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 Ruminococcus gnavus ATCC 29149, and R. bromii L2-63, a keystone species for the degradation of resistant starch (RS) in human colon. Using anaerobic individual and co-cultures of R. bromii and R. gnavus grown on mucin or starch as sole carbon source, we showed that starch degradation by R. bromii supported the growth of R. gnavus whereas R. bromii did not benefit from mucin degradation by R. gnavus. Further we analyzed the growth (quantitative PCR), metabolite production (1H NMR analysis), and bacterial transcriptional response (RNA-Seq) of R. bromii cultured with RS or soluble starch (SS) in the presence or absence of R. gnavus. In co-culture fermentations on starch, 1H NMR analysis showed that R. gnavus benefits from transient glucose and malto-oligosaccharides released by R. bromii 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 R. bromii induced changes in R. gnavus transcriptional response of genes encoding several maltose transporters and enzymes involved in its metabolism such as maltose phosphorylase, in line with the ability of R. gnavus to utilize R. bromii starch degradation products. In the RS co-culture, R. bromii 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 R. gnavus. Together this study showed a direct competition between R. bromii and R. gnavus on RS, suggesting that in vivo, the R. gnavus population inhabiting the mucus niche may be modulated by the supply of non-digestible carbohydrates reaching the colon such as RS.

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics

“…A similar pattern was observed for Lactobacillus in these categories as well, which further provided support of their mucin degrading capabilities. Interestingly, Ruminococcus also displayed this pattern in "carbohydrate transport and metabolism" and previous work have suggested that these are mucin degraders as well [40]. It is possible that these taxa may play important roles in foraging nitrogen from the host to the microbiome.…”

Consumption of Cooked Black Beans Stimulates a Cluster of Some Clostridia Class Bacteria Decreasing Inflammatory Response and Improving Insulin Sensitivity

“…Interestingly, we found that the consumption of BB increases alpha diversity and modifies the gut microbiota by increasing the diversity of bacterial communities, mainly of the major phyla Gram-positive Firmicutes and of the class Clostridia of the genus Ruminococcus, mainly R. bromii, a key species for the degradation of resistant starch in the human colon [16], R. callidus and R. flavefaciens. From the genus Butyriciccocus B. pullicaecorum mainly increased, and from the genus Coprococcus, mainly C. eutactus, key species for the degradation of resistant starch in the human colon [25].…”

“…A possible explanation for these findings could be the changes in gut microbiota, mainly in butyrate-producing bacteria, as has been described [14,15]. Furthermore, one of the main components of beans is resistant starch, and, although there is considerable information on the effect of the different types of resistant starch on gut microbiota [16], few studies have focused on the effect of beans containing naturally resistant starch on the intestinal microbiota. One of the major sources of energy for microbial growth in the human colon is dietary resistant starch, which escapes digestion in the small intestine and reaches the colon undigested.…”

“…On the other hand, it is known that, although BB has some limiting amino acids, recent studies have shown that R. bromii increases the induction of the tryptophan biosynthesis genes [16], and methionine [30], the limiting amino acids of BB. In addition to the fermentation of indigestible carbohydrates, gut microbes are able to convert dietary choline and L-carnitine, via microbial enzymes, into trimethylamine (TMA).…”

Bifidobacterium breveUCC2003 exopolysaccharide modulates the early life microbiota by acting as a dietary substrate

“…Furthermore, another member of the Lachnospiraceae family, Ruminococcus , degrades intestinal mucins (similar in structure to EPS) liberating metabolites for other members of the microbiota to consume [36]. Thus, the positive correlation of Tyzzerella with formate in the EPS+ vessels suggests that, similar to other members in the Lachnospiraceae family, Tyzzerella may be consuming EPS and producing formate as a fermentation end-product [37]. Moreover, we observed several other strong negative correlations between different genus (e.g.…”