Metabolic flux analysis of colonic microbiota using NMR

Abstract

Short chain fatty acids (SCFA) and especially butyrate, produced by the colonic microbiota, are important mediators of health and disease. Linking the biosynthesis of SCFA to specific gut microbial pathways holds promise for the development of prebiotics that specifically modulate these pathways in vivo. Therefore, 13C stable isotope labeling, NMR, and mathematical modeling of isotopomer distributions were employed to investigate colonic microbial metabolic pathway activities. An in vitro model of the colon was inoculated with a standardised human fecal microbiota. D-[U-13C]glucose was added at t=0, and samples were taken at various time points for metabolite and isotopomer analysis. A metabolic network model of key fermentative microbial pathways was constructed. Metabolic fluxes in this network were obtained by fitting predicted isotopomer distributions in SCFA and lactate to experimentally determined ones. The results indicated rapid transmembrane equilibration notably of formate, acetate and lactate in the microbiota, and demonstrated activity of special anaerobic pathways, such as the Wood-Ljungdahl pathway for acetate synthesis. In conclusion, this stable isotope study demonstrates successful quantitative probing of gut microbial pathways for SCFA synthesis from carbohydrates.