Lactate cross-feeding between <i>Bifidobacterium</i> species and <i>Megasphaera indica</i> contributes to butyrate formation in the human colonic environment

Abstract

Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing <i>Bifidobacterium</i> population and an unidentified <i>Megasphaera</i> species. Therefore, we hypothesized that a cross-feeding phenomenon exists between <i>Bifidobacterium</i> and <i>Megasphaera</i>, where <i>Megasphaera</i> is the butyrate producer, and its growth relies on the metabolites generated by <i>Bifidobacterium</i>. To validate this hypothesis, three bacterial species (<i>B. longum</i>, <i>B. pseudocatenulatum</i>, and <i>M. indica</i>) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the <i>Bifidobacterium</i> and <i>M. indica</i> isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two <i>Bifidobacterium</i> isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, <i>M. indica</i> alone scarcely grew on the xylose-based substrates. The growth of <i>M. indica</i> was significantly elevated by coculturing it with bifidobacteria, while the two <i>Bifidobacterium</i> species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of <i>M. indica</i> genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by <i>Bifidobacterium</i> through catabolizing xylose fueled the growth of <i>M. indica</i> and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between <i>Bifidobacterium</i> and <i>Faecalibacterium prausnitzii</i> and between <i>Bifidobacterium</i> and <i>Eubacterium rectale</i>. In this study, we provided an alternative butyrate synthetic pathway through the interaction between <i>Bifidobacterium</i> and <i>Megasphaera indica. M. indica</i> is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of <i>M. indica</i> in the human colon are still limited. Our results show that <i>M. indica</i> proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.