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DEVELOPMENT of MOLECULAR TOOLS to ASSESS WHETHER ARCOBACTER BUTZLERI IS an ENTERIC PATHOGEN of HUMAN BEINGS ANDREW L WEBB Bachel
DEVELOPMENT OF MOLECULAR TOOLS TO ASSESS WHETHER ARCOBACTER BUTZLERI IS AN ENTERIC PATHOGEN OF HUMAN BEINGS ANDREW L WEBB Bachelor of Science, University of Lethbridge, 2011 A Thesis Submitted to the School of Graduate Studies of the University of Lethbridge in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE Department of Biological Sciences University of Lethbridge LETHBRIDGE, ALBERTA, CANADA © Andrew Lawrence Webb, 2016 DEVELOPMENT OF MOLECULAR TOOLS TO ASSESS WHETHER ARCOBACTER BUTZLERI IS AN ENTERIC PATHOGEN OF HUMAN BEINGS ANDREW LAWRENCE WEBB Date of Defence: June 27, 2016 G. Douglas Inglis Research Scientist Ph.D. Thesis Co-Supervisor L. Brent Selinger Professor Ph.D. Thesis Co-Supervisor Eduardo N. Taboada Research Scientist Ph.D. Thesis Examination Committee Member Robert A. Laird Associate Professor Ph.D. Thesis Examination Committee Member Sylvia Checkley Associate Professor Ph.D., DVM External Examiner University of Calgary Calgary, Alberta, Canada Tony Russell Assistant Professor Ph.D. Chair, Thesis Examination Committee DEDICATION This thesis is dedicated to my partner Jen, who has been a source of endless patience and support. Furthermore, I dedicate this thesis to my parents, for their unwavering confidence in me and their desire to help me do what I love. iii ABSTRACT The pathogenicity of Arcobacter butzleri remains enigmatic, in part due to a lack of genomic data and tools for comprehensive detection and genotyping of this bacterium. Comparative whole genome sequence analysis was employed to develop a high throughput and high resolution subtyping method representative of whole genome phylogeny. In addition, primers targeting a taxon-specific gene (quinohemoprotein amine dehydrogenase) were designed to detect and quantitate A. -
(12) Patent Application Publication (10) Pub. No.: US 2012/0277127 A1 Hendrickson Et Al
US 20120277127A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0277127 A1 Hendrickson et al. (43) Pub. Date: Nov. 1, 2012 (54) METHODS, STRAINS, AND COMPOSITIONS Publication Classification USEFUL FOR MICROBALLY ENHANCED Int. C. OIL RECOVERY ARCOBACTER CLADE 1 (51) C09K 8/582 (2006.01) (75) Inventors: Edwin R. Hendrickson, Hockessin, CI2N L/20 (2006.01) DE (US); Scott Christopher Jackson, Wilmington, DE (US); Abigail K. Luckring, (US) (52) U.S. Cl. ...................................... 507/201:435/252.1 (73) Assignee: E. DUPONT DE NEMOURS AND COMPANY, Wilmington, DE (US) (57) ABSTRACT Appl. No.: Methods, microorganisms, and compositions are provided (21) 13/280,972 wherein oil reservoirs are inoculated with microorganisms (22) Filed: Oct. 25, 2011 belonging to Arcobacter clade 1 and medium including an electron acceptor. The Arcobacter strains grow in the oil Related U.S. Application Data reservoir to form plugging biofilms that reduce permeability (60) Provisional application No. 61/408,739, filed on Nov. in areas of Subterranean formations thereby increasing Sweep 1, 2010. efficiency, and thereby enhancing oil recovery. Patent Application Publication Nov. 1, 2012 Sheet 1 of 12 US 2012/0277127 A1 - - - - - - - us is us r u u ulu - ul |eunôl Patent Application Publication Nov. 1, 2012 Sheet 2 of 12 US 2012/0277127 A1 Patent Application Publication Nov. 1, 2012 Sheet 3 of 12 US 2012/0277127 A1 veenfil Patent Application Publication Nov. 1, 2012 Sheet 7 of 12 US 2012/0277127 A1 #7ºInfil Patent Application Publication Nov. 1, 2012 Sheet 8 of 12 US 2012/0277127 A1 G3Infil Patent Application Publication Nov. -
