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Using Prophylactics to Improve Resistance Against Enterobacteriaceae in Chickens

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Using Prophylactics to Improve Resistance Against Enterobacteriaceae in Chickens Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2021 Using prophylactics to improve resistance against Enterobacteriaceae in chickens Graham Redweik Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Redweik, Graham, "Using prophylactics to improve resistance against Enterobacteriaceae in chickens" (2021). Graduate Theses and Dissertations. 18597. https://lib.dr.iastate.edu/etd/18597 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Using prophylactics to improve resistance against Enterobacteriaceae in chickens by Graham Antony Joseph Redweik A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Microbiology Program of Study Committee: Melha Mellata, Major Professor Elizabeth Bobeck Susan Lamont Kevin Schalinske Stephan Schmitz-Esser Michael Wannemuehler The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2021 Copyright © Graham Antony Joseph Redweik, 2021. All rights reserved. ii DEDICATION I would not be where I am without my late grandfather, Bob Dillman. You were, and con- tinue to be, one of my greatest motivators. Thus, this work is in memoriam to you. iii TABLE OF CONTENTS Page DEDICATION ................................................................................................................................ ii TABLE OF CONTENTS ............................................................................................................... iii NOMENCLATURE ..................................................................................................................... vii ACKNOWLEDGMENTS ........................................................................................................... xiii ABSTRACT ...................................................................................................................................xv CHAPTER 1. GENERAL INTRODUCTION ................................................................................1 Background ................................................................................................................................ 1 Host Factors Affecting Intestinal Enterobacteriaceae Colonization in Chickens .................... 3 Live Bacterial Vaccines Improve Chicken Responses against Bacterial Pathogens ................. 6 Probiotics Improve Chicken Health through Numerous Mechanisms ...................................... 7 Knowledge Gaps and Limitations for Probiotics and Live Bacterial Vaccines in Poultry ....... 9 Summary Statement and Organization for Thesis Research ................................................... 12 References ............................................................................................................................... 13 Figure ....................................................................................................................................... 23 CHAPTER 2. ORAL TREATMENTS WITH PROBIOTICS AND LIVE SALMONELLA VACCINE INDUCE CHANGES IN GUT NEUROCHEMICALS AND MICROBIOME IN CHICKENS....................................................................................................................................24 Abstract .................................................................................................................................... 24 Introduction ............................................................................................................................. 25 Materials and Methods ............................................................................................................ 26 Ethics Statement and General Conditions .......................................................................... 26 In vivo Experiments ............................................................................................................ 27 Vaccine Preparation and Immunization ............................................................................. 27 Sample Collection .............................................................................................................. 28 Ultra-High Pressure Liquid Chromatography .................................................................... 29 DNA Isolation and Microbiome 16S rRNA Sequencing ................................................... 29 IgA Titers Measured by ELISA ......................................................................................... 30 Statistical Analysis ............................................................................................................. 31 Results ..................................................................................................................................... 31 Catecholamine, but Not Serotonin Metabolism, Was Altered in Treatment-Specific Manner................................................................................................................................ 31 Ceca Microbiome Diversity Changed by Treatment .......................................................... 32 Specific Microbial Abundances Are Influenced by Live Prophylactics ............................ 33 Enterobacteriaceae Antigen-Specific IgA Positively Associated with Enterobacteriaceae Levels ................................................................................................. 34 Certain Bacteria Positively Correlated with Specific Neurochemical Metabolites ........... 34 Discussion ................................................................................................................................ 35 iv Chicken Ceca Is a Major Site for Neurochemical Metabolism, Although Only Catecholamines Were Affected by Treatments .................................................................. 35 RASV Causes Major Rift in Gut Microbiome Diversity ................................................... 36 Certain Gut Bacteria Were Correlated with Neurochemical Metabolites .......................... 37 Ceca Enterobacteriaceae Levels Associated with Intestinal IgA Levels .......................... 39 Conclusion ............................................................................................................................... 40 Data availability statement ...................................................................................................... 40 Author Contributions ............................................................................................................... 40 References ............................................................................................................................... 41 Figures and Tables ................................................................................................................... 46 CHAPTER 3. EVALUATION OF LIVE BACTERIAL PROPHYLACTICS TO DECREASE INCF PLASMID TRANSFER IN CHICKEN GUT AND ASSOCIATION WITH INTESTINAL SMALL RNAS...........................................................................................59 Abstract .................................................................................................................................... 59 Introduction ............................................................................................................................. 60 Materials and Methods ............................................................................................................ 61 Ethics Statement ................................................................................................................. 61 Experimental Design and Sample Sizes ............................................................................. 62 Phenotypic and Genotypic Assays ..................................................................................... 62 Ceca smRNA Extraction and Quantification ..................................................................... 64 Inter-E. coli Conjugation-smRNA Assays ......................................................................... 64 RNAHybrid miRNA Target Predictions ............................................................................ 65 miRNA RT-qPCR and Mimic in vitro Assays ................................................................... 66 Statistical Analyses and Binary Heatmap Development .................................................... 66 Results ..................................................................................................................................... 67 Fecal E. coli from P+V Group Exhibited Absence in IncFIB+ ColV+ Plasmids, Virulence Genes, and Phenotype........................................................................................ 67 Lack of Large Plasmids in Isolates Is Associated with Decreased Ceca smRNA Concentration ....................................................................................................................
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