Date of Award

Summer 8-15-2016

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



Micronutrient deficiencies represent a form of "hidden hunger" that afflict two billion people worldwide. To test the hypothesis that dietary micronutrient deficiency has differential effects on members of the human gut microbiota, a consortium containing 92 sequenced phylogenetically diverse bacterial strains was introduced into germ-free mice. Recipient animals were subjected to a diet oscillation that began with highly defined micronutrient-sufficient diet followed by a derivative diet with one of four types of single micronutrient deficiency, or a diet representing combined deficiencies, followed by return to the original sufficient diet. Times-series studies of microbial community structure and transcriptome revealed that acute vitamin A deficiency had the largest effects. Bacteroides vulgatus, a member of the developing microbiota associated with healthy growth of children, was a prominent responder, increasing its abundance in the absence of dietary vitamin A, and manifesting robust changes in gene expression affecting a number of metabolic and other pathways. In vitro studies of different retinoids revealed that retinol was the most potent inhibitor of B. vulgatus growth. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of AcrR, a member of the TetR family of transcriptional repressors, abrogated retinol sensitivity. Genetic complementation studies, vitro RNA-Seq analysis, and transcription factor binding assays disclosed that AcrR (i) functions as a repressor of an adjacent AcrAB-TolC efflux system (and of dispersed genes comprising a larger regulon) and (ii) mediates retinol sensitivity. Measurement of retinol efflux from wild-type, acrR-mutant, and complemented acrR mutant strains of B. vulgatus, combined with studies of the effects of a pharmacologic inhibitor of this efflux system and of bile acids on growth provided additional support that members of the AcrR regulon, including AcrAB-TolC, function as determinants of retinol and bile acid sensitivity in gut Bacteroides. Our findings raise the possibility that dietary retinol availability, bile acids generated by microbial biotransformation, and this efflux system interact to influence the fitness of B. vulgatus and perhaps other gut bacterial species.


English (en)

Chair and Committee

Jeffrey I. Gordon

Committee Members

Gautam Dantas, Daniel E. Goldberg, Jeffrey P. Henderson, Scott J. Hultgren, Lora L. Iannotti


Permanent URL: https://doi.org/doi:10.7936/K7639N46