Characterizing the Fecal Microbiota and Resistome of Corvus Brachyrhynchos (American Crow) in Fresno and Davis, California

Total Page:16

File Type:pdf, Size:1020Kb

Characterizing the Fecal Microbiota and Resistome of Corvus Brachyrhynchos (American Crow) in Fresno and Davis, California ABSTRACT CHARACTERIZING THE FECAL MICROBIOTA AND RESISTOME OF CORVUS BRACHYRHYNCHOS (AMERICAN CROW) IN FRESNO AND DAVIS, CALIFORNIA American Crows are common across the United States, well adapted to human habitats, and congregate in large winter roosts. We aimed to characterize the bacterial community (microbiota) of the crows’ feces, with an emphasis on human pathogens. The antibiotic resistance (AR) of the bacteria was analyzed to gain insight into the role crows may play in the spread of AR genes. Through 16S rRNA gene and metagenomic sequencing, the microbiota and antibiotic resistance genes (resistome) were determined. The core microbiota (taxa found in all crows) contained Lactobacillales (22.2% relative abundance), Enterobacteriales (21.9%) and Pseudomonadales (13.2%). Among the microbiota were human pathogens including Legionella, Camplycobacter, Staphylococcus, Streptococcus, and Treponema, among others. The Fresno, California crows displayed antibiotic resistance genes for multiple drug efflux pumps, macrolide-lincosamide- streptogramin (MLS), and more. Ubiquitous, urban wildlife like the American Crow may play a role in the spread of AR pathogens to the environment and human populations. Rachel Lee Nelson August 2018 CHARACTERIZING THE FECAL MICROBIOTA AND RESISTOME OF CORVUS BRACHYRHYNCHOS (AMERICAN CROW) IN FRESNO AND DAVIS, CALIFORNIA by Rachel Lee Nelson A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology in the College of Science and Mathematics California State University, Fresno August 2018 APPROVED For the Department of Biology: We, the undersigned, certify that the thesis of the following student meets the required standards of scholarship, format, and style of the university and the student's graduate degree program for the awarding of the master's degree. Rachel Lee Nelson Thesis Author Tricia Van Laar (Chair) Biology John V. H. Constable Biology Krish Krishnan Chemistry For the University Graduate Committee: Dean, Division of Graduate Studies AUTHORIZATION FOR REPRODUCTION OF MASTER’S THESIS X I grant permission for the reproduction of this thesis in part or in its entirety without further authorization from me, on the condition that the person or agency requesting reproduction absorbs the cost and provides proper acknowledgment of authorship. Permission to reproduce this thesis in part or in its entirety must be obtained from me. Signature of thesis author: ACKNOWLEDGMENTS Python and Linux expertise - Wesley Leach Guidance - Tricia Van Laar and committee Funding - California State University, Fresno: Graduate Net Initiative, Faculty Student Research, Graduate Research and Creative Activities CSU Council on Ocean Affairs San Joaquin Valley Chapter of the Wildlife Society TABLE OF CONTENTS Page LIST OF TABLES ................................................................................................. vii LIST OF FIGURES ................................................................................................. ix INTRODUCTION .................................................................................................... 1 Corvus brachyrhynchos (American Crow) ....................................................... 1 Gut Microbiota .................................................................................................. 7 Antibiotic Resistance (AR) ............................................................................... 9 Aims, Hypotheses, and Significance ............................................................... 15 METHODS ............................................................................................................. 17 Field Work ...................................................................................................... 17 Experimental Design ....................................................................................... 21 DNA Extraction and Sequencing .................................................................... 23 Microbiota Analysis ........................................................................................ 24 Resistome Determination ................................................................................ 29 RESULTS ............................................................................................................... 34 American Crow Microbiota ............................................................................ 34 Diversity Analyses of Fecal Microbiota ......................................................... 47 American Crow Resistome ............................................................................. 52 DISCUSSION ......................................................................................................... 56 American Crow Microbiota ............................................................................ 56 Pathogens ........................................................................................................ 62 American Crow Resistome ............................................................................. 64 Future Directions ............................................................................................. 