Untargeted stable isotope probing of gut microbiota metabolome using 13C-labeled dietary fibers

Authors: DENG, PAN - University Of Kentucky; VALENTINO, TAYLOR - University Of Kentucky; Flythe, Michael; MOSELEY, HUNTER - University Of Kentucky; LEACHMAN, JACQUELINE - University Of Kentucky; MORRIS, ANDREW - University Of Kentucky; HENNING, BERNHARD - University Of Kentucky

Submitted to: Journal of Proteome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2021
Publication Date: 4/8/2021
Citation: Deng, P., Valentino, T., Flythe, M.D., Moseley, H., Leachman, J., Morris, A., Henning, B. 2021. Untargeted stable isotope probing of gut microbiota metabolome using 13C-labeled dietary fibers. Journal of Proteome Research. 20(5):2904-2913. https://doi.org/10.1021/acs.jproteome.1c00124.
DOI: https://doi.org/10.1021/acs.jproteome.1c00124

Interpretive Summary: It has long been known that fiber is an important energy source for grazing animals. It is now recognized that dietary fiber is nutritionally important for humans as well. The term, "fiber", includes a variety of complex carbohydrates that are not easily digested by mammals. Fiber passes through the digestive tract, unaltered by mammalian enzymes until it encounters bacteria and other microorganisms in the gut that can metabolize it. This study compared cellulose, a very stable polymer of glucose, to inulin, which is a fructan, or polymer of fructose. Each of the fiber types was made up with carbon-13, a non-radioactive, but heavy form of carbon. Any compounds made from the carbon-13 in the fiber could be detected and identified with a mass spectrometer. The each of the fiber types were given to gut microbiota that were extracted from the feces of mice. The microbiota were not cultures, but rather a mixture of the hundreds of bacteria and other microbial species from the gut microbiomes of the animals. The results showed that both of the fiber types were fermented by the microbiota, inulin to a greater extent than cellulose. A variety of metabolic end products, such as short chain fatty acids, were made. The carbon from the fiber types was also incorporated into anabolic products, in other words, the building blocks of the microbial cells. These products included amino acids and vitamins. One surprising product was gamma amino butyric acid, or GABA. Vitamins and short chain fatty acids benefit the animal host and GABA is known to serve as a neurotransmitter in animals. These results shows the diversity of products that the gut microbiome can produce from dietary fiber. The impact of this research is to provide new, basic information on the range of biologically important compounds made from dietary fiber by the gut microbiota for the host animal.

Technical Abstract: The gut microbiome generates numerous metabolites that exert local effects and enter the circulation to affect the functions of many organs. Despite extensive sequencing-based characterization of the gut microbiome, there remains a lack of understanding of microbial metabolism. Here, we reported an untargeted stable isotope-resolved metabolomics (SIRM) methodology for the holistic study of gut microbial metabolites. Viable microbial cells were extracted from the fresh feces of female mice without enrichment and incubated anaerobically with 13C labeled dietary fibers including inulin or cellulose. High resolution mass spectrometry was used to investigate extensive 13C enrichment in metabolites associated with glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleotide synthesis, and pyruvate catabolism in both microbial cells and the liquid medium. Carbon (13C) from soluble (inulin) and insoluble (cellulose) fibers were utilized by gut microbiome to a different extent in the biosynthesis of amino acids, pantothenic acid and co-factors. Comparison of these two types of fiber revealed significant higher 13C enrichment in inulin treated samples compared to cellulose, reflecting distinct metabolic pathways of dietary fibers in the gut microbiome, which could be related with host effects. This is the first study utilizing SIRM technologies to investigate gut microbiome metabolism. This technology facilitates deeper and holistic insights into the metabolic function of the gut microbiome.