DOCSLIB.ORG

Ecological Genetics of Dugongs (Dugong Dugon) in Queensland

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ecological Genetics of Dugongs (Dugong Dugon) in Queensland Ecological genetics of dugongs (Dugong dugon) in Queensland Alexandra May McGowan Bachelor of Science Bachelor of Applied Science (Honours) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2019 School of Veterinary Science i Abstract Effective management of species is paramount to their survival in the face of ever- increasing threats. To ensure appropriate conservation management, ongoing monitoring of a species’ dispersal patterns is required to assess the impact potential barriers can have on limiting the exchange of genetic material between populations. Additionally, threats to the overall health of species need to be identified to ensure conservation initiatives are effective. In this thesis, I used an array of genetic techniques to assess the impact of coastal threats to dugongs (Dugong dugong) along the Queensland, Australia coast in an effort to inform conservation management of the Queensland population. The dugong is a long-lived marine mammal that inhabits shallow sub-tropical and tropical coastal waters of the Indo-West Pacific region, feeding on meadows of seagrass. Australia is considered a stronghold for the species due to the large populations still found within its waters, although in Queensland, they are exposed to a number of threatening factors that have potentially contributed to observed population declines. For my first study, I used microsatellite and mitochondrial DNA (mtDNA) genetic markers to investigate the genetic diversity and population structure of dugong populations along the eastern coastline of Queensland, between Torres Strait and Moreton Bay. A seascape genetics approach evaluated the factors that may have influenced dugong dispersal. The microsatellite analysis identified an abrupt genetic break within the Queensland dugong population in the Whitsunday Islands region, with a northern and southern cluster identified. Additionally, Fst values from the mtDNA analysis supported the division of these two clusters. While sea surface temperature and seagrass distribution were not found to be significant factors influencing dugong population structure and genetic distance, an oceanographic phenomenon known as the ‘sticky water’ effect, which is associated with strong tidal currents, may potentially be influencing dugong dispersal. Next, I developed single nucleotide polymorphism (SNP) markers using the double-digest RAD-Seq method to better define Queensland dugong population structure and to identify highly discriminatory, genome-wide genetic markers. After filtering, a dataset of 10,690 loci detected the same abrupt genetic break as in the first study. However, the analysis also indicated a third genetic cluster, suggesting dugong dispersal may have occurred more often across the Whitsundays Islands region than the microsatellite and mtDNA analyses ii indicated. The identification of genome-wide genetic markers, including a subset of 464 highly differentiating SNPs, provides opportunities for future genomic studies of dugongs. My third study aimed to test the effectiveness of a novel method, the commensal bacterial network, to detect dugong contemporary movements. This method aimed to build a network demonstrating dugong groupings based on whether bacterial genotypes were shared, assuming the transfer of bacteria through either direct or indirect contact among dugongs. Faecal samples were collected and commensal bacterial species cultured and sequenced to determine bacterial genotypes for construction of a network. There was a surprisingly low rate of Escherichia coli culture (n=1, previously used commensal species). A 16S sequencing method identified Staphylococcus warneri as a potentially more suitable species, although low culture success and limited genetic diversity meant it was not possible to build a comprehensive commensal bacterial network to infer dugong contemporary movements. Characterisation and investigation of differences in the dugong faecal microbiome along the Queensland coast was the aim of my fourth study. Diversity profiling demonstrated that the faecal microbial composition of three southern Queensland populations (Clairview, Hervey Bay and Moreton Bay) were different to those of the more northern locations according to Principal Coordinate Analysis and relative abundance averages of the three main phyla, potentially due to differences in diet. Interestingly, the microbiome geographical divide did not align with the genetic divide, potentially indicating ranging movements across the genetic break. Additionally, core microbial families were identified throughout all locations, including Clostridiaceae_1, Lachnospiraceae, Peptostreptococcaceae, Ruminococcaceae, Bacteroidaceae and