Date of Award

Spring 5-15-2017

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Microbiology & Microbial Pathogenesis)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The adaptive immune response to the human gut microbiota consists of a complex repertoire of antibodies interacting with a broad range of taxa. In mammals, immunoglobulin A (IgA) is the major class of antibody secreted at mucosal surfaces, where it promotes gut barrier function by preventing microbial and food antigens from interacting with host cells/tissues. The organisms targeted by gut mucosal IgA responses, the molecular targets of these secreted antibodies, and the environmental and genetic factors that shape these responses in the gut remain poorly defined. The central hypotheses of my thesis are: (i) IgA responses to human gut bacteria help to establish and maintain the mutually beneficial relationship between members of the microbiota and the host, including the fitness and expressed features of these members, (ii) IgA-targeting of specific bacterial taxa can serve as a biomarker for barrier disruption and be used to purify bacterial consortia with disease-effecting or disease-attenuating properties, and (iii) during the course of the first two years of postnatal life gut mucosal immune responses converge on a shared pattern of IgA-targeting in healthy infants that can be modeled within and between twin pairs and in gnotobiotic mice colonized with human fecal microbiota and fed diets representative of the donor human population. The first chapter in my thesis provides a brief synopsis of our current understanding of interactions between the microbiota and gut mucosal immunity. The second chapter contrasts the functional effects of two naturally-primed monoclonal IgAs that recognize distinct surface epitopes on the model human gut symbiont, Bacteroides thetaiotaomicron. Studies in three collections of B. thetaiotaomicron isolates and in gnotobiotic mice monocolonized with B. thetaiotaomicron are used to explore strain- and species-level epitope conservation, the fitness effects of these conserved epitopes in vivo, and the effects of antibody binding on bacterial gene expression. In the third chapter, I examine interrelationships between the gut microbiota and intestinal IgA responses in children with varying degrees of undernutrition, and gut barrier function. This study used fluorescence-activated cell sorting to purify IgA-bound and unbound fractions of a fecal microbial community (‘BugFACS’). We applied this technique to (i) fecal samples collected from mice harboring the fecal microbial communities of a Malawian twin pair discordant for kwashiorkor (a form of severe acute malnutrition), and fed either a sterile macro- and micronutrient deficient diet designed to represent the diets of the donor population or a nutrient sufficient diet, (ii) fecal samples collected from other twin pairs in this cohort that were discordant for severe acute malnutrition, and (iii) fecal samples collected from a second cohort of Malawian children with moderate acute malnutrition. These experiments disclosed that IgA responses to the bacterial family Enterobacteriaceae were robust biomarkers for health status. Follow-up experiments in gnotobiotic mice disclosed that a BugFACS-purified IgA+ consortium of bacteria could transmit a severe enteropathy characterized by rapid barrier disruption in the colon and small intestine, weight loss, and sepsis. Fractionation of this bacterial consortium disclosed that members of the Enterobacteriaceae were necessary but not sufficient to cause the profound weight loss and barrier disruption, while IgA-targeted members of the ‘healthy’ co-twin’s microbiota could prevent these phenotypes. In the fourth chapter, I analyze the co-development of gut microbiota and gut mucosal IgA responses in a birth cohort of 40 healthy USA twin pairs. I model development of the gut microbiota using a Random Forests-based machine learning approach that yielded a set of 25 bacterial taxa that could describe the maturation of fecal microbial communities in unrelated children. Applying BugFACS to a subset of these fecal samples, I further characterize gut mucosal IgA responses to components of the microbiota, and show how they vary as a function of postnatal age, family, and diet. These analyses reveal that there is an identifiable pattern of progression of gut mucosal IgA responses to members of the microbiota from one that in the first several months of postnatal life is highly distinctive for family members sharing a common environment (exemplified by healthy twin pairs), to one that subsequently generalizes across families (twin pairs) during the second postnatal year. I then present data from gnotobiotic mouse experiments showing that IgA responses in these mice broadly mirrored those of the human donor population and recapitulated age-associated differences observed in the twin pairs. The fifth chapter of my thesis proposes several potential avenues for future research based on the findings in my thesis.


English (en)

Chair and Committee

Jeffrey I. Gordon

Committee Members

Marco Colonna, Gautam Dantas, Daniel Goldberg, Chyi-Song Hsieh,


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