut microbiota in healthy humans 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 likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated aB. fragilisstrain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impactB. fragilisfitness in DC and crude bile. Treatment ofB. fragiliswith a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further definedB. fragilisgenes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of aB. fragilisbile response and genetic determinants of its fitness in DC and crude bile.ImportanceThe Gram-negative bacterium,Bacteroides fragilis, is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enableB. fragilisto grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for aB. fragilisstrain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, whereB. fragilisoften blooms. Using this resource, we uncovered pathways and processes that impactB. fragilisfitness in bile and that may contribute to population expansions during bouts of gut inflammation.