Ten to 100 trillion microbes inhabit our gastrointestinal tract (Gl) and have co-evolved with us to form an optimized symbiosis. Reduced occurrence of food-borne bacteria and increased sanitation in westernized countries over the past century has resulted in our Gl tract and resident microbiota being deprived exposure to lactic acid bacteria common in the diets of our ancestors. This proposal employs a gnotobiotic mouse model host to assess the impact of lactic-acid-producing probiotic bacterial species on (i) a model human microbiota composed of sequenced representatives of the two dominant bacterial divisions in our intestinal ecosystem, Bacteroides thetaiotaomicron (Bacteroidetes division) and Eubacterium rectale (Firmicutes division), and (ii) on the host. Bifidobacterium longum and Lactobacillus case/will represent the two common genera of probiotic bacteria.
Aim 1 defines the impact of each probiotic species on the two-component model microbiota in the ceca of gnotobiotic mice. I will use whole genome transcriptional profiling of B. theta, E. rectale, and the probiotic species recovered from mouse ceca, transmission electron microscopy to assess bacterial localization, and mass-spectrometry of cecal nutrients.
Aim 2 characterizes host epithelial responses and mucin remodeling induced by probiotics using transcriptional profiling of laser-capturedcecal epithelium. Mass-spectrometric analysis of cecal mucin glycosylation will provide a structural view of how glycans, which are utilized by microbes for nutrients and tethering, are modified as a function of probiotic exposure.
Aim 3 assesses the impact of defined perturbations in the cecal nutrient environment on probiotic- symbiont-host interactions using (i) a defined inulin-rich diet, and (ii) a fucosyltransferase-deficient mouse that has altered cecal mucus composition. I have extensive training in host-microbial interactions, gnotobiotics, functional genomics, and glycobiology. The Washington University Center for Genome Sciences is a dynamic research environment that combines faculty and students with diverse expertise with state of the art technology, ensuring the support required as I transition into an independent faculty position. Relevance: This grant investigates the mechanisms by which probiotic bacteria affect the microbiota and Gl tract biology: given their wide use, these studies should provide a conceptual framework and biomarkers for hypothesis-based clinical studies designed to measure the impact of probiotics in healthy individuals and those with diseases inside and outside of the gut.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Scientist Development Award - Research & Training (K01)
Project #
Application #
Study Section
Diabetes, Endocrinology and Metabolic Diseases B Subcommittee (DDK)
Program Officer
Podskalny, Judith M,
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Stanford University
Schools of Medicine
United States
Zip Code
Marcobal, A; Sonnenburg, J L (2012) Human milk oligosaccharide consumption by intestinal microbiota. Clin Microbiol Infect 18 Suppl 4:12-5
Lynch, Jonathan B; Sonnenburg, Justin L (2012) Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Mol Microbiol 85:478-91
Sonnenburg, Erica D; Zheng, Hongjun; Joglekar, Payal et al. (2010) Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141:1241-52