Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates

Abstract

Dietary and host glycans shape the composition of the human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining the structure and function of gut microbial communities. Here, we focused on two major human gut symbionts, the mucin-degrader <i>Ruminococcus gnavus</i> ATCC 29149, and <i>R. bromii</i> L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of <i>R. bromii</i> and <i>R. gnavus</i> grown on mucin or starch as sole carbon source, we showed that starch degradation by <i>R. bromii</i> supported the growth of <i>R. gnavus</i> whereas <i>R. bromii</i> did not benefit from mucin degradation by <i>R. gnavus</i>. Further we analyzed the growth (quantitative PCR), metabolite production (¹H NMR analysis), and bacterial transcriptional response (RNA-Seq) of <i>R. bromii</i> cultured with RS or soluble starch (SS) in the presence or absence of <i>R. gnavus</i>. In co-culture fermentations on starch, ¹H NMR analysis showed that <i>R. gnavus</i> benefits from transient glucose and malto-oligosaccharides released by <i>R. bromii</i> upon starch degradation, producing acetate, formate, and lactate as main fermentation end-products. Differential expression analysis (DESeq 2) on starch (SS and RS) showed that the presence of <i>R. bromii</i> induced changes in <i>R. gnavus</i> transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of <i>R. gnavus</i> to utilize <i>R. bromii</i> starch degradation products. In the RS co-culture, <i>R. bromii</i> showed a significant increase in the induction of tryptophan (Trp) biosynthesis genes and a decrease of vitamin B12 (VitB12)-dependent methionine biosynthesis as compared to the mono-culture, suggesting that Trp and VitB12 availability become limited in the presence of <i>R. gnavus</i>. Together this study showed a direct competition between <i>R. bromii</i> and <i>R. gnavus</i> on RS, suggesting that <i>in vivo</i>, the <i>R. gnavus</i> population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.