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Crossland-Dissertation-2018 EFFICACY OF FEED-GRADE ANTIBIOTICS, ANTIBIOTIC ALTERNATIVES AND THE IMPACT OF THERMAL STRESS ON THE RUMINAL MICROBIOME, RUMINAL FERMENTATION, FEEDLOT PERFORMANCE, FEEDING BEHAVIOR, AND CARCASS CHARACTERISTICS OF BEEF CATTLE A Dissertation by WHITNEY LYNN CROSSLAND Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Luis O. Tedeschi Committee Members, Jason J. Gill Tryon A. Wickersham Andy D. Herring T. G. Nagaraja Head of Department, Cliff Lamb May 2018 Major Subject: Animal Science Copyright 2018 Whitney Lynn Crossland ABSTRACT Beef cattle production in the United States is faced with restricted access to previously used feed-grade antibiotics, deemed medically important, under the 2017 Veterinary Feed Directive. Suitable alternatives should be characterized and verified across different feeding scenarios to maintain production efficiency and implementation strategies should be investigated to ensure the best utilization of current technology. In the first study, continuous versus rotational feeding of two products, monensin and bambermycin, were investigated to determine their effects on volatile fatty acids, potential activity of methane production, and rumen microbial populations of steers. We found no evidence to suggest that rotational feeding schemes were more effective than the continuous feeding of monensin and bambermycin or that rotational regimens delay microbial adaptation. In the second study, the effects of supplemental yeast (ADY) in the diets of finishing steers were investigated under different environmental temperatures (TN = 18 ± 0.55°C or HS = 35 ± 0.55°C). We concluded that supplementing ADY in the diets of finishing steers improved digestibility, digestible energy, metabolizable energy, and mean ruminal pH under TN conditions, but not under extreme HS conditions, due to depressed intake and energetic demand. In the third study, we observed the effects of supplementing ADY to feedlot steers (n = 120) fed for 164 days. Final treatment assignments were designated on d 70, followed by a 14 d dietary transition to a finishing diet, resulting in four treatment groups (Balaam’s design: two parallel groups and two cross-over groups). There is evidence to suggest that the ii addition of ADY in the diets of beef cattle during the dietary transition may aid in ruminal stabilization without affecting growth performance or carcass traits. A fourth study was initiated to isolate and characterize bacteriophage that target hyper ammonia producing bacteria (HAB) in the rumen. HAB had poor bacterial lawn growth to detect phage plaques. Sequential transfer methods of Félix d'Hérelle are recommended to identify phage presence on these obligately anaerobic bacteria. Naturally occurring antimicrobial substances in environmental samples may have interfering effects. Future phage work should look to high impact bacteria that cause easily measurable losses to truly understand efficacy. iii DEDICATION This dissertation is dedicated to those who helped me become the scientist I am today. By now I have figured out that I still have quite a lot to learn. And I can’t wait to spend the rest of my career doing that very thing. To my advisor: Dr. Tedeschi, there aren’t enough words to tell you how much I appreciate you for giving me another opportunity to work with you in your research program (and for footing the bill). You have a lot to read here so I’ll keep it short. I know the last 4 years have not been easy. Thank you for the letters of recommendation for the many scholarships and applications. You have invested a great deal of time and money into cultivating me as a young scientist and I only hope I can promote that same passion in my own research program. I am proud to call you mentor. To my committee: Dr. Gill, Dr. Wickersham, Dr. Herring, and Dr. Nagaraja, thank you for allowing me to randomly show up and ask you questions and advice. Your contributions and perspective have given me a well-balanced perception of the intricate ways nutrition is tied to all aspects of beef production and how I should pursue grants in the future. To my husband, thank you for sticking by me through this venture. Without you, I would have crashed and burned in year 2. It was hard and there are some scars but I think we can both agree we are better people now than we were when we started. And now, through faith and perseverance (or hard-headedness?) we have achieved our goals of returning to the panhandle where we can raise our family in the cattle business. We are so very blessed. iv ACKNOWLEDGEMENTS Thank you to the Department of Animal Science for providing me the opportunity to be the instructor of record for Animal Science 320 and for covering my tuition