MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Kundi Yang Candidate for the Degree Doctor of Philosophy ______________________________________ Dr. Michael Crowder, Director ______________________________________ Dr. Neil Danielson, Reader ______________________________________ Dr. Rick Page, Reader ______________________________________ Dr. Scott Hartley, Reader ______________________________________ Dr. Xin Wang, Graduate School Representative ABSTRACT ASSESSING AND EVALUATING BIOMARKERS AND CHEMICAL MARKERS BY TARGETED AND UNTARGETED MASS SPECTROMETRY-BASED METABOLOMICS by Kundi Yang The features of high sensitivity, selectivity, and reproducibility make liquid chromatography coupled mass spectrometry (LC-MS) the mainstream analytical platform in metabolomics studies. In this dissertation work, we developed two LC-MS platforms with electrospray ionization (ESI) sources, including a LC-triple quadrupole (LC-QQQ) MS platform for targeted metabolomics analysis and a LC-Orbitrap MS platform for untargeted metabolomics analysis, to assess and evaluate either biomarkers or chemical markers in various sample matrices. The main focus of targeted metabolomics platform was to study human gut microbiota and how the gut microbiome responds to therapies. We utilized a LC-QQQ targeted platform for this focus and conducted three projects: (1) to evaluate the effects of four nutrients, mucin, bile salts, inorganic salts, and short chain fatty acids, on the gut microbiome in terms of their impact to the microbial metabolic profiles in vitro, (2) to examine the ability of Lactobacillus acidophilus (LA) to ferment black tea extract (BTE) and to investigate the enhancement of antimicrobial ability of the fermented BTE against Escherichia coli due to the increasing abundant of phenolic compounds in the fermentation process, (3) to determine the modulating effects of the exposure to gastrointestinal (GI) ultrafine particles (UFPs) on gut microbial composition and functions that may lead to a systematic evaluation of the impact of UFPs on host health by using an in vivo murine model. Two additional studies were accomplished by using an LC-Orbitrap untargeted/hybrid platform. In one study we used both LC-QQQ and LC-Orbitrap approaches to analyze polar metabolites from micro anaerobic bacterial culture matrices, to systematically differentiate four Lactobacillus species based on their metabolic profiles. In the other project, the LC-Orbitrap was incorporated with a Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) system to determine whether bourbons could be “fingerprinted” by their chemical compositions. ASSESSING AND EVALUATING BIOMARKERS AND CHEMICAL MARKERS BY TARGETED AND UNTARGETED MASS SPECTROMETRY-BASED METABOLOMICS A DISSERTATION Presented to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry and Biochemistry by Kundi Yang The Graduate School Miami University Oxford, Ohio 2020 Dissertation Director: Dr. Michael Crowder © Kundi Yang 2020 TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................................... iii LIST OF TABLES ......................................................................................................................... vi LIST OF FIGURES ...................................................................................................................... vii DEDICATION ................................................................................................................................ x ACKNOWLEDGEMENTS ........................................................................................................... xi CHAPTER 1 ................................................................................................................................... 1 Introduction ..................................................................................................................................... 1 1.1 Metabolomics and its applications .................................................................................... 1 Targeted/untargeted approaches in metabolomics .................................................................. 1 Mass spectrometry and MS-based metabolomics ................................................................... 3 Metabolomics in human gut microbiota research ................................................................... 4 Metabolomics in food science ................................................................................................ 6 1.2 Specific aims ........................................................................................................................ 7 CHAPTER 2 ................................................................................................................................. 16 Evaluating the Impact of Four Major Nutrients on Gut Microbial Metabolism by a Targeted Metabolomics Approach ............................................................................................................... 16 2.1 Introduction ....................................................................................................................... 18 2.2 Materials and Methods ..................................................................................................... 19 2.3 Results and Discussion ...................................................................................................... 22 Targeted metabolic profiling differentiates the gut microbial growth in LCIS and HCIS ... 22 Targeted metabolic profiling differentiates the gut microbial metabolic profiles with other nutrients in a defined inorganic salts level ............................................................................ 25 Metabolic pathway impact analyses ..................................................................................... 29 2.4 Conclusions ........................................................................................................................ 33 CHAPTER 3 ................................................................................................................................. 37 Metabolomics Study Reveals Enhanced Inhibition and Metabolic Dysregulation in Escherichia coli Induced by Lactobacillus acidophilus-Fermented Black Tea Extract ................................... 37 3.1 Introduction ....................................................................................................................... 39 3.2 Materials and Methods ..................................................................................................... 40 3.3 Results and Discussion ...................................................................................................... 44 CHAPTER 4 ................................................................................................................................. 60 iii Ultrafine Particles Altered Gut Microbial Population and Metabolic Profiles in a Sex-Specific Manner in an Obese Mouse Model ............................................................................................... 60 4.1 Introduction ....................................................................................................................... 62 4.2 Materials & Methods ........................................................................................................ 63 4.3 Results ................................................................................................................................ 67 UFP-Induced Changes in the Structures of Gut Microbial Communities ............................ 67 UFP-induced changes in the metabolic profile of the gut microbiome ................................ 71 UFP-induced metabolic pathway alteration .......................................................................... 74 4.4 Discussion ........................................................................................................................... 80 4.5 Conclusions ........................................................................................................................ 82 ASSOCIATED CONTENT .......................................................................................................... 83 CHAPTER 5 ................................................................................................................................. 91 Rapid Differentiation of Lactobacillus Species via Metabolic Profiling ...................................... 91 5.1 Introduction ....................................................................................................................... 93 5.2 Materials and method ....................................................................................................... 94 5.3 Results ................................................................................................................................ 96 5.4 Discussion ......................................................................................................................... 105 5.5 Conclusions ...................................................................................................................... 106 CHAPTER 6 ............................................................................................................................... 111 Analysis