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University of Florida Thesis Or Dissertation AN EXPLORATION OF FUSOBACTERIUM NECROPHORUM AND PORPHYROMONAS LEVII STRAINS ISOLATED FROM THE UTERI OF DAIRY COWS WITH METRITIS By AMYE MARIAH FRANCIS A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2019 © 2019 Amye M. Francis To my Lord Jesus Christ, I dedicate this, the first fruits of my scientific research ACKNOWLEDGMENTS I would like to thank my co-advisors Dr. Tim Hackmann and Dr. Klibs Galvao for supporting me during the process of transitioning from one thesis project to another when things didn't work out well. I want to thank them for their guidance and for putting my needs and my future first throughout this project, it is because of them that I was still able to complete a project in time without having to go an extra semester to earn my degree. I would also like to thank Federico Cunha and Soo Jin Jeon for giving me adivce throughout this project and to my other committee members, Dr. Lori Warren and Dr. Antonio Faciola for their continued support throughout my projects and for the advise they offered. Additional thanks goes to my friends and family who have been with me through the rough times and the exciting adventures I've experienced through the course of my studies. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ............................................................................................................ 7 LIST OF FIGURES .......................................................................................................... 8 LIST OF ABBREVIATIONS ............................................................................................. 9 ABSTRACT ................................................................................................................... 12 CHAPTER 1 INTRODUCTION .................................................................................................... 13 2 LITERATURE REVIEW .......................................................................................... 16 The Uterus .............................................................................................................. 16 Puerperium ............................................................................................................. 16 Description and Diagnosisof Metritis ....................................................................... 17 Negative Effects of Metritis ..................................................................................... 18 Risk Factors of Metritis ........................................................................................... 21 Retained Placenta, Dystocia and Stillbirths ...................................................... 23 Feeding, Nutrition and BCS .............................................................................. 24 Immunity and Immunosuppression ................................................................... 27 Bacterial Infection of the Uterus .............................................................................. 29 Culture Dependent Studies .............................................................................. 32 Culture Independent Studies ............................................................................ 33 Virulence Factors ............................................................................................. 37 3 FUSOBACTERIUM NECROPHORUM KG34 AND KG35 ...................................... 42 Methods .................................................................................................................. 42 Sample Collection and Culture ......................................................................... 42 16s rRNA Gene Amplification and Identification ............................................... 43 Illumina Whole Genome Sequencing ............................................................... 43 Genome Trimming, Quality Control, Assembly and Annotation ........................ 44 Virulence Factor Search ................................................................................... 45 Data Availability ................................................................................................ 46 Results .................................................................................................................... 46 Statistics ........................................................................................................... 46 Virulence Factor Coding Genes ....................................................................... 46 Discussion .............................................................................................................. 47 Virulence Factors and Proteins of Interest........................................................ 48 lktA Leukotoxin Family Filamentous Adhesin ................................................... 48 5 Hemolysin And Hemolysin Associated Proteins ............................................... 49 Filamentous Hemagglutinin .............................................................................. 49 Ecotin ............................................................................................................... 50 Hemin Receptors .............................................................................................. 50 Omptin Proteases ............................................................................................. 50 Clp Proteases and Associated Proteins ........................................................... 51 Adhesins ........................................................................................................... 51 Virulence-Associated Protein E ........................................................................ 52 BrkB Proteins ................................................................................................... 52 Closing Thoughts ............................................................................................. 52 4 PORPHYROMONAS LEVII KG45 .......................................................................... 66 Methods .................................................................................................................. 66 Sample Collection ............................................................................................ 66 Metritis Diagnosis ............................................................................................. 66 Plating and Growing Samples .......................................................................... 67 Isolation of P. levii ............................................................................................ 67 DNA Extraction ................................................................................................. 68 Illumina Whole Genome Sequencing ............................................................... 70 Quality Control, Assembly, and Annotation ...................................................... 70 Virulence Factor Search ................................................................................... 71 Results .................................................................................................................... 72 Statistics ........................................................................................................... 72 Species Identification ....................................................................................... 72 Virulence Factors ............................................................................................. 73 Genome Comparison ....................................................................................... 73 Discussion .............................................................................................................. 74 Proteases ......................................................................................................... 75 Aminopeptidases .............................................................................................. 76 Phospholipase .................................................................................................. 76 Nucleotidyl Transferase AbiEii/AbiGii Toxin Family Protein.............................. 77 Lipopolysaccharide ........................................................................................... 77 Superoxide Dismutase ..................................................................................... 77 Peroxidases ...................................................................................................... 78 Pilin Glycosylation Protein ................................................................................ 79 Virulence Protein E and YihY/Virulence Factor BrkB Family Protein ................ 79 Zinc-Dependent Metalloproteinase Lipoprotein ................................................ 79 Summary .......................................................................................................... 80 5 CONCLUSION ...................................................................................................... 107 LIST OF REFERENCES ............................................................................................. 112 BIOGRAPHICAL SKETCH .......................................................................................... 125 6 LIST OF TABLES Table page 3-1 Results
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