Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

Abstract

The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.

Fig. 1.

Summary of metabolic responses of E. rectale to B. thetaiotaomicron. (A) Overview of metabolic pathways. (B) GeneChip probeset intensities and qRT-PCR validation assays are shown for a subset of genes. Mean values for triplicate qRT-PCR determinations (n = 4 mice per group) ± SD are plotted. Pts, phosphotransferase systems; Gpd, glycerol 3-phosphate dehydrogenase; Pck, phosphoenolpyruvate carboxykinase; Por, pyruvate:ferredoxin oxidoreductase; Hyd, hydrogenase; Rnf, NADH: ferredoxin oxidoreductase complex; Fd_red, reduced ferredoxin; Fd_ox oxidized ferredoxin; Pta, phosphate acetyltransferase; Bcd, butyryl-CoA dehydrogenase; Etf electron transport flavoproteins; Cat, butyryl CoA: acetate CoA transferase; Glt, glutamate synthetase; GlnA, glutamine synthetase Gln, glutamine; Glu, glutamate; Mct1, monocarboxylate transporter 1.

Fig. 2.

Cocolonization affects the efficiency of fermentation. Cecal contents from 4 mice in each treatment group were assayed for NAD⁺, NADH acetate, butyrate and proprionate levels. Expression of Mct-1 mRNA, a monocarboxylate transporter whose preferred substrate is butyrate was defined by qRT-PCR in the proximal colon. Cecal propionate concentrations. Mean values ± SEM are plotted; n = 4–5 mice per group; ∗, P < 0.05, ∗∗, P < 0.001 compared with cocolonization (Student's t test).