Anaerobic riboflavin degradation by human gut Lachnospiraceae

Abstract

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-positives 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 Gram-positives in the human gut, produce many health-relevant metabolites, but are genetically intractable and are often grown in rich medium, complicating physiological studies. By performing a comparative study with chemically defined media, we identify for the first time a specific anaerobe that can break down riboflavin to lumichrome. Using transcriptomics, we also identify a specific gene neighborhood representing the first candidate pathway for anaerobic flavin degradation. This neighborhood is conserved in a handful of other Lachnospiraceae, including F. fissicatena, the only other anaerobe known to degrade riboflavin (to the related product hydroxyethylflavin). These results may explain decades-old observations implicating gut microbes in the formation of riboflavin degradation products. Furthermore, lumichrome and related metabolites 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.