Flavobacteriaceae, with these possibly important for seagrass digestion. In my final study, antibiotic resistance profiles of bacterial isolates cultured from dugong faecal samples (n=9) collected at two locations, Moreton Bay (urban) and Newry Region (rural), were investigated. Whole Genome Sequencing (WGS) was used to identify resistance and virulence genes. All S. warneri isolates were resistant to penicillin, with two S. warneri isolates displaying multidrug resistance, while E.coli isolates were all resistant to ampicillin. Together with the finding of resistance genes in some of the WGS, these iii preliminary findings suggest possible contamination of the dugong’s environment with antibiotics from human and agricultural wastewater or run-off. Overall, my findings indicated dugong dispersal is limited across the genetic break, although relatively unrestricted along the remainder of the Queensland coast, with sufficient gene flow to reduce the likelihood of inbreeding and other deleterious effects of low genetic diversity within the two identified clusters. The results from this thesis have the potential to improve dugong conservation management along the urbanised Queensland coast, with maintenance of movement corridors paramount to ensure genetic connectivity. iv Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. v Publications included in this thesis No publications included. Submitted manuscripts included in this thesis Chapter 3, Seascape genetics of a mobile marine mammal: evidence of an abrupt break in dugong (Dugong dugon, Müller) gene flow along Australia’s eastern Queensland coast, has been submitted as a manuscript to Conservation Genetics. Contributions by authors, Alexandra M. McGowan, Janet M. Lanyon, Nicholas Clark, David Blair, Helene Marsh, Eric Wolanski, Jennifer M. Seddon, to the manuscript are presented in the page preceding Chapter 3. Other publications during candidature No other publications. Contributions by others to the thesis Contributions to the research design, interpretation of data, structure, editing and proof- reading of this thesis was provided by my supervisors Prof Jennifer Seddon, Dr Janet Lanyon, Dr Nicholas Clark and Dr Justine Gibson. Additionally, Dr Janet Lanyon supervised and assisted with sample collection, Dr Nicholas Clark assisted with analyses for Chapters 3 and 4 and Dr Justine Gibson assisted with interpretation of Chapter 7 results. Dr Deirdre Mikkelsen from The University of Queensland Centre for Nutrition and Food Science and QAAFI assisted with the analysis and interpretation of the microbiome data in Chapter 6. Contributions by Prof David Blair, Prof Helene Marsh and Prof Eric Wolanski to Chapter 3 are outlined in the ‘Contributions by authors to submitted manuscript’ section preceding the chapter. Antimicrobial resistance testing services were conducted by Rochelle Price, Tina Maguire and Hester Rynhoud from UQ Veterinary Laboratory Services. Sequencing services for Chapters 3 and 5 were conducted by the Animal Genetics Laboratory, Gatton. SNP and diversity profiling sequencing services were conducted by the Australian Genome Research Facility. vi Statement of parts of the thesis
Load more

Recommended publications
  • Omics Based Approaches to Study Campylobacter Jejuni Pathogenesis
    Omics based approaches to study Campylobacter jejuni pathogenesis Ozan Gundogdu 2020 This research dissertation is submitted for the MSc in Bioinformatics at Queen Mary, University of London 1 Table of Contents Abstract .................................................................................................................................. 3 Acknowledgements ................................................................................................................ 5 1. Introduction ........................................................................................................................ 6 1.1 Campylobacter ............................................................................................................. 6 1.1 Next-generation sequencing ......................................................................................... 6 1.3 16S metagenomics ....................................................................................................... 7 1.4 Operational Taxonomic Units (OTUs) ......................................................................... 8 1.5 Amplicon Sequence Variants (ASVs) .......................................................................... 9 1.6 Data analysis .............................................................................................................. 10 1.6 Bacterial transcriptomics ............................................................................................ 11 1.7 Bacterial transcriptomics data analysis .....................................................................
