Understanding small molecule uptake by the Bacteroidetes

The human gut microbiome has a profound influence on virtually all aspects of human health. The composition and therefore collective function of the colonic microbiota depends on the ability of individual micro-organisms to acquire nutrients in a highly competitive environment. While very diverse at the species level, the gut microbiome is dominated by just two bacterial phyla, Gram-positive Firmicutes and Gram-negative Bacteroidetes. In the Bacteroidetes, the outer membrane (OM) is the first, and for hydrophobic molecules only, barrier for cell entry. Therefore, the intracellular fate (metabolism, bioconversion) of any small molecule is linked to its ability to traverse the OM via active transporters and diffusion channels. While extensively characterized in Proteobacteria, OM transport in the phylogenetically distant Bacteroidetes is terra incognita. In this proposal we will define the OM protein landscape of an abundant and representative member of the genus Bacteroides via quantitative proteomics under various conditions. We will also gain a thorough mechanistic understanding of (i) active import via TonB-dependent transporters and (ii) passive uptake via OM diffusion channels, using X-ray crystallography, cryo-EM and electrophysiology. The work will transform our understanding of nutrient acquisition by Bacteroidetes and will suggest ways for microbiota manipulation to benefit human health.