66 CONCLUSION ...................................................................................................... 67 vi vi Page REFERENCES ....................................................................................................... 68 APPENDICES ........................................................................................................ 84 APPENDIX A: QIIME2 SYSTEM DETAILS AND COMMANDS .................... 85 APPENDIX B: MICROBIOTA DETAILS ........................................................... 89 APPENDIX C: RESISTOME RESULTS VIA ARGS-OAP ............................... 108 LIST OF TABLES Page Table 1. FeatureTable (table.qzv) Displaying Number of Aequences Per Sample Remaining After Quality Control (DADA2). .......................................... 25 Table 2. Isolation Agars Used to Select Organisms from Fecal Samples .............. 30 Table 3. Test Antibiotics Modes of Action ............................................................ 31 Table 4. 96 Well Plate Set Up Used to Determine Minimal Inhibitory Concentrations ......................................................................................... 31 Table 5. Taxonomic Richness of Fresno, Davis, and Critter Creek Microbiota .... 34 Table 6. Relative Abundance of Phyla and Orders in the American Crow Microbiota ................................................................................................ 35 Table 7. Taxa Identified in All Fecal Samples, Comprising the Core Fecal Microbiota of the American Crow ........................................................... 40 Table 8. Fresno American Crow Core Fecal Microbiota ....................................... 41 Table 9. Critter Creek American Crow Core Fecal Microbiota ............................. 42 Table 10. Davis American Crow Core Fecal Microbiota ....................................... 43 Table 11. Fresno American Crow Variable Fecal Microbiota ............................... 44 Table 12. Critter Creek American Crow Variable Fecal Microbiota ..................... 44 Table 13. Davis American Crow Variable Fecal Microbiota ................................. 45 Table 14. Number of Pathogen-Containing Taxa in American Crow Microbiota . 46 Table 15. Summary of Microbiota Diversity Statistical Analyses ......................... 48 Table 16. Antibiotic Resistance Genes Identified in Fresno Resistome ................ 52 Table 17. Minimum Inhibitory Concentrations (µg/mL) of Critter Creek Isolates ........................................................................................... 53 Table 18. Minimal Inhibitory Concentration (µg/mL) Observed in Fresno, California Fecal Microbiota ..................................................................... 54 Table 19. Antibiotic Resistant Organisms Isolated from Fresno Crow MIC ......... 54 viii viii Page Table 20. Minimum Inhibitory Concentrations (µg/mL) of CSU, Fresno Farm Animals Isolates ....................................................................................... 55 Table 21. Full Microbiota of American Crow Feces ............................................. 90 Table 22. Complete Relative Abundance of Phyla in the Fresno Crow Microbiota .................................................................................... 105 Table 23. Complete Relative Abundance of Phyla in the Critter Creek Crow Microbiota .............................................................................................. 106 Table 24. Complete Relative Abundance of Phyla in the Davis Crow Microbiota .................................................................................... 107 Table 25. Complete List of Antibiotic Resistance Genes Identified by ARGs-OAP. ...................................................................................... 109 LIST OF FIGURES Page Figure 1. Map of American Crow staging and roosting locations in Fresno, California. ............................................................................................... 18 Figure 2. Map of American Crow staging and roosting locations in Davis, California. ............................................................................................... 20 Figure 3. Forward and reverse reads quality (Demux.qzv). ................................... 26 Figure 4. Average relative abundance of
Recommended publications
  • Spatio-Temporal Study of Microbiology in the Stratified Oxic-Hypoxic-Euxinic, Freshwater- To-Hypersaline Ursu Lake
    Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake Baricz, A., Chiriac, C. M., Andrei, A-., Bulzu, P-A., Levei, E. A., Cadar, O., Battes, K. P., Cîmpean, M., enila, M., Cristea, A., Muntean, V., Alexe, M., Coman, C., Szekeres, E. K., Sicora, C. I., Ionescu, A., Blain, D., O’Neill, W. K., Edwards, J., ... Banciu, H. L. (2020). Spatio-temporal insights into microbiology of the freshwater-to- hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake. Environmental Microbiology. https://doi.org/10.1111/1462-2920.14909, https://doi.org/10.1111/1462-2920.14909 Published in: Environmental Microbiology Document Version: Peer reviewed version Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2019 Wiley. This work is made available online in accordance with the publisher’s policies. Please refer to any applicable terms of use of the publisher. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected].
