Dynamic genetic requirements for B. theta colonization of the murine gut

Successful invasion of the gut environment by a commensal microbe requires the organism to adapt rapidly to a variety of biotic and abiotic factors. Although previous studies have begun to elucidate some of the most salient determinants of gut colonization, our understanding of how these fitness landscapes shift over time is still lacking. To address this gap in knowledge, we tracked Bacteroides thetaiotaomicron (Bt), a prominent human gut bacterium, in a time-resolved manner after its introduction into the murine gut. First, we compared the transcriptomic profiles of Bt 1-, 7-, and 14-days post gavage. Our data revealed that large global transcriptional changes occur quickly after penetration of the gut, then shifted again within the first week. Genes involved in proteomic remodeling and capsular polysaccharide biosynthesis were upregulated immediately upon introduction of Bt, whereas later in colonization, polysaccharide utilization genes were more prominently upregulated. Expression of PUL24, involved in raffinose family oligosaccharide metabolism, continued to increase into the second week when the rest of the transcriptome had stabilized. Second, we performed a TnSeq mutant screen. Overall, the results validated the functional significance of the genes identified by RNA-seq. Moreover, spontaneous Bt mutations that increased alpha-galactosidase activity were selected for within the murine gut, which highlights efficient carbohydrate metabolism as the most important determinant for the growth and persistence of Bt. Together, these results show that the genetic requirements for colonization shift over time, and the successful colonizer must respond rapidly and appropriately to the changing pressures.