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Genomic Insights Into Mycobacterium Tuberculosis and Its Interaction with the Microbiota

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GENOMIC INSIGHTS INTO MYCOBACTERIUM TUBERCULOSIS AND ITS INTERACTION WITH THE MICROBIOTA by Kathryn Winglee A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland May 2015 Abstract Tuberculosis (TB) is the leading cause of death from a bacterial infection in humans. Despite its impact throughout history on humans across the globe, it remains challenging to diagnose and treat. This work used molecular biology and next generation sequencing to explore these issues. First, in a study to identify potential biomarkers of TB infection, the interaction between Mycobacterium tuberculosis (the causative agent of TB), the mouse immune system, and the murine gut microbiota was examined. The murine gut microbiota was observed to respond specifically to M. tuberculosis infection in several host genotypes, and these changes were most likely mediated by the adaptive immune system. Together, these data confirm that the response of the gut microbiota can be further explored for TB diagnostics. A second study was aimed at understanding the genetic mechanisms of resistance to a novel anti- mycobacterial compound. Resistance was mediated through loss of function of Rv2887, a previously unannotated gene that was found to be a multiple antibiotic resistance repressor (MarR) transcriptional regulator. Analysis of the function of Rv2887 led to the identification of a gene regulation mechanism that could be a potential new drug target. Finally, in a third study the genetic basis of geographic restriction of M. africanum, a mycobacterial species that causes similar disease to human TB but is usually only found in West Africa, was elucidated. Despite conventional dogma, analysis of M. africanum using new bioinformatics tools revealed that it is not a separate species from M. tuberculosis. Furthermore, M. africanum is unimpaired in transmission or virulence compared to M. tuberculosis, thus suggesting that the geographic restriction may be due to host factors. Taken together, this work explores the host-pathogen interactions and genetics of mycobacteria and provides novel insights into how these bacteria cause TB. ii Thesis Advisor: William R. Bishai, MD, PhD, Professor of Medicine and Pathology, Johns Hopkins University School of Medicine Second Reader: Srinivasan Yegnasubramanian, M.D., Ph.D., Assistant Professor of Oncology, Johns Hopkins University School of Medicine Thesis Committee: Srinivasan Yegnasubramanian, M.D., Ph.D., Assistant Professor of Oncology, Johns Hopkins University School of Medicine (Chair) Brendan Cormack, Ph.D., Professor of Molecular Biology and Genetics, Johns Hopkins University School of Medicine Joel Bader, Ph.D., Associate Professor of Biomedical Engineering, Johns Hopkins University School of Medicine iii Acknowledgments My Ph.D. was a great learning experience, and there are a number of people that made it possible. First, I would like to thank my Ph.D. supervisor, Dr. William Bishai, who gave me numerous opportunities to explore different topics and helped to foster collaborations that greatly enriched this experience. I would also like to thank my thesis committee, Dr. Srinivasan Yegnasubramanian, Dr. Brendan Cormack and Dr. Joel Bader for their valuable time and insight, especially Dr. Yegnasubramanian for chairing my committee and reading my thesis. I would also like to acknowledge all past and present members of the Center for Tuberculosis Research, and particularly the members of the Bishai lab. All of you have made this a wonderful work environment and have taught me a lot. In particular, I would like to thank Dr. Shashank Gupta, who provided mentorship, advice and friendship. We have had an amazing time working together and none of this would have been possible without him. I would also like to thank all of my collaborators outside of Johns Hopkins University, particularly Dr. Ashlee Earl at the Broad Institute for providing advice and guidance and giving me the opportunity to work closely with her team. For their assistance with chapter 2, I would additionally like to acknowledge Dr. Emiley Eloe-Fadrosh and Dr. Claire Fraser from the University of Maryland. For chapter 3, I would like to thank Dr. Curtis Huttenhower and Dr. Galeb Abu-Ali from Harvard School of Public Health for their guidance on data analysis. For chapter 4, I would like to thank Dr. Shichun Lun from Johns Hopkins University, Dr. Marco Pieroni from Università di Parma and Dr. Alan Kozikowski from the University of Illinois at Chicago for their assistance with the compound. For chapter 5, I would like to thank Dr. Thomas Abeel, Dr. Terrance Shea, Dr. Christopher Desjardins, and especially Dr. Abigail Manson McGuire from the Broad Institute for their assistance with iv sequencing analysis. In addition, this project would not have been possible without Dr. Mamoudou Maiga, now at the National Institute of Health, and everyone at SEREFO. Finally, I would like to thank my parents, Jennifer and Robert Winglee, my brother Matthew, and the rest of my family for their support all of these years. I would not have gotten here without them. There are a number of friends and colleagues who were not mentioned here, but who have still had a positive impact on this work. Thank you to everyone for your support and guidance during the past 6 years. v Table of Contents Abstract ............................................................................................................................................ ii Acknowledgments........................................................................................................................... iv Table of Contents ............................................................................................................................ vi List of Figures ................................................................................................................................. xii List of Tables ................................................................................................................................. xvii Chapter 1: Introduction ................................................................................................................... 1 Chapter 2: Aerosol Mycobacterium tuberculosis Infection Causes Rapid Loss of Diversity in Gut Microbiota........................................................................................................................................ 3 2.1 Abstract .................................................................................................................................. 3 2.2 Introduction ........................................................................................................................... 3 2.3 Materials and Methods .......................................................................................................... 5 2.3.1 Ethics Statement ............................................................................................................. 5 2.3.2 Bacterial Strains .............................................................................................................. 5 2.3.3 Animals ............................................................................................................................ 5 2.3.4 Stool Collection and Storage ........................................................................................... 6 2.3.5 Aerosol Infection ............................................................................................................. 6 2.3.6 DNA Extraction and 16S rRNA Sequencing ..................................................................... 6 2.3.7 16S rRNA sequence processing and analysis .................................................................. 7 vi 2.3.8 Nucleotide accession numbers ....................................................................................... 8 2.4 Results .................................................................................................................................... 8 2.4.1 Compositional changes in the gut microbiota during M. tuberculosis infection ............ 8 2.4.2 Gut community composition and structure differ based on infection status ................ 9 2.4.3 Distinct changes in the gut community is independent of M. tuberculosis strain ....... 10 2.5 Discussion............................................................................................................................. 11 2.6 Figures .................................................................................................................................. 14 2.7 Table ..................................................................................................................................... 22 Chapter 3: Interaction between M. tuberculosis, the immune system, and the microbiota results in specific changes and is mediated by the adaptive immune system .......................................... 23 3.1 Abstract ................................................................................................................................ 23 3.2 Introduction ......................................................................................................................... 24 3.3 Materials and Methods ........................................................................................................ 25 3.3.1 Bacterial Strains ...........................................................................................................
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