Date of Award

Summer 8-15-2015

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type




A Gnotobiotic Mouse Model for Studying the Effect of Human Gut Community Ecology on a Pathobiont, Bacteroides fragilis


Vitas Wagner

Doctor of Philosophy in Biology and Biomedical Sciences

Evolution, Ecology, and Population Biology

Washington University in St. Louis, 2015

Professor Jeffrey I. Gordon, Chair

Childhood undernutrition represents a pressing global health challenge. Epidemiologic studies have shown that undernutrition is not due to food insecurity alone, but rather represents a complex set of interactions between intra- and intergenerational factors. The gut microbiota has been implicated as one such factor. This thesis tested the hypothesis that enteropathogen burden affects the structure and expressed functions of the gut microbiota, and reciprocally, the gut microbiota affects susceptibility to the effects of enteropathogen invasion. To examine this hypothesis, groups of adult germ-free C57Bl/6 mice were colonized with fecal microbiota sampled from two 24 month-old members of a birth-cohort living in an urban slum in the Mirpur district of Dhaka, Bangladesh: one child had a healthy growth phenotype as judged by anthropometry, and the undernourished child was severely stunted and underweight and exhibited relative microbiota immaturity. The microbiota of both children contained Bacteroides fragilis, a pathobiont. Both groups of colonized mice were fed three diets that embodied the diets consumed by the population from which the microbiota donors were selected. Mice harboring the intact uncultured microbiota from the stunted donor exhibited severe weight-loss, while those receiving the healthy donor’s microbiota maintained weight on these diets. Clonally-arrayed, sequenced collections of cultured anaerobic bacteria strains, generated from the donors’ fecal microbiota, transmitted (i) the discordant weight phenotypes within and across generations of animals (in a diet-dependent fashion), as well as (ii) distinct host metabolic phenotypes (manifest by marked differences in tissue organic acid, amino acid and ceramide profiles as defined by mass spectrometry). The B. fragilis strain in the stunted donor’s culture collection was enterotoxigenic (ETBF), while the two B. fragilis strains in the healthy donor’s culture collection were non-toxigenic (NTBF). Through a series of experiments in which mice were colonized with either the stunted or healthy culture collection ± ETBF or ± NTBF, I demonstrated that ETBF was associated with weight loss as a member of the stunted donor’s community, but not the healthy donor’s community. Microbial RNA-Seq analysis revealed marked differences in ETBF gene expression in the two different community contexts, and as a function of the presence or absence of NTBF. Strikingly, ETBF induced expression of a large repertoire of virulence factor genes encoded in the genomes of the healthy culture collection members; these effects were mitigated when NTBF was present. The effects of ETBF on host metabolism were also community context-dependent. These results provide preclinical evidence that enteropathogen effects on host physiology and metabolism are greatly impacted by gut community ecology and illustrate the value of combining gnotobiotic mouse models, human diet embodiments, and ‘personal’ culture collections for dissecting microbial-microbial and microbial-host interactions. A parallel study using gnotobiotic mice and subsets of the culture collection from the healthy donor revealed how turmeric, a culturally relevant spice in the Bangladeshi diet, and microbial bile acid production/metabolism interact to impact gut motility.


English (en)

Chair and Committee

Jeffrey I Gordon

Committee Members

Gautam Dantas, Daniel E Goldberg, Scott Mangan, David Queller, Alan Templeton,


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