Anaerobic riboflavin degradation by human gut Lachnospiraceae

Vitamins mediate a web of cross-feeding interactions in the human gut. Many gram-positive gut microbes, in particular, are predicted to be vitamin auxotrophs. Previous studies of these microbes, however, have tended to use rich media, precluding controlled perturbations of low-abundance nutrients. We tested the ability of diverse Lachnospiraceae, the most common gram-positive bacteria in the gut, to grow on a chemically defined medium. Even though this medium contained riboflavin, we found that predicted riboflavin auxotrophs grew poorly, including the bile metabolizer Clostridium scindens. High-dose riboflavin supplementation enhanced growth, but also revealed that, surprisingly, C. scindens catabolizes riboflavin into lumichrome, making it the first reported anaerobe to do so. The only previously described catabolic pathway for riboflavin requires oxygen and has no homologs in C. scindens. In high-dose riboflavin, a single gene neighborhood with an aldolase, oxidoreductases, and a riboflavin kinase/adenylyltransferase was upregulated, suggesting an alternative anaerobic degradation or overflow pathway. Similar neighborhoods were detected in several other Lachnospiraceae, including Faecalicatena fissicatena, the only other anaerobe reported to degrade riboflavin. Reanalysis of published metabolomic data showed that, in vivo, both riboflavin and lumichrome were more abundant in colonized (vs germ-free) mouse ceca, and that, in vitro, Lachnospiraceae isolates depleted riboflavin while certain gram-negative isolates overproduced it. These results demonstrate that a member of the Lachnospiraceae can anaerobically convert an essential B vitamin into lumichrome, a molecule recently shown to have anti-inflammatory properties. Vitamin catabolism may both structure cross-feeding interactions in the gut and affect host health.IMPORTANCELachnospiraceae, the most prevalent human gut gram-positive bacteria, produce many health-relevant metabolites, but are genetically intractable and often grown in rich medium, complicating physiological studies. Unexpectedly, through comparative experiments in a chemically defined medium, we identify the first anaerobe that can catabolize riboflavin to lumichrome and show that it induces a specific gene neighborhood while doing so, suggesting a novel pathway. Variants of this neighborhood are conserved in a handful of Lachnospiraceae, including the only other anaerobe reported to degrade riboflavin (to hydroxyethylflavin). These results potentially explain decades-old observations implicating gut microbes in riboflavin catabolism. Furthermore, riboflavin catabolites have recently been shown to inhibit host mucosal-associated invariant T (MAIT) cell activation, suggesting an additional mechanism by which commensal Lachnospiraceae may dampen inflammation.