DOCSLIB.ORG

An Exploration of Ecological Concepts in the Context of Antimicrobial Resistance and the Use

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Exploration of Ecological Concepts in the Context of Antimicrobial Resistance and the Use An exploration of ecological concepts in the context of antimicrobial resistance and the use of phytochemical compounds within the ruminant gut microbiome by Natalie Cécile Knox A thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY Department of Animal Science University of Manitoba Copyright © 2013 by Natalie Cécile Knox ii ACKNOWLEDGMENTS I would like to express my sincere gratitude to the late Dr. Denis Krause for serving as my advisor and Dr. Rick Holley for serving as my co-advisor. To Dr. Krause, I will always be indebted to you for being a great mentor and teacher. You will be greatly missed. In addition, I would like to thank Dr. Holley for your kind advice and guidance throughout my program. Special thank you to Dr. Kim Ominski for your kind support and advice as you have, in my mind, acted as another co-advisor throughout my degree. Special thanks to my committee members Drs. Karin Wittenberg, George Zhanel, and Tim McAllister for their time and insightful contributions along the way. I would also like to thank Dr. Gary Crow for his sound statistical advice throughout my research. And thank you to the Canadian Dairy Commission for the financial support throughout my graduate degree. The animal trial would not have been possible without the help of Terri Garner, Janice Haines, Chad Malfait, Darcy Catellier and staff at the Glenlea Research Centre, many thanks to all of you. And of course a huge thank you to Jenelle Hamblin and Kristen Bouchard-Teasdale for their friendships and patience while teaching me what agriculture was all about. A special thank you also goes out to Ehsan Khafipoor, Sanjiv Bhandari, Amit Setia, Juan Hernandez, Stephanie Cheng, and Roman Kotlowski for teaching me all the fundamentals of molecular biology and statistical methods. To Victoria Tkachuk and Ainsley Little, thank you for always being there to help me with lab work but most of all, thank you for your friendship! Many thanks to all the graduate students, faculty, and staff of the Department of Animal Science for your support and friendships along the way, you’ve made the last 5 years memorable. Finally, I would like to express my utmost gratitude to my mom and dad for their endless iii support and encouragement. No words can express how grateful I am for everything you have done for me. Thank you to my brothers, Jude and Serge for always being there for me whenever I needed them. To my new family, Fran, Ted, Angie, Dustin, Pam, and Marc, thank you for all your patience and support throughout what seemed to you as a never ending degree. And lastly, a special thank you to my husband Greg for his love and encouragement throughout this journey! iv DEDICATION I dedicate this thesis to my parents. You are the reason I’ve made it this far! Thank you. v ABSTRACT Secondary plant metabolites have recently been gaining interest in livestock production systems following the ban of in-feed antibiotics within the European Union. The rise in antimicrobial resistance found in pathogenic and non-pathogenic bacteria has lead to increased interest in the research community regarding the use of phythochemicals as an alternative to antibiotics. The purpose of this research was to evaluate the impact of including phytochemicals in a livestock production system. Specifically, a high tannin-containing forage, sainfoin (Onobrychis viciifolia), was evaluated in vitro for its antimicrobial effect on Escherichia coli. We determined that phytochemicals alone are not as inhibitory as synthetic antibiotics. Thus, the use of combination therapy to deter the development of antimicrobial resistance was evaluated. A myriad of plant compounds were screened for their synergistic interactions with ciprofloxacin. Geraniol, an essential oil, was identified to possess good antimicrobial activity and synergistic interactions with ciprofloxacin. Therefore the effect of long term exposure to both ciprofloxacin and geraniol were examined. Results demonstrated that once an antimicrobial concentration threshold was reached, resistance to ciprofloxacin increased markedly in the presence of both geraniol and ciprofloxacin. Finally, an in vivo trial was conducted in which forty steers were fed sainfoin or alfalfa over a 9-week period to evaluate its ability to reduce E. coli shedding and its impact on gut microbiota in the context of popular theoretical ecology concepts. Results from the in vivo study indicate that sainfoin was able to promote a slight decrease in generic E. coli shedding which could be maintained throughout the trial. Using high-throughput sequencing, the effect of sainfoin on the microbial ecosystem of the ruminant gut was evaluated. Sainfoin induced a significant shift in the microbial community structure of the rumen and to a lesser vi extent in the hindgut. Using ecology theories, a hypothesis was formulated regarding the mechanisms that mediate the development of tolerance and the fundamental ecological processes controlling microbial population shifts. Understanding how the gut ecosystem functions and predicting its behaviour in the presence of various fluctuating environmental conditions will enable more efficient manipulation of the rumen and promote best management practices in livestock production. vii FOREWARD This thesis was prepared following a manuscript format. The thesis is comprised of five manuscripts each corresponding to a chapter. Manuscript I and II have been published in the Canadian Journal of Plant Science and the Journal of Applied and Environmental