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Characterization of a Ribose Metabolism Pathway in Bacteroides Thetaiotaomicron and New Insights Into the Nutrients Degraded by This Bacterium By

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Characterization of a Ribose Metabolism Pathway in Bacteroides Thetaiotaomicron and New Insights Into the Nutrients Degraded by This Bacterium By Characterization of A Ribose Metabolism Pathway in Bacteroides thetaiotaomicron and New Insights into the Nutrients Degraded by this Bacterium by Robert W.P. Glowacki A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Microbiology and Immunology) at the University of Michigan 2020 Doctoral Committee: Associate Professor Eric C. Martens, Chair Professor Matthew R. Chapman Assistant Professor Nicole K. Koropatkin Professor Thomas M. Schmidt Robert W.P. Glowacki [email protected] ORCID iD: 0000-0001-7718-5056 © Robert W.P. Glowacki 2020 Dedication There is one person who stands out in my mind that, without her guidance, I would not be where I am today. Therefore, I am dedicating my dissertation to the memory of Dr. Jody Modarelli. Jody was my undergraduate mentor and head of the Biochemistry department at Hiram College. When I began my college journey, I was undecided in major field of study, but leaning towards political science. Well, the way my liberal arts education was structure allowed for the crossing of our paths via a semester long colloquium in my first year. I chose to take “The molecular basis of infectious disease”, having given few thoughts to a science major, Jody made learning about the science of diseases fun and engaging. So, at my first year advising meeting, Jody convinced me that I needed to be a biochemistry major and that she would support me in any way possible throughout my undergraduate education and beyond. She truly exemplified the joy that comes with discoveries in science and had a passion for teaching that I don’t know I’ve experienced since taking her classes. Jody was the first person to make me truly believe that I had what it takes to be a scientist and her countless letters of recommendation allowed me to get research experience while an undergraduate. Her reference letter undoubtedly aided greatly, my entrance into the University of Michigan PIBS program. Halfway through the first semester of biochemistry Jody was diagnosed with pancreatic cancer. Of course, Jody being Jody, she would not let this get her down, she continued to lecture and mentor and live the happiest and fullest life possible. Sadly, Jody passed away not long after I had decided on my thesis lab. Prior to her death and in failing health, she emailed me just weeks before her passing to ask how graduate school was treating me and to offer advice on how to survive. Her memory, and in some ways her life, lives on in the trainees that she advised and inspired. Jody continues to inspire me and I strive to be as wonderful of a mentor and researcher as she was. I truly would not have been here today if not for the guidance and support of Dr. Jody Modarelli. ii Acknowledgements I would first like to thank my thesis advisor Dr. Eric Martens for his support and guidance in developing my research skills and for career development during the extent of my doctoral training. He has taught me the knowledge required to become an independent scientist and how to formulate testable and interesting hypothesis. He has always been a proponent of going where the data leads to build a better, more complete picture of underlying biological mechanisms. Most importantly, he has always been understanding when science has dealt setbacks. Eric, thank you for providing me the research and writing skills necessary to complete this body of work and for allowing me to pursue my teaching and outreach interests. I would also like to thank my thesis committee members, Dr. Nicole Koropatkin, Dr. Matthew Chapman, and Dr. Thomas Schmidt for helpful guidance throughout the years and for their commitment to my training and career goals. I also appreciate the Department of Microbiology and Immunology as a whole for being an excellent resource for reagents, tools, and scientific discussion. I want to call special attention to Dr. David Friedman for providing plasmids and strains as well as being an excellent conversationalist for both science, and general discussions. Further, I want to recognize the unwavering support of the department administrators who ensure everything in the background runs smoothly. Beyond the department, the staff of the Germ Free Facility have been invaluable in completion of the work within this dissertation. Additionally, I would like to thank the collaborators in other departments at the University of Michigan and Dr. Anton Terekov and Dr. Bruce Hamaker of the Department of Food Science at Purdue University for running samples and training me in analytical techniques. This work would not have been possible if not for the generous support of the Rackham Merit Fellowship, the Molecular Mechanisms of Microbial Pathogenesis training grant and the support of NIH grants. iii One of the most important groups of people I need to thank is my lab family. Getting through this journey would not have been possible without their support and encouragement and helpful troubleshooting of failed experiments. Although many individuals have come through the lab, each helping me along the way, Nick Pudlo stands out as the person who I owe the most gratitude. Nick is our lab manager, our science Sherpa, the labs motivational speaker, and guidance counselor, all while being a fantastic and easy going person who is generally fun to hang out with, and for these qualities I must say thanks for everything you do Nick for me, the lab, and the trainees within the Martens lab. Outside of lab, I have had the pleasure of having many friends that I met during my first year at Michigan, all from a wide range of departments under the PIBS umbrella. These friends have gotten me through a lot of tough times, provided so many laughs and memories, and were even on board when I formed a softball team from a motley crew of graduate students. My friends have made being in Michigan a much more enjoyable experience and I know, our forged friendships are lifelong. Finally, I would not be here without the love and support of my family. As a first generation college graduate and now a soon-to-be first generation PhD, my mother, father, and step-mother have always encouraged me to do the best that I could, work hard, and stay strong. To my fiancée Jessica Cory, if it were not for your love and the support of your family, the last few years would have been so much harder and way less fun. Thank you for putting up with my late nights, my science discussions over dinner, your willingness to proofread my jargon-laden writing, and especially for being my rock through the last few hectic months. iv Table of Contents Dedication ....................................................................................................................................ii Acknowledgements ......................................................................................................................iii List of Tables ...............................................................................................................................x List of Figures ..............................................................................................................................xi Abstract ........................................................................................................................................xiv CHAPTER I: Introduction Introduction .............................................................................................................................1 The impact of gut bacterial metabolites on host physiology ......................................2 Metabolism of drugs and other xenobiotics by gut microbes .....................................5 A way forward in the search for better therapeutics: detailed mechanistic studies ....6 If you eat it or secrete it, they will grow: The expanding cornucopia of nutrients that gut bacteria, especially Bacteroides utilize ..........................................................7 Mechanisms of Polysaccharide Utilization in the Human Gut Microbiota ................9 Marine Bacteroidetes use similar PUL-encoded mechanisms to utilize polysaccharides and may transfer these abilities to human gut Bacteroides ..............11 Gram-positive bacteria utilize polysaccharides via alternative multi- protein systems............................................................................................................12 Monosaccharides and other overlooked nutrients.......................................................13 To cook or not to cook, let’s ask the microbiota: cooking, food preservation, and ultra-refined foods alter the gut microbiota ................................................................14 The central bank, how Bacteroides regulate their carbohydrate intake ......................15 Synthetic engineering of gut bacteria and generation of synthetic communities ................................................................................................................18 v Prospectus ...................................................................................................................20 Chapter outline .......................................................................................................................21 Notes ......................................................................................................................................22 References ..............................................................................................................................23 CHAPTER II: A Genetically Adaptable
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