    [Show full text]
  • Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
    ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co.
    [Show full text]
  • Development of a Seroprevalence Map for Mycoplasma Gallisepticum
    Original Paper Veterinarni Medicina, 61, 2016 (3): 136–140 doi: 10.17221/8764-VETMED Development of a seroprevalence map for Mycoplasma gallisepticum in broilers and its application to broilers from Comunidad Valenciana (Spain) over the course of two years (2009–2010) C. Garcia1, J.M. Soriano2, P. Catala-Gregori1 1Poultry Quality and Animal Nutrition Center of Comunidad Valenciana (CECAV), Castellon, Spain 2Faculty of Pharmacy, University of Valencia, Burjassot, Spain ABSTRACT: The aim of this study was to design and implement a Seroprevalence Map based on Business Intelligence for Mycoplasma gallisepticum (M. gallisepticum) in broilers in Comunidad Valenciana (Spain). To obtain the sero- logical data we analysed 7363 samples from broiler farms over 30 days of age over the course of two years (3813 and 3550 samples in 2009 and 2010, respectively, from 189 and 193 broiler farms in 2009 and 2010, respectively). Data were represented on a map of Comunidad Valenciana to include geographical information of flock location and to facilitate the monitoring. Only one region presented with average ELISA titre values of over 500 in the 2009 period, indicating previous contact with M. gallisepticum in broiler flocks. None of the other regions showed any pressure of infection, indicating a low seroprevalence for M. gallisepticum. In addition, data from this study represent a novel tool for easy monitoring of the serological response that incorporates geographical information. Keywords: Mycoplasma gallisepticum; broiler; seroprevalence map; ELISA, Comunidad Valenciana Mycoplasma gallisepticum (M. gallisepticum) is a matic for several days or months before experiencing bacterium causing poultry disease that is listed by stress (Dingfelder et al.
    [Show full text]
  • Quantitative and Qualitative Evaluation of the Impact of the G2 Enhancer
    bioRxiv preprint doi: https://doi.org/10.1101/365395; this version posted July 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Quantitative and qualitative evaluation of the impact of the G2 2 enhancer, bead sizes and lysing tubes on the bacterial community 3 composition during DNA extraction from recalcitrant soil core 4 samples based on community sequencing and qPCR 5 6 Alex Gobbi1¶, Rui G. Santini2¶, Elisa Filippi1, Lea Ellegaard-Jensen1, Carsten S. 7 Jacobsen1, Lars H. Hansen1* 8 9 1 Department of Environmental Science, Aarhus University, Roskilde, Denmark 10 2 Natural History Museum, Centre for GeoGenetics, University of Copenhagen, Copenhagen, 11 Denmark 12 13 14 * Corresponding author 15 E-mail: [email protected] (LHH) 16 17 18 ¶ These authors contributed equally to this work. 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/365395; this version posted July 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 21 Abstract 22 Soil DNA extraction encounters numerous challenges that can affect both yield and 23 purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, 24 and PCR inhibitors from the soil matrix can negatively affect downstream analyses 25 when applying DNA sequencing.
    [Show full text]
  • Bacterial Communities of the Upper Respiratory Tract of Turkeys
    www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11.
