Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated colitis and is responsible for significant morbidity, mortality and increased healthcare costs. Despite the significance of CDI, there are major gaps in our understanding of the pathogenesis of this infection. Antibiotics disrupt the indigenous gut microbiota, reducing resistance to C. difficile colonization. However, our knowledge of how the gut microbiota confers resistance to CDI is rudimentary, presenting a significant roadblock to improving preventative and therapeutic approaches against this infection. My long-term goal is to understand how the gastrointestinal tract microbiota mediates colonization resistance against C. difficile. The overall objective of this application is to define metabolites associated with changes in the gut microbiota that contribute to C. difficile colonization and pathogenesis. Using an untargeted metabolomics approach, we have shown that the intestinal environment of antibiotic-treated mice was characterized by major shifts in metabolic profiles. Following antibiotic administration, we detected increases in primary bile acids, carbohydrates, and amino acids and decreased free fatty acids, secondary bile acids and dipeptides;reflecting the diminished metabolic activity of the gut microbiome. Subsequently, we demonstrated that C. difficile could utilize many of these metabolites for in vitro germination and growth. The central hypothesis is that the availability of specific nutrients that support C. difficile growth in the gt after antibiotic treatment is responsible for the observed decrease in colonization resistance. The rationale for the proposed research is that understanding the role the gastrointestinal metabolome plays in C. difficile pathogenesis has the potential to improve preventative and therapeutic approaches for this infection. Guided by strong preliminary data, this hypothesis will be tested by pursuing two specific aims: 1) Identify metabolites in the gastrointestinal tract that contribute to C. difficile colonization and pathogenesis;and 2) Determine the physiological concentrations of gut metabolites that modulate C. difficile pathogenesis. Under the first specific aim, we will use an untargeted metabolomics approach to identify candidate biomarkers from the murine gastrointestinal tract prior to CDI and during different stages of infection. Under the second specific aim, we will use a targeted metabolomics approach to confirm and quantitate metabolites that were significantly affected in specific aim 1, prior to CDI and during different stages of infection. We will also use in vitro studies to confirm their role in C. difficile germination, growth and toxin production. The approach is innovative, because we are using new mass spectrometry technology in a different way, to help solve important biological questions that will improve public health. The proposed research is significant, because it will lead to the identification of novel biomarkers and potential targets for therapeutic interventions to prevent or treat CDI. My overall career goal is to establish an independent research career bridging the field of metabolomics and biomedical infectious diseases, with emphasis on understanding Clostridium difficile pathogenesis. My long-term research interests have always included studying the impact of disease and how it impacts human health. With the advent of """"""""omics"""""""" technologies complex communities, including the gastrointestinal tract, can be defined. The expertise and co-mentorship of both Dr. Vincent Young and Dr. Charles Burant ensures success of this research project and my continued success a research scientist. The combined resources that my mentors and collaborators share will allow me access to mouse models of C. difficile infection and the Metabolomics Core Facility, which includes access to state of the art mass spectrometry equipment and trained experts in metabolomics. Finally, these studies will provide me with the opportunity to learn the methodologies related to the emerging field of metabolomic profiling, including the design of studies, sample preparation, metabolite extraction and analysis by the latest mass spectrometer based methods and the processes of data analysis and bioinformatics interpretation of the acquired data. The mentorship plan detailed in this proposal and further didactic coursework in ethics, bioinformatics, statistics, and workshops on metabolomics will help me to become an independent researcher in the field of biomedical infectious diseases and metabolomics.

Public Health Relevance

The proposed research is relevant to public health because understanding how the gastrointestinal tract metabolome contributes to Clostridium difficile pathogenesis will lead to the development of therapeutic interventions for CDI. Thus, the proposed research is relevant to the part of the NIH's mission that pertains to developing fundamental knowledge that will reduce the burdens of human illness.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Scientist Development Award - Research & Training (K01)
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Special Emphasis Panel (ZRG1)
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Okita, Richard T
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University of Michigan Ann Arbor
Internal Medicine/Medicine
Schools of Medicine
Ann Arbor
United States
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Fletcher, Joshua R; Erwin, Samantha; Lanzas, Cristina et al. (2018) Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model. mSphere 3:
Theriot, Casey M (2018) Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics. mSystems 3:
Seekatz, Anna M; Theriot, Casey M; Rao, Krishna et al. (2018) Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe :
Thanissery, Rajani; Winston, Jenessa A; Theriot, Casey M (2017) Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids. Anaerobe 45:86-100
Winston, Jenessa A; Theriot, Casey M (2016) Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract. Anaerobe 41:44-50
Winston, Jenessa A; Thanissery, Rajani; Montgomery, Stephanie A et al. (2016) Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291. J Vis Exp :
Theriot, Casey M; Bowman, Alison A; Young, Vincent B (2016) Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine. mSphere 1:
Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha et al. (2016) Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. mSystems 1:
Theriot, Casey M; Young, Vincent B (2015) Interactions Between the Gastrointestinal Microbiome and Clostridium difficile. Annu Rev Microbiol 69:445-61
Koenigsknecht, Mark J; Theriot, Casey M; Bergin, Ingrid L et al. (2015) Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract. Infect Immun 83:934-41

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