Date of Award

Winter 12-15-2014

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Human & Statistical Genetics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



A species' niche is the description of all the environmental conditions required to permit a population of that species to persist, including the effects of the population on those conditions. This definition includes the species' resource requirements, as well as stress tolerances and interactions with other species acting as competitors, predators, parasites, and mutualists. The human gut microbiota serves as a microbial `metabolic organ' tasked in part with the biotransformation of many components of our diet. Relatively little is known about the factors that allow members of the human gut microbiota to persist in a habitat that experiences marked changes in its nutrient environment. Identification of these factors is important for understanding the mechanisms that determine community assembly, community responses to and recovery after various perturbations, and the food webs that link microbes to one another and to their host. Therefore, in my thesis, I developed an experimental and computational pipeline for multi-taxon insertion sequencing (multi-taxon INSeq) to identify fitness determinants in multiple species and strains of human gut Bacteroides. Libraries of tens of thousands of transposon (Tn) mutants for each of four human gut Bacteroides strains, two of which represented the same species, were generated. These libraries were then introduced into adult germ-free mice as part of a 15-member artificial defined human gut microbiota containing 11 other wild-type bacterial species. Mice were fed diets either low in fat and high in plant polysaccharides (LF/HPP), or high in fat and simple sugars (HF/HS). Fecal samples, collected over time, were subjected to multi-taxon INSeq and my analysis pipeline, which was based on maximum likelihood estimation. A total of 86 core fitness determinants were identified across all four strains; a large fraction of these determinants were involved in various aspects of amino acid biosynthesis. Significant intra-species differences were detected in response to diet between two strains of Bacteroides thetaiotaomicron, highlighting differential strategies facilitating their co-existence within a complex community. By combining information gleaned from in vivo and in vitro INSeq experiments, as well as from in vivo and in vitro microbial RNA-Seq, I determined that arabinoxylan, the most common hemicellulose in cereals, was able to drive expression of a polysaccharide utilization locus that represented a key fitness factor in Bacteroides cellulosilyticus WH2 when mice consumed HF/HS diet. Supplementation of the drinking water with this glycan in turn significantly increased the representation of B. cellulosilyticus WH2 within the defined community in the context of the high fat diet. Multi-taxon INSeq defined the changes in fitness determinants of this and the other Bacteroides in response to arabinoxylan supplementation. Collectively, these studies revealed multiple mechanisms by which our microbial symbionts establish themselves in the gut, including species-specific, strain-specific, as well as core responses, which mapped to a variety of metabolic/nutrient processing pathways. The approach described for mapping fitness landscapes in a community context should facilitate discovery efforts aimed at identifying the niches of microbiota members, as well as ways to deliberately reshape community structure and function through dietary interventions.


English (en)

Chair and Committee

Jeffrey I. Gordon

Committee Members

Justin C. Fay, Daniel E. Goldberg, Robi D. Mitra, Michael A. Province, Clay F. Semenkovich


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