High-throughput analyses of Phocaeicola vulgatus reveal fitness determinants for gut colonization and during colitis.

Phocaeicola vulgatus is one of the most ubiquitous and abundant bacterial members of the human gut microbiota; however, the genetic factors that are essential for its survival and persistence in the mammalian gut and in a colitic host have not been analyzed. Using both RB-TnSeq and transcriptomic analyses, we performed genome-wide, unbiased analyses to identify genes important for growth in rich medium, those contributing to gut colonization, and those important during dextran sulfate sodium (DSS)-induced colitis. RB-TnSeq analyses of P. vulgatus from the feces of monocolonized mice identified 1189 genes that contribute to fitness in the gut. Transcriptomic analysis showed that the alternate sigma/anti-sigma factor gene pair ecfO-reo and the nigD genes of its regulon are amongst the most highly expressed genes in the mono-colonized mouse gut. Analyses of genes important during DSS-induced colitis identified a distinct set of genes, many of which are involved in nutrient acquisition. We extensively studied several genes affecting fitness by deletion mutant analysis with subsequent phenotypic characterization and by mouse competitive colonization analyses. Finally, we identified a previously undescribed sigma/anti-sigma factor pair that is drastically upregulated during DSS-induced colitis, along with a co-transcribed spy chaperone gene, known to help protect bacteria against numerous stressors. Altogether, this study provides the first comprehensive genome-wide analysis of P. vulgatus from the mouse gut and of any gut Bacteroidales strain during colitis.