Host-Associated Microbial Communities as Mediators of Dietary Effects on Host Health

Abstract

Host-associated microbial communities evolve with their host. They depend on the host for energy substrates and stability and must adapt to host-specific selective pressures. Evidence for how complex communities respond to certain exposures, such as host diet or medication use, is inconsistent across populations (both within and between host species) due to biological (e.g., interindividual variation) and technical (e.g., varying sequencing and quantification methods) complexities, coupled with evolving methods for analysis. Thus, deriving generalizable conclusions for how gut communities respond to chemical perturbations, particularly host diet, remains a challenge. In Chapter 1 of this dissertation, I discuss efforts made to systematically compare the effects of dietary exposure on the healthy human gut microbiome in relation to diverse gut contexts (across diets, health and disease phenotypes, and host species). In Chapter 2, I share a large-scale characterization of the gut microbiomes of canine and feline companion animals, which will contribute to our understanding of how diet interacts with the gut microbiome in different hosts. Additionally, this work was the first to provide community-wide evidence of microbial transmission of commensals between humans and companion animals, for which the health impacts remain unknown. In Chapter 3, themes of the two preceding chapters come together as I explore how the gut microbiome contributes to obesity, a diet-linked phenotype, in the feline gut microbiome.