    [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]
  • Study of the Oral Virome and Microbiome Associated to the Proliferative Verrucous Leukoplakia
    Study of the oral virome and microbiome associated to the proliferative verrucous leukoplakia Doctorando: Rodrigo García López Programa: 1393/2007 Biotecnología, FACULTAT DE CIÈNCIES BIOLÒGIQUES Directores: Andrés Moya Simarro Vicente Pérez Brocal Valencia, 2017 D. Andrés Moya, Catedrático del Departamento de Genética de la Universitat de València y D. Vicente Pérez Brocal, Investigador del Centro de Investigación Biomédica en Red (Epidemiología y Salud Pública) (CIBERESP), certifican que la memoria titulada “Study of the oral virome and microbiome associated to the proliferative verrucous leukoplakia” ha sido realizada bajo su dirección en la Unidad Mixta de Investigación en Genómica y Salud FISABIO-Salud Pública -Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de València. Y para que así conste, firman el presente certificado. Fdo. Dr. Andrés Moya Fdo. Dr. Vicente Pérez Brocal Valencia, a _____________________________________________ Agradecimientos A mi esposa, Letty por el enorme apoyo y cariño en estos momentos tan complicados. A Andrés por su interminable paciencia y la motivación para seguir adelante. A Vicente y Ma. José por la valiosa guía tanto en lo académico como en la vida. A Jorge y Bea por la amistad que tanta falta hace para poder disfrutar del trabajo. A Maria por marcar la pauta y recordarme siempre hay algo positivo en todo. A los compañeros del laboratorio por la convivencia y a los técnicos por su imprescindible ayuda. A los que ya no están, los que nos dejaron pero a quienes recordamos con mucho cariño. A mi papá, por los valiosos consejos que quisiera seguir más frecuentemente. A mi mamá por ser quien me aterriza en la realidad cuando divago.
    [Show full text]
  • 26Sor Tm3rray /Mmucd
    D4006- Gut Microbiota Analysis UC Davis MMPC - Microbiome & Host Response Core Contents 1 Methods: 1 1.1 Sequencing . .1 1.2 Data processing . .1 2 Summary of Findings: 2 2.1 Sequencing analysis . .2 2.2 Microbial diversity . .2 2.2.1 Alpha Diversity . .2 2.2.2 Beta Diversity . 10 2.3 Data analysis using taxa abundance data . 13 2.3.1 Stacked bar graphs of Taxa abundances at each level . 14 A Appendix 1 (Taxa Abundance Tables) 30 B Appendix 2 (Taxa removed from filtered datasets at each level) 37 References: 43 Core Contacts: Helen E. Raybould, Ph.D., Core Leader ([email protected]) Trina A. Knotts, Ph.D., Core Co-Leader ([email protected]) Michael L. Goodson, Ph.D., Core Scientist ([email protected]) Client(s): Kent Lloyd, DVM PhD ;MMRRC; UC Davis Project #: MBP-2079 MMRRC strain ID: MMRRC_043518 Animal Information: The strain was donated to the MMRRC by Russell Ray at Baylor College of Medicine. Fecal samples were obtained from animals housed under the care of Russell Ray at Baylor College of Medicine. 1 Methods: Brief Project Description: MMRRC strains are often contributed to the MMRRC to fulfill the resource sharing aspects of NIH grants. Since transporting mice to another facilty often causes a microbiota shift, having a record of the original fecal microbiota from the donor institution where the original phenotyping or testing was performed may prove helpful if a phenotype is lost after transfer. Several MMRRC mouse lines were selected for fecal microbiota profiling of the microbiota. Table 1: Animal-Strain Information X.SampleID TreatmentGroup Animal_ID Genotype Line Sex MMRRC.043518.M493 MMRRC.043518_Het_M M493 Het MMRRC.043518 M MMRRC.043518.M494 MMRRC.043518_Het_M M494 Het MMRRC.043518 M 1 1.1 Sequencing Frozen fecal or regional gut samples were shipped on dry ice to UC Davis MMPC and Host Microbe Systems Biology Core.
