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Comparison of Rumen Microbe Taxa Among Wild and Domestic Ruminants

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Comparison of Rumen Microbe Taxa Among Wild and Domestic Ruminants COMPARISON OF RUMEN MICROBE TAXA AMONG WILD AND DOMESTIC RUMINANTS A thesis presented to the Faculty of the Graduate School University of Missouri In partial fulfillment of the requirements for the Degree PhD By TASIA MARIE TAXIS Dr. William R. Lamberson Thesis Advisor DECEMBER 2015 The undersigned, appointed by the Dean of the Graduate School, have examined the thesis entitled COMPARISON OF RUMEN MICROBE TAXA AMONG WILD AND DOMESTIC RUMINANTS Presented by Tasia Marie Taxis A candidate for the degree of PhD And hereby certify that in their opinion it is worthy of acceptance. Dr. William R. Lamberson, advisor University of Missouri, Columbia, MO Dr. Robert L. Kallenbach, external committee member University of Missouri, Columbia, MO Dr. Gavin C. Conant University of Missouri, Columbia, MO Dr. Kristi M. Cammack University of Wyoming, Laramie, WY DEDICATION My professional and personal growth would have been stunted if it weren’t for the guidance and support of so many people, too many to mention. I would like to acknowledge my biological, academic, and adopted-Mizzou family. My biological family provided my foundation on which I still stand. While physically 1,000 miles away, they were always close. My mother, Mary Ann Taxis, has always grounded me back to the ‘go get it’ girl she raised. My father, Craig Taxis, has always sent extra hugs and love, which in a note or voice, could always be felt. My brother, Travis Taxis, was honest and provided the kick when I needed it and support when I didn’t. He will forever be my best friend and favorite hunting partner. My academic family contains too many to name here, but Mike Carson was one of the first voices that encouraged me to reach for the stars and remain driven towards my goals. Having Drs. Chris Bidwell, Jolena Wadell-Fleming, Eduardo Casas, Bob Weaber, and Bill Lamberson as mentors has made me a better person in life and research. My adopted-Mizzou families, The Mallory Family and the Kendrick Family have always provided support and encouragement. The Mallory family is responsible for introducing me to Grant Kendrick, of which kind words will never be enough. Grant has been there to celebrate the small accomplishments and great victories, and he has been support through the stressful and hard times. I am fortunate to have paved this road, but I wouldn’t have gotten here without the support, love, and encouragement from so many. For that, I am forever grateful. ACKNOWLEDGEMENTS There are many individuals that have played an important role over the past several years in assisting me to reach this point. While it is impossible to thank everyone, I would like to express my appreciation to several individuals for their assistance and guidance towards my Doctoral experience. Foremost, I would like to thank my advisor, Bill Lamberson for his guidance, patience, and enthusiasm for me to succeed. He is one of the best! As a mentor, not only does Dr. Lamberson provide the right amount of control and freedom, but he listens. He has provided encouragement and advice when needed, and not only has improved my statistical knowledge but has been a great resource for discussion. I have learned everything from research to generalities of life. I hope he is proud of me and I strive to become a professor/mentor like him. I’d also like to thank, Dr. Gavin Conant. He has had patience in guiding me and has helped build my bioinformatics toolbox needed for research. I would also like to thank Dr. Kristi Cammack and Dr. Robert Kallenbach for being committee members and providing help when needed. I was fortunate to travel and work in various labs, and would like to thank the scientists that hosted me. I extracted my rumen samples in Dr. Andre Wright’s laboratory at the University of Vermont, Burlington, VT. I utilized my bioinformatics toolbox and analyzed data with Dr. Ben Hayes, Keith Savin, and Min Wang at AgriBio in Melbourne, Australia. Last, but not least, I would like to thank Sara Wolff. Without her I would not have been able to complete this research. It was with the help of all the listed individuals, and many that are not, that I have learned how to be a true professional and example of excellence in the scientific community. I not only received an education, but gained friendships I hope to never lose. Thank you. ii TABLE OF CONTENTS Acknowledgements ............................................................................................................. ii List of Tables ...................................................................................................................... v List of Figures ................................................................................................................... vii Abbreviations ................................................................................................................... viii Abstract .............................................................................................................................. ix Chapter One Literature Review................................................................................................................ 1 Introduction ..................................................................................................................... 1 Metagenomic Analysis Techniques ................................................................................. 5 Microbiome of Ruminants ............................................................................................. 13 The Rumen Methanogens .............................................................................................. 25 Research Objectives ...................................................................................................... 26 Chapter Two Distribution of Microbial Taxa and Identification of A Core Microbiome in Ruminant Host Species..................................... 28 Summary ........................................................................................................................ 28 Introduction ................................................................................................................... 30 Materials and Methods.................................................................................................. 33 Results and Discussion .................................................................................................. 40 Chapter Three Effects of Host Diet, Species, and Domestication Status on Microbiome........................ 59 Summary ........................................................................................................................ 59 iii Introduction ................................................................................................................... 61 Materials and Methods.................................................................................................. 66 Results and Discussion .................................................................................................. 71 Chapter Four Conclusions and Future Directions ................................................................................... 95 Overall Conclusions ...................................................................................................... 95 Future Directions .......................................................................................................... 99 Appendix SAS Program: PROC DISCRIM (Step-Wise Discriminate Function) ....................... 102 SAS Program: PROC DISCRIM................................................................................. 103 SAS Program: PROC NLIN (Exponential Decay Model) .......................................... 104 SAS Program: PROC GLM ........................................................................................ 105 PERL Script: Total OTUs and Common OTUs .......................................................... 106 SAS Program: PROC VARCOMP (Type 1 Method) ................................................. 112 Literature Cited ............................................................................................................ 113 Vita ................................................................................................................................. 123 iv LIST OF TABLES Table 2.1: Metadata for Domesticated Host Animals ...................................................... 46 Table 2.2: Metadata for Wild Host Animals .................................................................... 47 Table 2.3: Average Number of Reads for Each Host Species at Each Analysis Step ............................................................ 48 Table 2.4: Estimated Coefficients and Standard Errors of the Exponential Decay Curve for Each Host Species ........................................... 49 Table 2.5: Percent Increase in Total Observed OTUs and Decrease in Common ‘Core’ OTUs as Additional Host Species are Included in Analysis .................................................... 50 Table 2.6: Identified Core Microbial Community ........................................................... 51 Table 3.1: Metadata for Domesticated Host Animals ...................................................... 81 Table 3.2: Metadata for Wild Host Animals .................................................................... 82 Table 3.3: Ingredients of Host Diets ................................................................................ 83 Table 3.4: Average Number of Reads for Each Host Species at Each Analysis
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