    [Show full text]
  • High Quality Permanent Draft Genome Sequence of Chryseobacterium Bovis DSM 19482T, Isolated from Raw Cow Milk
    Lawrence Berkeley National Laboratory Recent Work Title High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Permalink https://escholarship.org/uc/item/4b48v7v8 Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Laviad-Shitrit, Sivan Göker, Markus Huntemann, Marcel et al. Publication Date 2017 DOI 10.1186/s40793-017-0242-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laviad-Shitrit et al. Standards in Genomic Sciences (2017) 12:31 DOI 10.1186/s40793-017-0242-6 SHORT GENOME REPORT Open Access High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk Sivan Laviad-Shitrit1, Markus Göker2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, T. B. K. Reddy3, Chris Daum3, Nicole Shapiro3, Victor Markowitz3, Natalia Ivanova3, Tanja Woyke3, Hans-Peter Klenk4, Nikos C. Kyrpides3 and Malka Halpern1,5* Abstract Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.
    [Show full text]
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • Bacterial Microbiome of the Nose of Healthy Dogs and Dogs with Nasal Disease
    RESEARCH ARTICLE Bacterial microbiome of the nose of healthy dogs and dogs with nasal disease Barbara Tress1, Elisabeth S. Dorn1, Jan S. Suchodolski2, Tariq Nisar2, Prajesh Ravindran2, Karin Weber1, Katrin Hartmann1, Bianka S. Schulz1* 1 Clinic of Small Animal Medicine, LMU Munich, Munich, Germany, 2 Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America * [email protected] Abstract a1111111111 The role of bacterial communities in canine nasal disease has not been studied so far a1111111111 a1111111111 using next generation sequencing methods. Sequencing of bacterial 16S rRNA genes has a1111111111 revealed that the canine upper respiratory tract harbors a diverse microbial community; a1111111111 however, changes in the composition of nasal bacterial communities in dogs with nasal dis- ease have not been described so far. Aim of the study was to characterize the nasal micro- biome of healthy dogs and compare it to that of dogs with histologically confirmed nasal neoplasia and chronic rhinitis. Nasal swabs were collected from healthy dogs (n = 23), dogs OPEN ACCESS with malignant nasal neoplasia (n = 16), and dogs with chronic rhinitis (n = 8). Bacterial DNA was extracted and sequencing of the bacterial 16S rRNA gene was performed. Data were Citation: Tress B, Dorn ES, Suchodolski JS, Nisar T, Ravindran P, Weber K, et al. (2017) Bacterial analyzed using Quantitative Insights Into Microbial Ecology (QIIME). A total of 376 Opera- microbiome of the nose of healthy dogs and dogs tional Taxonomic Units out of 26 bacterial phyla were detected.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
    Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Influence of External and Internal Environmental Factors on Intestinal Microbiota of Wild and Domestic Animals A
    Influence of external and internal environmental factors on intestinal microbiota of wild and domestic of animals factors on intestinal microbiota Influence of external and internal environmental Influence of external and internal environmental factors on intestinal microbiota of wild and domestic animals A. Umanets Alexander Umanets Propositions 1. Intestinal microbiota and resistome composition of wild animals are mostly shaped by the animals’ diet and lifestyle. (this thesis) 2. When other environmental factors are controlled, genetics of the host lead to species- or breed specific microbiota patterns. (this thesis) 3. Identifying the response of microbial communities to factors that only have a minor contribution to overall microbiota variation faces the same problems as the discovery of exoplanets. 4. Observational studies in microbial ecology using cultivation- independent methods should be considered only as a guide for further investigations that employ controlled experimental conditions and mechanistic studies of cause-effect relationships. 5. Public fear of genetic engineering and artificial intelligence is not helped by insufficient public education and misleading images created through mass- and social media. 6. Principles of positive (Darwinian) and negative selection govern the repertoire of techniques used within martial arts. Propositions belonging to the thesis, entitled Influence of external and internal environmental factors on intestinal microbiota of wild and domestic animals Alexander Umanets Wageningen, 17 October
    [Show full text]