Microbiology, respectively. Manuscript III, IV, and V will be submitted to the Journal of Applied and Environmental Microbiology. All manuscripts are formatted in accordance with the guidelines of the Canadian Journal of Plant Science. viii TABLE OF CONTENTS ACKNOWLEDGEMENTS..............................................................................................ii DEDICATION...................................................................................................................iv ABSTRACT........................................................................................................................v FOREWARD....................................................................................................................vii TABLE OF CONTENTS................................................................................................viii LIST OF TABLES............................................................................................................xii LIST OF FIGURES.........................................................................................................xiv LIST OF COPYRIGHTED MATERIAL FOR WHICH PERMISSION WAS OBTAINED.....................................................................................................................xvii LIST OF ABBREVIATIONS.........................................................................................xix CHAPTER ONE: GENERAL INTRODUCTION..........................................................1 CHAPTER TWO: LITERATURE REVIEW.................................................................3 2.1 Microbial ecosystem of the ruminant gut............................................................3 2.2 How to study microbial ecosystems?..................................................................7 2.3 Next-generation sequencing technology.............................................................8 2.4 Introduction to antimicrobial resistance..............................................................9 2.5 Microbial mechanisms of antimicrobial resistance.............................................9 2.6 Agriculture and antimicrobial resistance...........................................................12 2.7 Combination therapy and methodologies to assess antimicrobial synergism, additivity, and antagonism..................................................................................................16 2.8 Phytochemicals..................................................................................................26 ix 2.9 Tannins..............................................................................................................33 2.10 Ecology theories................................................................................................54 2.11 Research hypothesis and objectives...............................................................60 CHAPTER THREE: MANUSCRIPT I.........................................................................61 Condensed tannin concentrations found in vegetative and mature forage legumes grown in western Canada….....................................................................................................61 3.1 Abstract..................................................................................................................62 3.2 Introduction............................................................................................................63 3.3 Material and methods.............................................................................................64 3.4 Results and discussion............................................................................................68 CHAPTER BRIDGE TO CHAPTER FOUR................................................................80 CHAPTER FOUR: MANUSCRIPT II...........................................................................81 Potential to reduce Escherichia
Load more

Recommended publications
  • Serpula Hyodysenteriae Comb
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1991, p. 50-58 Vol. 41, No. 1 0020-7713/91/0 10050-09$02.00/0 Copyright 0 1991, International Union of Microbiological Societies Reclassification of Treponema hyodysenteriae and Treponema innocens in a New Genus, Serpula gen. nov., as Serpula hyodysenteriae comb. nov. and Serpula innocens comb. nov. T. B. STANTON,l* N. S. JENSEN,l T. A. CASEY,l L. A. TORDOFF,2 F. E. DEWHIRST,2 AND B. J. PASTER2 Physiopathology Research Unit, National Animal Disease Center, Agricultural Research Service, U.S.Department of Agriculture, Ames, Iowa 50010,l and Forsyth Dental Center, Boston, Massachusetts 021152 The intestinal anaerobic spirochetes Treponema hyodysenteriae B7ST (T = type strain), B204, B169, and A-1, Treponema innocens B256T and 4/71, Treponema succinifaciens 6091T, and Treponema bryantii RUS-lT were compared by performing DNA-DNA reassociation experiments, sodium dodecyl sulfate-polyacrylamide gel electrophoresis of cell proteins, restriction endonuclease analysis of bNA, and 16s rRNA sequence analysis. DNA-DNA relative reassociation experiments in which the S1 nuclease method was used showed that T. hyodysenteriae B78T and B204 had 93% sequence homology with each other and approximately 40% sequence homology with T. innocens B256T and 4/71. Both T. hyodysenteriae B7ST and T. innocens B256T exhibited negligible levels of DNA homology (55%)with T. succinifaciens 6091T. The results of comparisons of protein electrophoretic profiles corroborated the DNA-DNA reassociation results. We found high levels of similarity (296%) in electrophoretic profiles among T. hyodysenteriae strains, moderate levels of similarity (43 to 49%) between T. hyodysenteriae and T. innocens, and no detectable similarity between the profiles of either T.
