Metabolomic Profiling of Nutrient Solutions for Characterization of Human Gut Microbiota

Abstract

Studying the metabolite output, the “exometabolome,” of bacterial communities provides insight into the metabolic interactions occurring within that ecosystem. As such, a metabolomic approach can be used to gain further understanding of the human gut microbiota. As the microbes that reside in the human gastrointestinal (GI) system, the ecosystem has extensive impacts on the human body. In vitro systems for culturing gut microbes circumvents the ethical and technical challenges of in vivo studies, while, at the same time, lends itself to metabolomic investigations. The nutrient solutions in which microbial communities representative of the human gut microbiota are cultured contain a wealth of metabolomic data. In this thesis, metabolomic characterization is used to validate an in vitro gut-mimicking bioreactor system. This provided support for the ability to establish standardized protocols on preparing, culturing and reporting on in vitro gut microbiota. Furthermore, the metabolomic approach to studying gut microbes was used in applications relevant to clinical and industrial research. The findings from this thesis demonstrate the application of a metabolomic approach to studying the human gut microbiota in a single-stage continuous stirred tank reactor (CSTR) system. More importantly, the research here exemplifies the ways in which metabolomic insight can be translated into deciphering the complex interactions of the human gut microbiota.