Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut

Diet selectively shapes the human gut microbiota and fuels production of diverse metabolites that influence host health. Responses of the microbiota to diet are highly personalized, yet mechanistically not well understood because the metabolic capabilities of human gut microorganisms remain largely unknown. Here we show that sulfoquinovose (SQ), an omnipresent monosaccharide in green vegetables, is a selective substrate for few but ubiquitous bacteria in the human gut. In anoxic incubations of human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia both use previously unrecognized pathways to cooperatively catabolize SQ to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. We find SQ degradation capability encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. Re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, suggesting their active contribution to gut functioning. The discovery of green diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.