    [Show full text]
  • ( 12 ) United States Patent
    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
    [Show full text]
  • Bacterial Community Ecology of the Colon in Mus Musculus
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2017-07-01 Bacterial Community Ecology of the Colon in Mus musculus Rachel Marie Nettles Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Nettles, Rachel Marie, "Bacterial Community Ecology of the Colon in Mus musculus" (2017). Theses and Dissertations. 6912. https://scholarsarchive.byu.edu/etd/6912 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bacterial Community Ecology of the Colon in Mus musculus TITLE PAGE Rachel Marie Nettles A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Roger T. Koide, Chair John Chaston Laura Bridgewater Department of Biology Brigham Young University Copyright © 2017 Rachel Marie Nettles All Rights Reserved ABSTRACT Bacterial Community Ecology of the Colon in Mus musculus Rachel Marie Nettles Department of Biology, BYU Master of Science The gut microbiome is a community of closely interacting microbes living in the gastrointestinal tract. Its structure has direct relevance to health. Disturbances to the microbiome, such as due to antibiotic use, have been implicated in various diseases. The goal of this study was to determine how the gut microbiome reacts to and recovers from disturbance caused by antibiotics. Because diet also influences the microbiome, this study included the interaction between diet and antibiotics.
    [Show full text]
  • Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
    microorganisms Article Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study Hend Alqaderi 1,2,3,†, Meganathan P. Ramakodi 4,†, Rasheeba Nizam 2,† , Sindhu Jacob 2, Sriraman Devarajan 5 , Muthukrishnan Eaaswarkhanth 2,* and Fahd Al-Mulla 2,* 1 Department of Oral Health Policy & Epidemiology, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA; [email protected] 2 Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait; [email protected] (R.N.); [email protected] (S.J.) 3 Kuwait School Oral Health Program, Ministry of Health, Salmiya 20005, Kuwait 4 Hyderabad Zonal Centre, CSIR-IICT Campus, CSIR-National Environmental Engineering Research Institute, Hyderabad 500007, India; [email protected] 5 National Dasman Diabetes Biobank, Special Services Facility, Dasman Diabetes Institute, Dasman 15462, Kuwait; [email protected] * Correspondence: [email protected] (M.E.); [email protected] (F.A.-M.); Tel.: +965-22242999 (ext. 2328) (M.E.); +965-22242999 (ext. 2211) (F.A.-M.) † These authors contributed equally to this work. Abstract: The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except Citation: Alqaderi, H.; Ramakodi, the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti M.P.; Nizam, R.; Jacob, S.; Devarajan, adolescents with varied body mass indexes (BMI). The analyses of core microbiome composition S.; Eaaswarkhanth, M.; Al-Mulla, F. showed Firmicutes, Bacteroidota, Proteobacteria, Patescibacteria, Fusobacteriota, Actinobacteriota, and Salivary Microbiome Diversity in Campylobacterota as the common phylum found in the Kuwaiti adolescent population.
    [Show full text]
  • Alterations in Gut Microbiota Linked to Provenance, Sex, and Chronic
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.11.426270; this version posted January 11, 2021. 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 Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in 2 white-tailed deer (Odocoileus virginianus) 3 4 David Minich1, Christopher Madden2, Morgan V. Evans2, Gregory A. Ballash1, Daniel J. Barr3, 5 Keith P. Poulsen3, Patricia M. Dennis2,4, Vanessa L. Hale2 6 7 1The Ohio State University College of Veterinary Medicine, Columbus, OH 8 2Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 9 3Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, WI 10 4Cleveland Metroparks Zoo, Cleveland, OH 11 12 Abstract 13 Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting 14 both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral 15 ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells 16 (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore 17 potential links between the gut microbiota and CWD, we collected fecal samples from farmed 18 and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest. Farmed deer 19 orignated from farms that were depopulated due to CWD. Free-ranging deer were sampled 20 during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we 21 used 16S rRNA gene sequencing to characterize the gut microbiota.
