UNIVERSITY OF CALIFORNIA SAN DIEGO SAN DIEGO STATE UNIVERSITY EXPLORING THE GLOBAL VIROME AND DECIPHERING THE ROLE OF PHAGES IN CYSTIC FIBROSIS A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Ana Georgina Cobián Güemes Committee in charge: University of California San Diego Professor Douglass Conrad Professor Justin Meyer Professor Joseph Pogliano San Diego State University Professor Forest Rohwer, Chair Professor Robert Edwards 2019 The Dissertation of Ana Georgina Cobián Güemes is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ ___________________________________________________________________________ Chair University of California San Diego San Diego State University 2019 iii Dedication To Adrian, Pilar and Jorge for always supporting me through this unique journey. iv Epigraph “No temas a la perfección, nunca la alcanzarás” Salvador Dali v Table of Contents Signature page ........................................................................................................................... iii Dedication .................................................................................................................................. iv Epigraph ..................................................................................................................................... v Table of Contents ...................................................................................................................... vi List of Figures ............................................................................................................................ xi List of Tables ........................................................................................................................... xiii List of Equations ...................................................................................................................... xiv Acknowledgments .................................................................................................................... xv Vita .......................................................................................................................................... xix Abstract of the Dissertation ....................................................................................................... iv Chapter 1 : Viruses as Winners in the Game of Life .................................................................. 1 Abstract ................................................................................................................................... 1 How many viruses? ................................................................................................................ 1 A Global Census ................................................................................................................. 3 Phages Matter ..................................................................................................................... 8 How many different viruses? ................................................................................................ 11 Signature Genes ................................................................................................................ 12 Phage Metagenomics ........................................................................................................ 15 Virome Meta-analysis .......................................................................................................... 16 How many different phages on Earth? ............................................................................. 22 Which are the most abundant phage genes? ..................................................................... 23 The future for FRAP ......................................................................................................... 25 Summary Points .................................................................................................................... 26 Future Issues ......................................................................................................................... 26 Definition of terms ............................................................................................................... 28 Acknowledgements .............................................................................................................. 29 References ............................................................................................................................ 30 Appendix for Chapter 1 ........................................................................................................ 39 Supplemental methods ...................................................................................................... 39 Chapter 2: Fragment Recruitment Assembly Purification (FRAP): Put bioinformatics back into the hands of biologists. ...................................................................................................... 45 Abstract ................................................................................................................................. 45 vi Introduction .......................................................................................................................... 46 Current bioinformatics ...................................................................................................... 46 Why use FRAP? ............................................................................................................... 47 How to use FRAP? ........................................................................................................... 48 Challenges in the development of FRAP ......................................................................... 49 Results and Discussion ......................................................................................................... 50 Basic FRAP ...................................................................................................................... 51 Blind FRAP ...................................................................................................................... 60 The future of FRAP .......................................................................................................... 65 Biological insights from FRAP ........................................................................................ 65 Methods ................................................................................................................................ 65 File types .......................................................................................................................... 65 FRAP implementations .................................................................................................... 66 FRAP-tools ....................................................................................................................... 69 Reference databases .......................................................................................................... 69 Denovo assemblies ........................................................................................................... 69 Acknowledgments ................................................................................................................ 69 References ............................................................................................................................ 70 Appendix for Chapter 2 ........................................................................................................ 73 Supplemental tables .......................................................................................................... 73 Chapter 3 : Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information ................................................................................................................ 76 Abstract ................................................................................................................................. 76 Introduction .......................................................................................................................... 76 Results .................................................................................................................................. 79 Patient CF01 fatal exacerbation expedited monitoring: metatranscriptomes and metabolomes ..................................................................................................................... 79 Bacterial small molecule profiles before and during fatal exacerbation. ......................... 85 Active members of the microbial community during a stable period and the fatal exacerbation. ..................................................................................................................... 86 Microbial community dynamics during a non-fatal exacerbation. ................................... 88 Discussion ............................................................................................................................. 89 CF01