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Microbial Partners in Health: Broadening Our Understanding of Host-Microbiome Relationships

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Microbial Partners in Health: Broadening Our Understanding of Host-Microbiome Relationships University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2018 MICROBIAL PARTNERS IN HEALTH: BROADENING OUR UNDERSTANDING OF HOST-MICROBIOME RELATIONSHIPS Sarah Stuart Chewning University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Chewning, Sarah Stuart, "MICROBIAL PARTNERS IN HEALTH: BROADENING OUR UNDERSTANDING OF HOST-MICROBIOME RELATIONSHIPS. " PhD diss., University of Tennessee, 2018. https://trace.tennessee.edu/utk_graddiss/5262 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Sarah Stuart Chewning entitled "MICROBIAL PARTNERS IN HEALTH: BROADENING OUR UNDERSTANDING OF HOST-MICROBIOME RELATIONSHIPS." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Sarah L. Lebeis, Major Professor We have read this dissertation and recommend its acceptance: Gladys Alexandre, Alison Buchan, Chunlei Su Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) MICROBIAL PARTNERS IN HEALTH: BROADENING OUR UNDERSTANDING OF HOST-MICROBIOME RELATIONSHIPS A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Sarah Stuart Chewning December 2018 Copyright Ó 2018 by Sarah Stuart Chewning All rights reserved. ii DEDICATION To God be the glory. For Zack who showed me that with faith and perseverance, my dreams can come true. “It was not by accident that the greatest thinkers of all ages were deeply religious souls." -Max Planck "I was taught that the way of progress was neither swift nor easy." -Marie Curie iii ACKNOWLEDGEMENTS I had a crazy idea. I was going to quit my job, that paid well, and go back to school—full time— and live like a student again. I’ve never taken the easy path, and I’m honestly not sure why. What I am certain of is that embarking on this journey was the absolute right decision. It was a decision made with much prayer, doubt, and finally, resolution. Jesus intentionally designed every part of this plan and surrounded me with people and places for my good and His glory. I thank Sarah. She took a chance on me in so many ways. She was continually patient, gracious and supportive through emotionally, physically and psychologically brutal life circumstances. She kept me on track, gave me time when needed most, and challenged me in ways no one else could. Sarah taught me how to be a good scientist. She taught me to accept scientific rejection and push forward. She taught me I could accomplish things I doubted. She was a gift and I am grateful. I thank David. He’s been a dear friend, a reflection of Christ’s Truth, a steady support, and the scientist by my side for many of these years. Thank you to my committee, Alison Buchan, Gladys Alexandre, Chunlei Su, and again Sarah Lebeis, for support, guidance and patience. You have individually and collectively taught me how to be a good scientist and have led by example. My dearest girls Karen, April, Sam, Beth, Margo and Katie, you are a source of joy, Truth, generosity and rest. I thank my parents, with God, you molded and guided me. You are a constant, steadfast source of love and grace. You have consistently given me the best and I am grateful. Finally, I thank the love of my life, the one for which “it” was all worth, Zack. You have shown me what God intended love on this Earth to be. Your selflessness, encouragement, grace, and love reflect His goodness. You are a good man. I am grateful. iv ABSTRACT While microbes inhabit a wide array of environments, their ability to live within host tissue and become tolerated as part of a select microbial community is perhaps one of the most impressive feats of microbial resilience and survival. Host microbiome establishment and maintenance requires both host-microbe and microbe-microbe interactions. Among plant hosts, benefits from associated microbiomes are known to include improved growth, development and resistance to abiotic and biotic stresses. Mammalian microbiomes are known to improve host digestion, influence inflammation and even improve immune response to pathogens. While host-associated microbial communities across all domains of life are incredibly diverse, a growing number of studies are finding host-specific taxonomic trends, suggesting microbiome conservation and evolutionary selection. However, we have come to recognize that there is often functional redundancy between taxa. Therefore, investigative focus on microbiome composition potentially neglects pivotal and influential microbial players. Shifting focus to function over form creates the opportunity to tease apart the driving forces of unique microbiome constituents. This allows for identification of strains and genes of interest as well as microbial selections. To that end, here we describe the relationships between hosts and microbiomes as well as between microbes in two vastly different host systems (Figure 1.1). First, we suggest that plant root-associated Streptomyces isolates harboring genes encoding an enzyme and its co-factor are more tolerant of phenolic compounds generated by roots. Next, we address the capability of these Streptomyces isolates to employ their metabolic repertoires to influence the composition of the root microbiome. Finally, we define a previously under-described role for the gut microbiome in malaria immunology and suggest that gut microbial composition can modulate the severity of malarial disease. Together, these findings demonstrate the broad implications of microbiome composition across diverse hosts and environments, revealing unexplored opportunities for therapeutic interventions aimed at improving plant and human health. v TABLE OF CONTENTS CHAPTER ONE - INTRODUCTION ......................................................................................... 1 I. MICROBIOMES ACROSS HOST SPECIES .................................................................. 3 I. THE PLANT ROOT MICROBIOME.............................................................................. 5 Plant-microbe interactions ................................................................................................... 5 Microbe-microbe interactions .............................................................................................. 9 II. THE MAMMALIAN GUT MICROBIOME.................................................................. 10 Chronic diseases ................................................................................................................ 11 Infectious diseases ............................................................................................................. 14 III. OBJECTIVES ........................................................................................................... 16 IV. REFERENCES .......................................................................................................... 17 V. APPENDIX: FIGURES ................................................................................................. 29 CHAPTER TWO - ROOT-ASSOCIATED STREPTOMYCES ISOLATES HARBORING MEL GENES DEMONSTRATE ENHANCED PLANT COLONIZATION ...................................... 30 I. ABSTRACT .................................................................................................................. 32 I. INTRODUCTION ......................................................................................................... 33 II. MATERIALS AND METHODS ................................................................................... 35 Streptomyces culture preparation....................................................................................... 35 Extracellular pigment extraction ........................................................................................ 36 Liquid-chromatography mass spectrometry ....................................................................... 36 Pangenomic visualization. ................................................................................................. 37 Phylogenetic trees and identification of mel operons ......................................................... 38 Tyrosinase Assay .............................................................................................................. 38 Phenolic compound challenges on agar ............................................................................. 39 Salicylic acid challenge in liquid media ............................................................................. 40 Seed sterilization and germination ..................................................................................... 40 Plant colonization experiments .......................................................................................... 41 Statistical analysis ............................................................................................................. 42 III. RESULTS ................................................................................................................
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