University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2021 Impact of Different Plant-Based Foods Consumption on the Composition and Diversity of Gut Microbiota Ayoub Al Othaim University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Food Microbiology Commons, and the Human and Clinical Nutrition Commons Citation Al Othaim, A. (2021). Impact of Different Plant-Based Foods Consumption on the Composition and Diversity of Gut Microbiota. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/ 3992 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. Impact of Different Plant-Based Foods Consumption on the Composition and Diversity of Gut Microbiota A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Cell and Molecular Biology by Ayoub Al Othaim Qassim University Bachelor of Medical Microbiology, 2009 Quinnipiac University Master of Heath Science, Medical Laboratory Sciences, 2014 May 2021 University of Arkansas This dissertation is approved for recommendation to the Graduate Council. _______________________________ Franck Carbonero, Ph.D. Dissertation Director _______________________________ ______________________________ Luke R. Howard, Ph.D. Jiangchao Zhao, Ph.D. Committee Member Committee Member _______________________________ Charles Rosenkrans, Ph.D. Committee Member ABSTRACT Plant-based diets are primarily derived from plant sources, including fruits and vegetables. Such patterns are associated with health benefits by promoting general health and preventing many diseases and metabolic disorders. Fruits and vegetables are key sources of high- quality nutrients such as dietary fibers and polyphenols. Since they are rich in dietary fibers and polyphenols, whole fruits and vegetables represent unique and somewhat understudied modulators of the gut microbiota and its associated functions. This study aims to (i) investigate the impact of varying dilutions of cherry juices concentrate on the composition of the murine gut microbiota, (ii) investigate the impact of cranberry juice consumption on the bacterial composition of gut and vaginal microbiota in postmenopausal women, and (iii) investigate the impact of the amounts and botanical diversity of fruits and vegetables on gut microbiota profiles in healthy adults. Fecal samples were collected from mice consuming increasing tart cherry juice concentrations in their drinking water. A randomized, crossover controlled dietary intervention was conducted with cranberry juice and a matched control, and postmenopausal female volunteers provided stool and vaginal swabs for microbiota analyses. Two pilot studies looking at the impact of low and adequate intake of fruits and vegetables (SMART-Diet), as well as low versus high botanical diversity (SMART-Valid), were conducted at Colorado State University; stool samples were collected for gut microbiota analyses and short-chain fatty acids measurements. Microbial analyses were performed using Illumina following a dual-indexing 16S rRNA gene amplicon. Each dietary intervention resulted in distinct microbiota modulations and effects. Cherry juices consumption significantly increased the relative abundance of Akkermansia and Barnesiella and decreased the relative abundance of Bacteroides. Consumption of cranberry juice modulated the gut microbiota composition by elevating the relative abundance of Bifidobacterium, Clostridium XIVa members, Eggerthella, and Prevotella. Cranberry juice consumption also resulted in a beneficial impact on vaginal microbiota by decreasing the relative abundance of Streptococcus compared to a placebo. Finally, the SMART-Diet study showed that fruit and vegetable consumption resulted in a reduction of the Firmicutes/Bacteroidetes ratio whereas the SMART-Valid study showed an increase in the Firmicutes/Bacteroidetes ratio after fruit and vegetable consumption, and a significant increase in production of beneficial short- chain fatty acids. Our findings suggest that consumption of cherry juices, cranberry juice, and fruit and vegetable inclusive diets all have a beneficial impact on the composition of gut microbiota. This body of work is consistent with the emerging concept that whole foods should be considered rather than extracts when it comes to gut microbiota and microbiome studies. Human dietary studies with larger sample size are warranted by these suggested beneficial modulations. ACKNOWLEDGMENTS First and foremost, praise and thanks be to God, the Almighty, the greatest of all, for the blessings He has bestowed upon me and for giving me the strength and wisdom to achieve this dream. Without His grace, this research would not have been possible. This doctoral thesis exists in its current form due to the assistance and encouragement of several people. With immeasurable love and appreciation, I would like to express my deepest gratitude to the people who have had the greatest impact on my success during my Ph.D. journey. First, I would like to extend my sincere gratitude to my supervisor, Dr. Franck Carbonero, who expertly guided me through this study. I gratefully acknowledge his motivation, encouragement, invaluable insights, constructive suggestions and feedback, and continuous support throughout this work. I would also like to extend my gratitude to my thesis committee, Dr. Luke Howard, Dr. Charles Rosenkrans, and Dr. Jiangchao Zhao, for their constructive suggestions, insightful comments, and wonderful contributions and support; to Dr. Tiffany Weir for the opportunity to use her lab at Colorado State University and for providing the necessary equipment; and to my laboratory colleagues, who have generously supported me with their skill. Lastly, I extend my special thanks and appreciation to my sponsor, Majmaah University, for supporting me throughout my graduate studies. DEDICATION This study is dedicated to my beloved parents, Abdulaziz Al Othaim and Helah Al Othaim, who have been my source of inspiration and have given me endless love and encouragement to complete my studies. My dream of completing this research would not have come true without their support, sacrifice, and prayers. I also dedicate this work to my wife, soulmate, and best friend, Dr. Sarah Alajaji, with my heartfelt thanks for her mental strength, support, encouragement, and patience; and to my dear little boy, Feras, the most precious gift in my life, to whom I express my deep love. Though I did not deliberately neglect him, he has missed out on some of my love, care, and affection during this busy period. I also extend my gratitude to my siblings, Huda, Wafa, Sumayyah, Mohammed, Ibraheem, Younes, Yousef, Motaz, Adeeb, and Jory, whose continued support has motivated me to pursue my education and complete this accomplishment. Last but not least, I express my sincere thanks to my parents-in- law, Mansour and Zainab, for their blessings, affection, and support during my studies. TABLE OF CONTENT GENERAL INTRODUCTION ....................................................................................................... 1 CHAPTER 1: .................................................................................................................................. 3 Impact of Fruit and Vegetable Inclusive Diets on Gut Microbiota Composition and Diversity .... 3 Abstract ....................................................................................................................................... 3 Keywords: ................................................................................................................................... 4 1.1 Introduction ........................................................................................................................... 4 1.2 Plant-based dietary patterns .................................................................................................. 5 1.2.1 Health benefits of plant-based diets ............................................................................... 6 1.2.1.1 Lower risk of obesity .............................................................................................. 6 1.2.1.2 Lower risk of diabetes ............................................................................................. 8 1.2.1.3 Lower risk of cardiovascular diseases .................................................................... 9 1.2.1.4 Lower risk of cancers ............................................................................................ 10 1.3 Gut Microbiota Modulation by Plant-Based Foods ............................................................ 11 1.3.1 Gut Microbiota: General Aspects ................................................................................. 11 1.3.2 Effect of Plant-Based Diets on Gut Microbiota Composition ...................................... 15 1.3.3 Impact of Fruits and Vegetables on Gut Microbiota Composition .............................. 18 1.3.3.1 Berries ................................................................................................................... 18 1.3.3.2 Cherries ................................................................................................................. 26 1.3.3.3 Mangoes ...............................................................................................................