    [Show full text]
  • Perilla Frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows
    microorganisms Article Perilla frutescens Leaf Alters the Rumen Microbial Community of Lactating Dairy Cows Zhiqiang Sun, Zhu Yu and Bing Wang * College of Grass Science and Technology, China Agricultural University, Beijing 100193, China; [email protected] (Z.S.); [email protected] (Z.Y.) * Correspondence: [email protected] Received: 25 September 2019; Accepted: 12 November 2019; Published: 13 November 2019 Abstract: Perilla frutescens (L.) Britt., an annual herbaceous plant, has antibacterial, anti-inflammation, and antioxidant properties. To understand the effects of P. frutescens leaf on the ruminal microbial ecology of cattle, Illumina MiSeq 16S rRNA sequencing technology was used. Fourteen cows were used in a randomized complete block design trial. Two diets were fed to these cattle: a control diet (CON); and CON supplemented with 300 g/d P. frutescens leaf (PFL) per cow. Ruminal fluid was sampled at the end of the experiment for microbial DNA extraction. Overall, our findings revealed that supplementation with PFL could increase ruminal fluid pH value. The ruminal bacterial community of cattle was dominated by Bacteroidetes, Firmicutes, and Proteobacteria. The addition of PFL had a positive effect on Firmicutes, Actinobacteria, and Spirochaetes, but had no effect on Bacteroidetes and Proteobacteria compared with the CON. The supplementation with PFL significantly increased the abundance of Marvinbryantia, Acetitomaculum, Ruminococcus gauvreauii, Eubacterium coprostanoligenes, Selenomonas_1, Pseudoscardovia, norank_f__Muribaculaceae, and Sharpea, and decreased the abundance of Treponema_2 compared to CON. Eubacterium coprostanoligenes, and norank_f__Muribaculaceae were positively correlated with ruminal pH value. It was found that norank_f__Muribaculaceae and Acetitomaculum were positively correlated with milk yield, indicating that these different genera are PFL associated bacteria.
    [Show full text]
  • Microbial Communities Mediating Algal Detritus Turnover Under Anaerobic Conditions
    Microbial communities mediating algal detritus turnover under anaerobic conditions Jessica M. Morrison1,*, Chelsea L. Murphy1,*, Kristina Baker1, Richard M. Zamor2, Steve J. Nikolai2, Shawn Wilder3, Mostafa S. Elshahed1 and Noha H. Youssef1 1 Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA 2 Grand River Dam Authority, Vinita, OK, USA 3 Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA * These authors contributed equally to this work. ABSTRACT Background. Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results. Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake
    [Show full text]
  • Gut Microbiome Differences Between Wild and Captive Black Rhinoceros – Implications for Rhino Health Keylie M. Gibson1,2, Brya
    Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health Keylie M. Gibson1,2, Bryan N. Nguyen1,2, Laura M. Neumann3, Michele Miller4, Peter Buss5, Savel Daniels6, Michelle Ahn1,2, Keith A. Crandall1,7*, & Budhan Pukazhenthi8* 1 Computational Biology Institute, The Milken Institute School of Public Health, George Washington University, Washington, DC, USA 2 Department of Biological Sciences, George Washington University, Washington, DC, USA 3 Department of Environmental and Occupational Health, The Milken Institute School of Public Health, The George Washington University, Washington, DC, USA 4 DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. 5 South African National Parks, Veterinary Wildlife Services, Kruger National Park, Skukuza, South Africa 6 Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa 7 Department of Epidemiology and Biostatistics, The Milken Institute School of Public Health, George Washington University, Washington, DC, USA 8 Smithsonian’s National Zoo and Conservation Biology Institute, Front Royal, VA, USA * Co-Senior Authors Corresponding author: Budhan Pukazhenthi Smithsonian Conservation Biology Institute 1500 Remount Road, Front Royal, VA 22630 [email protected] Supplemental table legends Table S1a. Core rhino microbiome species in wild rhinos. Table S1b. Core rhino microbiome species in captive rhinos. Table S2. Differentially gene ontology terms between wild and captive rhino samples. Table S3. Differentially abundant pathways between wild and captive rhino samples. Table S1a. Core rhino microbiome species in wild rhinos.
    [Show full text]
  • Treponema Caldaria Comb. Nov
    Lawrence Berkeley National Laboratory Recent Work Title Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov.,... Permalink https://escholarship.org/uc/item/3qr1w6qx Journal Standards in genomic sciences, 8(1) ISSN 1944-3277 Authors Abt, Birte Göker, Markus Scheuner, Carmen et al. Publication Date 2013-04-15 DOI 10.4056/sigs.3096473 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2013) 8:88-105 DOI:10.4056/sigs.3096473 Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Treponema Birte Abt1†, Markus Göker1†, Carmen Scheuner1, Cliff Han2,3, Megan Lu2,3, Monica Misra2,3, Alla Lapidus2, Matt Nolan2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxanne Tapia2,3, Lynne A. Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Marcel Huntemann2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Stefan Spring1, Sabine
    [Show full text]