Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Strains

Genomic differences between gut-resident bacterial strains likely underlie significant interindividual variation in microbiome function. Traditional methods of determining community composition, such as 16S rRNA gene amplicon sequencing, fail to capture this functional diversity. Metagenomic approaches are a significant step forward in identifying strain-level sequence variants; however, given the current paucity of biochemical information, they too are limited to mainly low-resolution and incomplete functional predictions. Using genomic, biochemical, and molecular approaches, we identified differences in the fructan utilization profiles of two closely related strains. 8736 () contains a fructan polysaccharide utilization locus (PUL) with a divergent / homolog gene pair that enables it to utilize inulin, differentiating this strain from other characterized strains. Transfer of the distinct pair of / genes from into the noninulin using type strain resulted in inulin use by the recipient strain, (). The presence of the divergent / gene pair alone enabled the hybrid () strain to outcompete the wild-type strain in mice fed an inulin diet. Further, we discovered that the / homolog gene pair facilitated import of inulin into the periplasm without surface predigestion by an endo-acting enzyme, possibly due to the short average chain length of inulin compared to many other polysaccharides. Our data builds upon recent reports of dietary polysaccharide utilization mechanisms found in members of the genus and demonstrates how the acquisition of two genes can alter the functionality and success of a strain within the gut. Dietary polysaccharides play a dominant role in shaping the composition and functionality of our gut microbiota. Dietary interventions using these icrobiota-ccessible arbohydrates (MACs) serve as a promising tool for manipulating the gut microbial community. However, our current gap in knowledge regarding microbial metabolic pathways that are involved in the degradation of these MACs has made the design of rational interventions difficult. The issue is further complicated by the diversity of pathways observed for the utilization of similar MACs, even in closely related microbial strains. Our current work focuses on divergent fructan utilization pathways in two closely related strains and provides an integrated approach to characterize the molecular basis for strain-level functional differences.