UC Davis

Advances in DNA sequencing technologies have galvanized research efforts into understanding the effects of host-associated microbiomes on host health. While a staggering amount of data has been generated to describe taxonomic differences between “healthy” and “dysbiotic” microbiomes, the functions performed by microbiomes during homeostasis remain incompletely understood. This in turn makes understanding dysbiosis in the context of different etiologies difficult. Thus, it is paramount to develop new frameworks to expand our knowledge on the beneficial functions of host-associated microbiomes. To accomplish that goal, we created metabolic footprinting, a methodological framework which utilizes gnotobiotics, comparative-untargeted metabolomics, and growth assays to determine what microbes consume in vivo. Using metabolic footprinting, we determined that commensal Clostridia perform an important digestive function for the mammalian host by consuming sugar alcohols in the large bowel. Sugar alcohol intolerance is commonly reported by patients with irritable bowel syndrome or inflammatory bowel disease, suggesting the loss of Clostridia may be an important factor in these etiologies. Additionally, we used metabolic footprinting to discover that the human fungal pathogen Candida albicans consumes small sugars in the gut. Interestingly, C. albicans required oxygen to utilize these sugars in vitro, and we found that the gut microbiota prevented the expansion of C. albicans in the gut by restricting access to oxygen in vivo. The finding that oxygen is a critical resource for C. albicans in the large bowel could improve prophylaxis aimed at preventing invasive candidiasis in susceptible patients. Collectively, the results in this thesis demonstrate that metabolic footprinting is a useful tool for elucidating the functions performed by host-associated microbiomes.