    [Show full text]
  • Characteristics of Mouse Intestinal Microbiota During Acute Liver Injury and Repair Following 50% Partial Hepatectomy
    EXPERIMENTAL AND THERAPEUTIC MEDICINE 22: 953, 2021 Characteristics of mouse intestinal microbiota during acute liver injury and repair following 50% partial hepatectomy YI SHAO1, YUANCONG JIANG1, HUI LI2, FENG ZHANG2, ZHENHUA HU1 and SHUSEN ZHENG1,2 1Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University; 2Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang 310003, P.R. China Received November 23, 2020; Accepted May 7, 2021 DOI: 10.3892/etm.2021.10385 Abstract. Dysbiosis of the gut microbiota has important LR3 group, the operational taxonomic units, species richness roles in various diseases and pathological states of the host. (Chao1) and species diversity (Shannon and Simpson indices) However, the changes of the gut microbiota during partial were decreased, although without any significant difference. hepatectomy (PH)‑induced acute liver injury have so far Furthermore, in the LR3 group, significant Cyanobacteria remained elusive. The present study investigated the gut enrichment and Fusobacteria depletion compared with the NC microbiome and its related pathways following PH‑induced and Sham3 groups was observed, while in the LR14 group, acute liver injury. A total of 50 male C57/BL6 mice were a significant depletion of the abundance of Verrucomicrobia, divided into a normal control (NC), sham‑operation and Chloroflexi and Deferribacteres compared to the LR3 group liver resection (LR) group (50% PH). Samples were collected was obtained. The abundance of Firmicutes was increased at 3 and 14 days post‑operation to obtain specimens for the in the LR3 group and decreased again in the LR14 group.
    [Show full text]
  • C G M 2 0 1 8 [0 4 on D Er Z O E K S R a Pp O
    Update of the bacterial the of bacterial Update intaxonomy the classification lists of COGEM CGM 2018 - 04 ONDERZOEKSRAPPORT report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly.
    [Show full text]
  • Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From
    bioRxiv preprint doi: https://doi.org/10.1101/341842; this version posted June 11, 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-NC-ND 4.0 International license. 1 Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from 2 competitive to environmental drivers and a window of opportunity for Campylobacter 3 4 Umer Zeeshan Ijaz&1, Lojika Sivaloganathan&2, Aaron Mckenna&3, Anne Richmond3, Carmel Kelly4, Mark 5 Linton4, Alexandros Stratakos4, Ursula Lavery3, Abdi Elmi2, Brendan Wren2, Nick Dorrell*2, Nicolae 6 Corcionivoschi*4 and Ozan Gundogdu*2 7 8 1School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK 9 2Faculty of Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel 10 Street, London, WC1E 7HT, UK 11 3Moy Park, 39 Seagoe Industrial Estate, Portadown, Craigavon, Co. Armagh, BT63 5QE, UK 12 4Agri-Food and Biosciences Institute, Food Microbiology, Newforge Lane, Belfast, BT9 5PX, UK 13 14 &These authors are joint first authors. 15 *These authors jointly directed this work. 16 For correspondence, contact: 17 Ozan Gundogdu ([email protected]) 18 Nicolae Corcionivoschi ([email protected]) 19 Nick Dorrell ([email protected]) 20 21 Abstract 22 Chickens are a key food source for humans yet their microbiome contains bacteria that can be pathogenic to 23 humans, and indeed potentially to chickens themselves. Campylobacter is present within the chicken gut and 24 is the leading cause of bacterial foodborne gastroenteritis within humans worldwide.
    [Show full text]
  • The Microbial Ecology of Human-Associated Bacterial Communities
    UNIVERSITY COLLEGE LONDON The microbial ecology of human-associated bacterial communities Liam Shaw January 2018 A thesis submitted to University College London for the degree of DOCTOR OF PHILOSOPHY Declaration I confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Liam Shaw London, April 2018 2 Abstract The bacterial communities within the human body have important associations with health and disease. Understanding their complexity requires ecological approaches. In this thesis, I apply ecological techniques and models to explore the microbial ecology of human-associated bacterial communities at multiple scales. In the first half of this the- sis, I explore the oral microbiome using 16S rRNA gene sequencing data to characterise the effect of various factors on its diversity. Multiple factors apart from disease can also affect the oral microbiome, but their relative importance remains a matter of debate. In Chapter 2, I use a dataset of saliva samples from a family of related Ashkenazi Jewish individuals to show that host genetics plays much less of a role than shared household in explaining bacterial community composition. In Chapter 3, I use a large dataset of plaque samples from women in Malawi to investigate associations between bacterial taxa and periodontal disease. I show that the signals from gingivitis and periodontitis can be distinguished, and use correlation networks to identify important taxa for the develop- ment of disease. The second half of this thesis deals with the effect of antibiotics on the human microbiome.
    [Show full text]