Functional analysis of colonic bacterial metabolism: relevant to health?

Abstract

With the use of molecular techniques, numerous studies have evaluated the composition of the intestinal microbiota in health and disease. However, it is of major interest to supplement this with a functional analysis of the microbiota. In this review, the different approaches that have been used to characterize microbial metabolites, yielding information on the functional end products of microbial metabolism, have been summarized. To analyze colonic microbial metabolites, the most conventional way is by application of a hypothesis-driven targeted approach, through quantification of selected metabolites from carbohydrate (e.g., short-chain fatty acids) and protein fermentation (e.g., p-cresol, phenol, ammonia, or H(2)S), secondary bile acids, or colonic enzymes. The application of stable isotope-labeled substrates can provide an elegant solution to study these metabolic pathways in vivo. On the other hand, a top-down approach can be followed by applying metabolite fingerprinting techniques based on (1)H-NMR or mass spectrometric analysis. Quantification of known metabolites and characterization of metabolite patterns in urine, breath, plasma, and fecal samples can reveal new pathways and give insight into physiological regulatory processes of the colonic microbiota. In addition, specific metabolic profiles can function as a diagnostic tool for the identification of several gastrointestinal diseases, such as ulcerative colitis and Crohn's disease. Nevertheless, future research will have to evaluate the relevance of associations between metabolites and different disease states.

Fig. 1.

Simplified scheme of the metabolites produced by the interplay between the microbial and human metabolome. After passing through the small intestine, unabsorbed dietary substrates (mainly unabsorbed carbohydrates and proteins) along with other endogenous substrates (such as bile enzymes, mucus and exfoliated cells) reach the large intestine, where they are fermented by the intestinal microbiota. These microbial metabolites are excreted in feces or absorbed and transported to the liver. Subsequently, these absorbed metabolites are subject to further human metabolism and can be excreted in urine and breath (50).

Fig. 2.

Different metabolites produced from colonic fermentation of carbohydrates and proteins. BCFA, branched-chain fatty acids; SCFA, short-chain fatty acids.

Fig. 3.

Proposed mechanism of action of prebiotics. IBD, inflammatory bowel disease; IBS, irritable bowel syndrome.

Fig. 4.

Lactose[¹⁵N,¹⁵N′]ureide is resistant to digestion but is fermented by colonic bacterial enzymes into [¹⁵N,¹⁵N′]urea and subsequently [¹⁵N]ammonia (NH₃). The formed [¹⁵N]ammonia can either be taken by the microbiota and excreted via the feces or be absorbed through the mucosa and renally excreted after conversion to [¹⁵N,¹⁴N′]urea in the liver. The proportionate recovery of ¹⁵N in feces or urine indicates the degree of colonic protein fermentation.

Fig. 5.

Enterohepatic circulation of bile acids. After each meal, gallbladder contraction empties bile acids into the intestinal tract. When passing through the intestinal tract, some bile acids are reabsorbed in the upper intestine by passive diffusion, but most bile acids (±95%) are reabsorbed in the ileum. Bile acids are transdiffused across the enterocyte to the basolateral membrane and excreted into portal blood circulation back to the liver. In the colon, secondary bile acids are formed by bacterial 7α-dehydroxylation of their primary bile acid precursor. Secondary bile acids may have a cytotoxic effect on the colonic epithelium. Bile acids lost in the feces (0.2–0.6 g/day) are replenished by de novo synthesis in the liver to maintain a constant bile acid pool. BA, bile acids; CA, cholic acid; CDCA, chenodeoxycholic acid; DCA, deoxycholic acid; LCA, lithocholic acid.