Fate of Arcobacter Spp. Upon Exposure to Environmental
FATE OF ARCOBACTER SPP. UPON EXPOSURE TO ENVIRONMENTAL STRESSES AND PREDICTIVE MODEL DEVELOPMENT by ELAINE M. D’SA (Under the direction of Dr. Mark A. Harrison) ABSTRACT Growth and survival characteristics of two species of the ‘emerging’ pathogenic genus Arcobacter were determined. The optimal pH growth range of most A. butzleri (4 strains) and A. cryaerophilus (2 strains) was 6.0-7.0 and 7.0-7.5 respectively. The optimal NaCl growth range was 0.09-0.5 % (A. butzleri) and 0.5-1.0% (A. cryaerophilus), while growth limits were 0.09-3.5% and 0.09-3.0% for A. butzleri and A. cryaerophilus, respectively. A. butzleri 3556, 3539 and A. cryaerophilus 1B were able to survive at NaCl concentrations of up to 5% for 48 h at 25°C, but the survival limit dropped to 3.5-4.0% NaCl after 96 h. Thermal tolerance studies on three strains of A. butzleri determined that the D-values at pH 7.3 had a range of 0.07-0.12 min (60°C), 0.38-0.76 min (55°C) and 5.12-5.81 min (50°C). At pH 5.5, thermotolerance decreased under the synergistic effects of heat and acidity. D-values decreased for strains 3556 and 3257 by 26-50% and 21- 66%, respectively, while the reduction for strain 3494 was lower: 0-28%. Actual D- values of the three strains at pH 5.5 had a range of 0.03-0.11 (60°C), 0.30-0.42 (55°C) and 1.97-4.42 (50°C). -
The Best Paper Ever
University of São Paulo “Luiz de Queiroz” College of Agriculture Isolation, identification and genotypic and phenotypic characterization of Arcobacter spp. isolated from Minas frescal cheese and raw milk Melina Luz Mary Cruzado Bravo Thesis presented to obtain the degree of Doctor in Science. Area: Food Science and Technology Piracicaba 2020 Melina Luz Mary Cruzado Bravo Agroindustrial Engineering Isolation, identification and genotypic and phenotypic characterization of Arcobacter spp. isolated from Minas frescal cheese and raw milk versão revisada de acordo com a resolução CoPGr 6018 de 2011 Advisor: Profa. Dra. CARMEN JOSEFINA CONTRERAS CASTILLO Co-Advisor: Prof. Dr. LUIS ROBERTO COLLADO GONZÁLEZ Thesis presented to obtain the degree of Doctor in Science. Area: Food Science and Technology Piracicaba 2020 Dados Internacionais de Catalogação na Publicação DIVISÃO DE BIBLIOTECA – DIBD/ESALQ/USP Cruzado Bravo, Melina Luz Mary Isolation, identification and genotypic and phenotypic characterization of Arcobacter spp. isolated from Minas frescal cheese and raw milk / Melina Luz Mary Cruzado Bravo. - - versão revisada de acordo com a resolução CoPGr 6018 de 2011. - - Piracicaba, 2020. 88 p. Tese (Doutorado) - - USP / Escola Superior de Agricultura “Luiz de Queiroz”. 1. Patógeno emergente 2. Produtos lácteos 3. Genes de virulência 4. Resistência aos antibióticos 5. Biofilmes I. Título DEDICATION Dedico este trabajo a mis padres Isabel y Nery, mis hermanitas Vanessa y Jheny, mis sobrinos Alexa, Antonio y Nerick y a mi querida Sunchubamba. ACKNOWLEDGEMENTS -
Diversity of Mat-Forming Sulfide-Oxidizing Bacteria at Continental Margins
Diversity of Mat-forming Sulfide-oxidizing Bacteria at Continental Margins Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Stefanie Grünke Bremen, April 2010 Die vorliegende Doktorarbeit wurde in der Zeit von Juni 2006 bis April 2010 am Max- Planck-Institut für Marine Mikrobiologie und am Alfred-Wegener-Institut für Polar- und Meeresforschung angefertigt. 1. Gutachterin: Prof. Dr. Antje Boetius 2. Gutachter: Prof. Dr. Rudolf Amann Tag des Promotionskolloquiums: 4. Juni 2010 Diese Arbeit ist all denjenigen gewidmet, die ihre Segel setzen, um neue Welten gu erkunden. