BIOMESEQ: A QUANTITATIVE APPROACH FOR THE ANALYSIS OF ANIMAL MICROBIOMES AND ITS APPLICATION IN CHARACTERIZING THE MICROBIAL ECOLOGY OF AVIAN SPECIES by Kelly Ann Mulholland A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics and Systems Biology Spring 2020 © 2020 Kelly A. Mulholland All Rights Reserved BIOMESEQ: A QUANTITATIVE APPROACH FOR THE ANALYSIS OF ANIMAL MICROBIOMES AND ITS APPLICATION IN CHARACTERIZING THE MICROBIAL ECOLOGY OF AVIAN SPECIES by Kelly Ann Mulholland Approved: __________________________________________________________ Cathy H. Wu, Ph.D. Chair of Bioinformatics and Computational Biology Approved: __________________________________________________________ Mark Rieger, Ph.D. Dean of the College of Agriculture and Natural Resources Approved: __________________________________________________________ Douglas J. Doren, Ph.D. Interim Vice Provost for Graduate & Professional Education and Dean of the Graduate College I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Calvin L. Keeler, Jr., Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Carl Schmidt, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Shawn Polson, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Timothy Johnson, Ph.D. Member of dissertation committee DEDICATION To my father for the lifetime of love and support you gave me in the short time we shared together. To Tyler for your overflowing love, your uplifting spirit and your unwavering patience after all this time. iv ACKNOWLEDGMENTS I would like to extend my gratitude to several people for their contribution to this work. First, I give my sincere thanks to my advisor and mentor, Dr. Calvin Keeler, for his immeasurable support, advice and guidance throughout this process. His enthusiasm and dedication to his work have been very inspiring to me. I would like to thank my committee members, Dr. Shawn Polson, Dr. Carl Schmidt and Dr. Timothy Johnson for their time and invaluable insight. Thank you to the members of the Keeler Research Group, both past and present. I would especially like to thank Monique for her many contributions to this work and Sharon for sharing her knowledge and insight over the years. I also wish to thank the many friends that I have made during my time in the Bioinformatics Student Association and the EmPOWER mentoring program that have made my time at the University of Delaware so wonderful. I would like to acknowledge the University of Delaware CANR Unique Strengths Dissertation Award and the Agriculture and Food Research Initiative Competitive Grant for the financial support to make this work possible. I am incredibly grateful to all of my family and friends for always believing in me and for their encouragement over these past few years. This dissertation would not have been possible without them. I wish to express my most sincere gratitude to my v partner, Tyler, for being my greatest supporter throughout this entire journey and for all he has done to ensure that I accomplished this goal. It was his love and belief in me that gave me the strength to continue during some of the more difficult times. Thank you to Bob for his guidance and endless support in all of my endeavors. I will always cherish our conversations and laughs over coffee and breakfast. I wish to thank Kathy, David and Kari for their generosity, advice and love over the years. Thank you to Amy for her unparalleled friendship and for making these past few years so enjoyable with our many adventures. I would also like to thank Gibbs for being such a great companion and source of happiness. I am grateful to my father for instilling his work ethic in me and for always encouraging me to achieve my goals no matter how big or small. Although we are unable to celebrate this milestone together, I know that he is immensely proud. Finally, I would like to thank my mother and sisters for all of their support. vi TABLE OF CONTENTS LIST OF TABLES ........................................................................................................ xi LIST OF FIGURES ..................................................................................................... xiii ABSTRACT ................................................................................................................ xvi Chapter 1 INTRODUCTION AND REVIEW OF LITERATURE .................................... 1 1.1 Microbiomes .............................................................................................. 1 1.1.1 Symbiotic Microbial Interactions with Healthy Host and Other Microbes ........................................................................................ 3 1.1.2 Dysbiotic Microbial Interactions with Diseased Host and Other Microbes ........................................................................................ 6 1.2 Respiratory Microbiome ............................................................................ 7 1.2.1 Healthy Mammalian Respiratory Microbiome .............................. 7 1.2.2 Mammalian Respiratory Microbiome Diseases ............................ 9 1.2.3 Avian Respiratory Microbiome ................................................... 11 1.2.4 Multifactorial Avian Respiratory Disease Complex ................... 12 1.3 Advancement of Technology for Detection of Microorganisms ............. 14 1.3.1 Next-Generation Sequencing Technology .................................. 16 1.3.2 16S Ribosomal RNA Sequencing ............................................... 17 1.3.3 Metagenomic Shotgun Sequencing ............................................. 19 1.4 Characterization of the Virome ............................................................... 20 1.4.1 Characterizing the Virome Using a Culture-Independent Approach ..................................................................................... 21 1.4.2 Challenges with Developing Comprehensive Computational Tools for Analysis of the Virome ................................................ 22 1.4.2.1 Quantification of the Virome ........................................ 23 vii 1.4.3 Existing Culture-Independent Tools for Virome Characterization and their Limitations ........................................ 24 1.5 Rationale and Objectives ......................................................................... 25 REFERENCES ................................................................................................. 27 2 BIOMESEQ: A TOOL FOR THE CHARACTERIZATION OF ANIMAL MICROBIOMES FROM METAGENOMIC DATA ...................................... 48 2.1 Summary .................................................................................................. 48 2.2 Introduction ............................................................................................. 49 2.3 Results ..................................................................................................... 52 2.3.1 Design and Development of BiomeSeq ...................................... 52 2.3.2 Validation of BiomeSeq .............................................................. 54 2.3.3 A Longitudinal Study of the Microbial Ecology of a Healthy Broiler Flock ................................................................................ 58 2.3.4 A Comparison of BiomeSeq bacterial results to 16S rRNA Results ......................................................................................... 60 2.4 Discussion ................................................................................................ 60 2.5 Materials and Methods ............................................................................ 66 2.5.1 Quality Trimming and Host Decontamination ............................ 67 2.5.2 Microbial Database Alignment .................................................... 67 2.5.3 Quantification and Output ........................................................... 68 2.5.4 Performance Metrics ................................................................... 69 2.5.5 A Longitudinal Study of the Microbial Ecology of a Healthy Broiler Flock ................................................................................ 71 2.5.6 Comparison of BiomeSeq Bacterial Results to 16S rRNA Results ......................................................................................... 72 REFERENCES ................................................................................................. 85 3 METAGENOMIC ANALYSIS OF THE RESPIRATORY MICROBIOME OF A HEALTHY