Mass spectrometry-based approaches to evaluate the bidirectional relationship between microbial communities and metabolites in food products

Abstract

The relationship between microbial communities and the metabolites they produce is highly complex and deeply influential in human health. Advanced analytical instrumentation, particularly mass spectrometry, is essential for gaining a systems level understanding of these interactions. This dissertation investigates the bidirectional relationship between microbiomes and microbial derived metabolites through the application of robust analytical tools, including mass spectrometry and 16S rRNA sequencing. The three chapters of this dissertation explore microbial metabolite dynamics across clinical, in vitro, and in vivo contexts. Chapter One reviews current food-based clinical trials and emphasizes the need for more rigorous chemical characterization of dietary interventions, as analytical approaches applied to clinical biospecimens often far exceed those used for the foods themselves. Chapter Two examines how sourdough microbial communities shape the chemical composition of fermented foods, with the goal of leveraging this knowledge to intentionally design microbiomes that enhance nutritional functionality and shelf stability. Chapter Three evaluates the effects of the phytocannabinoids, CBD and CBG, on host metabolism and gut microbiome health in vivo. Together, this work highlights the necessity of standardized, high-resolution analytical techniques to better understand the complexity of microbial systems and their impact on human health.