Project description:Urolithins are a class of bioactive metabolites derived from the metabolism of dietary ellagitannins by the human gut microbiota. In the gut, urolithins are dehydroxylated regioselectively based on microbiota composition and activity. A single 9-hydroxy urolithin dehydroxylase (ucd) operon in gut resident Enterocloster species has been described to date; however, most enzymes in the urolithin metabolic pathway remain uncharacterized. Here, we investigate urolithin cross-feeding between members of the gut microbiota and discover a novel urolithin dehydroxylase in a subset of Enterocloster species. We show that urolithin intermediates, released by gut resident Gordonibacter species during ellagic acid metabolism, are dehydroxylated at both the 9- and 10-positions by E. asparagiformis, E. citroniae, and E. pacaense, but not E. bolteae. Using untargeted proteomics, we uncover a 10-hydroxy urolithin dehydroxylase operon, termed uxd, responsible for these species-specific differences in urolithin metabolism. By inducing uxd expression with diverse urolithins, we show that 9-hydroxy urolithins are required for uxd transcription and 10-position dehydroxylation. Collectively, this study reveals some of the genes, proteins, and substrate features underlying differences in urolithin metabolism by the human gut microbiota.
Project description:Urolithin A is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota which can affect host health. Most, but not all, individuals harbor a microbiota capable of urolithin A production; however, the enzymes that dehydroxylate its dietary precursor, urolithin C, are unknown. Here, we used a combination of transcriptomics and proteomics to reveal a urolithin C dehydroxylase (ucd) operon that dehydroxylates 9-hydroxy urolithin compounds in Enterocloster spp. Using comparative genomics, we identified Lachnoclostridium pacaense as a novel urolithin C metabolizer. Biochemical characterization and structure predictions of proteins in the Ucd complex demonstrated that dehydroxylation was both NADH- and molybdopterin-dependent and used urolithin C as a terminal electron acceptor. A meta-analysis publicly available metagenomic data revealed that both bacteria and ucd operon genes are widely distributed in gut metagenomes and likely comprise keystone species in the metabolism of urolithins by the human gut microbiota.
