Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2017 Human Gut Microbiota and Obesity: How Is Gut Microbiota Associated with Obesity Improvement Induced by Bariatric Surgeries or Low-Calorie Diet Treatment? Rui Zhang Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Environmental Sciences Commons Recommended Citation Zhang, Rui, "Human Gut Microbiota and Obesity: How Is Gut Microbiota Associated with Obesity Improvement Induced by Bariatric Surgeries or Low-Calorie Diet Treatment?" (2017). LSU Doctoral Dissertations. 4272. https://digitalcommons.lsu.edu/gradschool_dissertations/4272 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. HUMAN GUT MICROBIOTA AND OBESITY: HOW IS GUT MICROBIOTA ASSOCIATED WITH OBESITY IMPROVEMENT INDUCED BY BARIATRIC SURGERIES OR LOW- CALORIE DIET TREATMENT? A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Environmental Sciences by Rui Zhang B.S., North China Coal Medical University, 2003 M.S., Huazhong University of Science and Technology, 2008 M.S., Louisiana State University, 2012 May 2017 ACKNOWLEDGMENTS First and foremost, I would like to thank my advisor Dr. Aixin Hou for her generous direction, inspiration, and support in countless aspects during the process of the study. I appreciate my dissertation committee, Dr. Vince Wilson, Dr. Edward Laws, and the dean’s representative Dr. Jan Hondzinski for their insightful comments and suggestions. I also thank Dr. Eric Ravussin, Dr. Frank Greenway, Dr. Jizhong Zhou, Dr. Edward Overton and Dr. Jolene Zheng for their open-handed cooperation in the lab collaborative projects. I also thank Dr. Gary King for his kind enlightening, thoughts, comments and recommendations during the discussion of research topics. Next, I thank the Dean of the School of the Coast & Environment, Christopher D’Elia, Chair of Department of Environmental Sciences, Dr. Kevin Armbrust, former chair of Department of Environmental Sciences Dr. Lawrence J. Rouse, our department academic coordinator Ms. Charlotte St. Romain, administrative staff Ms. Barbara Porche, Ms. Katherine Grimes, research associate Dr. Roberto Wong, and Mr. Ric Pincomb for their work on my academic files, computer settings, and presentation schedules. Furthermore, I thank my lab colleagues Lauren Navarre, Kris Ackoury, Corwin Hess, Grace Cagle, and Brian Matherne for their different forms of help. In addition, I thank Dr. Joy van Nostrand, Dr. Tong Yuan, Dr. Ye Deng, Dr. Daliang Ning, Dr. Jiabao Li, Dr. Liyou Wu, Dr. Zhili He, Dr. Pin Zhang, Dr. Chongqin, Dr. Qichao Tu, Dr. Zhou Shi, Dr. Qingyun Yan, Dr. Kai Xue, Ms. Yujia Qin, Dr. Xishu Zhou, Dr. Jie Deng, and Dr. Aifeng Zhou, for their many forms of guidance and assistance. Last but not least, I want to thank my family for all their support and encouragement. ii Table of Contents ACKNOWLEDGMENTS .............................................................................................................. ii ABSTRACT .................................................................................................................................. vii CHAPTER ONE: INTRODUCTION ............................................................................................. 1 1.1 Obesity .................................................................................................................................. 1 1.1.1 History of Obesity .......................................................................................................... 1 1.1.2 Causes of Obesity ........................................................................................................... 2 1.1.3 Harmful Effects of Obesity ............................................................................................. 4 1.1.4 Treatment of Obesity ...................................................................................................... 5 1.2 Gut Microbiota ...................................................................................................................... 6 1.2.1 Microbiota ...................................................................................................................... 6 1.2.2 Human Microbiota .......................................................................................................... 6 1.2.3 Human Intestinal Microbiota .......................................................................................... 6 1.2.4 The Microbiota in Human Gut May Play an Important Role in Regulating Adiposity . 7 1.3 Bariatric Surgeries (BRS)...................................................................................................... 8 1.3.1 Bariatric Surgical Treatments Show Extremely Promising Results in Severe Obesity . 8 1.3.2 A Comparison between Gastric Bypass, Sleeve Gastrectomy, and Gastric Banding .... 8 1.3.3 Bariatric Surgeries Help Weight Loss .......................................................................... 10 1.4 Low-Calorie Diet Treatment (LCD) ................................................................................... 12 1.5 The ‘BARIA’ Project .......................................................................................................... 13 1.6 Hypotheses and Experimental Design ................................................................................ 13 CHAPTER TWO: MATERIALS AND METHODS ................................................................... 17 2.1 Stool Sample Collection ...................................................................................................... 17 2.2 DNA Extraction................................................................................................................... 17 2.3 Illumina Sequencing ............................................................................................................ 17 2.4 HumiChip Analysis ............................................................................................................. 19 2.5 Quantitative Polymerase Chain Reaction (qPCR) .............................................................. 22 2.6 Gas Chromatography........................................................................................................... 24 2.6.1 Instrumentation ............................................................................................................. 26 2.6.2 GC condition................................................................................................................. 26 iii 2.6.4 Sample Preparation ....................................................................................................... 27 2.6.5 Standard Solution Preparation ...................................................................................... 27 2.7 Obesity-related Physiological Variables ............................................................................. 27 2.8 Statistical Methods .............................................................................................................. 28 CHAPTER THREE: STATISTICAL METHODS IN ECOLOGY STUDIES ............................ 29 3.1 Analysis of Variance ........................................................................................................... 29 3.1.1 Abstract ......................................................................................................................... 29 3.1.2 Introduction .................................................................................................................. 29 3.1.3 Materials and Methods ................................................................................................. 34 3.1.4 Results and Discussions................................................................................................ 35 3.2 Analysis of Covariance ....................................................................................................... 41 3.2.1 Abstract ......................................................................................................................... 41 3.2.2 Introduction .................................................................................................................. 41 3.2.3 Materials and Methods ................................................................................................. 42 3.2.4 Results and Discussions................................................................................................ 42 3.3 Principal Component Analysis ............................................................................................ 49 3.3.1 Abstract ......................................................................................................................... 49 3.3.2 Introduction .................................................................................................................. 49 3.3.3 Materials and Methods ................................................................................................. 50 3.3.4 Results and Discussions...............................................................................................