during those years. Thank you also to the College of Agriculture and Life Science for selecting me to receive and Excellence Fellowship and the Willie Mae Harris Teaching Fellowship. Thank you to the business coordination staff Robbie, Linda, Jennifer, Kori and Sarah for your help with the details that goes with raising a graduate student. Thank you to Kerry Dean, Kendrick LeBlanc and Kenton Krueger for all their help with feed services and facilities. Thank you to my committee, Dr. Tedeschi, Dr. Gill, Dr. Wickersham, Dr. Herring and Dr. Nagaraja for their guidance and support throughout the course of this research. Thanks also go to my friends and colleagues and the department faculty and staff for making my time at Texas A&M University a great experience. A huge amount of gratitude to my colleague Aaron Norris for his skill and ability in helping me complete my research projects and for all the laughs we shared doing “Re-re-search”. Finally, thanks to my encouraging family for their support and patience through my late-blooming desire for a career in academia. v CONTRIBUTORS AND FUNDING SOURCES This work was supervised by the dissertation committee chair, Dr. Luis O. Tedeschi of the Texas A&M University Department of Animal Science, and committee members: Dr. Jason J. Gill, Dr. Tryon A. Wickersham, Dr. Andy D. Herring of the Texs A&M University Department of Animal Science, and Dr. T. G. Nagaraja of Kansas State University, adjunct member to the Texas A&M Univesity Department Animal Science. Graduate study was partially supported by the Excellence Fellowship and Willie Mae Harris Fellowship from the Texas A&M University College of Agriculture and Natural Resources. Graduate studies were also partially supported by the Department of Animal Science for teaching and research responsibilities. Graduate studies were also partially supported by the committee chair for research responsibilities. Research was made possible in part by the Texas A&M AgriLife Beef Initiative (02- 513406-20000) and also in part by ABVista LLC (06-407988-91230). vi TABLE OF CONTENTS Page ABSTRACT……………………………………………………………………………… ii DEDICATION…………………………………………………………………………. iv ACKNOWLEDGEMENTS………………………………………………………………. v CONTRIBUTORS AND FUNDING SOURCES………………………………………… vi TABLE OF CONTENTS…………………………………………………………………. vii LIST OF FIGURES……………………………………………………………………… ix LIST OF TABLES………………………………………………………………………. xi CHAPTER I INTRODUCTION AND LITERATURE REVIEW…............................... 1 Introduction…………………………………………………………………….. 1 Literature Cited………………………………………………………………… 26 CHAPTER II EFFECTS OF ROTATING ANTIBIOTIC AND IONOPHORE FEED ADDITIVES ON VOLATILE FATTY ACID PRODUCTION, POTENTIAL FOR METHANE PRODUCTION, AND MICROBIAL POPULATIONS OF STEERS CONSUMING A MODERATE-FORAGE DIET……………............. 43 Synopsis...…………………………………………………………………….... 43 Introduction…………………………………………………………………….... 44 Materials and Methods…………………………………………………………... 46 Results and Discussion………………………………………………………….. 52 Conclusion………………………………………………………………………. 62 Literature Cited………………………………………………………………….. 63 CHAPTER III EFFECTS OF ACTIVE DRY YEAST ON RUMINAL pH CHARACTERISTICS AND ENERGY PARTITIONING OF FINISHING STEERS UNDER THERMONEUTRAL OR HEAT-STRESSED ENVIRONMENT………………………………………………………………… 84 Synopsis………………………………………………………………………….. 84 Introduction………………………………………………………………………. 85 Materials and Methods…………………………………………………………... 87 vii Results and Discussion………………………………………………………….. 96 Conclusion……………………………………………………………………… 109 Literature Cited…………………………………………………………………. 110 CHAPTER IV EFFECTS OF ACTIVE DRIED YEAST ON GROWTH PERFORMANCE, RUMEN pH AND CARCASS CHARACTERISTICS OF GROWING BEEF STEERS……………………………………………………. 125 Synopsis………………………………………………………………………… 125 Introduction…………………………………………………………………….. 126 Materials and Methods………………………………………………………... 127 Results and Discussion……………………………………………………….. 135 Conclusion……………………………………………………………...………. 145 Literature Cited...……………………………………………………….…......... 146 CHAPTER V IDENTIFYING BACTERIOPHAGES THAT TARGET HYPER AMMONIA-PRODUCING BACTERIA OF THE BOVINE RUMEN……….. 165 Introduction…………………………………………………………………….. 165 Materials and Methods.………………………………………………….......… 166 Results and Discussion ........................................................................................ 171 Conclusion…………………………………………………………………...… 176 Literature Cited………………………………………………………...………. 178 CHAPTER VI CONCLUSIONS AND FUTURE OUTLOOK ………………………. 186 viii LIST OF FIGURES FIGURE Page 1.1 Schematic of the flow of energy in the net energy system of beef cattle......... 42 2.1 Interaction of treatment and week on the acetate-to-propionate ratio in the rumen fluid of steers…………………………………………….……........... 80 2.2 Interaction
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