Integrated Analysis of the Gut Microbiota and Their Fermentation Products in Mice Treated with the Longevity Enhancing Drug Acarbose

Abstract

During the last two decades, the predominant view of the microbial inhabitants of the mammalian digestive system has evolved from passive commensals to important drivers of health and disease. Processes now known to be affected by the gut microbiome include digestion, immune development and regulation, drug metabolism, pathogen resistance, and many more. Discoveries like these have been driven by revolutionary new methods for the untargeted, high-throughput characterization of the genetic and metabolic composition of microbial communities. However, going from these high-dimensional observations to mechanistic understanding is not trivial and is limited by experimental challenges in studying complex communities in realistic environments. The gut microbiome is particularly difficult, given its taxonomic diversity, physical inaccessibility, and intimate interface with host physiology. In this dissertation, I describe several contributions to our understanding of this important ecological system, with a particular focus on the analysis of bacteria and their metabolic roles in situ through the integration of diverse data.

The drug acarbose inhibits the breakdown and absorption of starch in the upper digestive system, resulting in increased availability of this polysaccharide in the lower gut. Interestingly, acarbose has been shown in mice to substantially increase lifespan. This work explores the effects in mice of experimental treatment with acarbose on the composition and function of the gut microbiome. Resulting dramatic increases in the abundance of members of the largely uncultivated bacterial family Muribaculaceae are linked to higher concentrations in feces of several short-chain fatty acids—in particular propionate—and these metabolic products of bacterial fermentation are in turn found to be associated with increased mouse lifespan. Furthermore, based on the culture-free reconstruction of bacterial genomes, we propose a metabolic role of Muribaculaceae in the breakdown of starch. Genetic features with homology to the starch utilization system in Bacteroides are identified in specific members of this family, possibly explaining their increased abundance in acarbose treated mice. In addition, for one taxon, two distinct genomic variants are found, predicting differences in physiology that could explain variable response to acarbose across replications of the experiment at multiple study sites. Finally, I develop experimental and analysis methods for measurements of absolute abundance in microbial communities using a recently proposed spike-in quantification approach. A novel, model-based inference procedure harnessing these data is found to outperform other methods in identifying changes in bacterial abundance.

This dissertation presents a comprehensive exploration of the dynamics and importance of the gut microbiome in an experimental model with implications for human health. Simultaneously, we develop and refine methods that can be applied to a variety of systems for deriving new understanding about complex microbial communities.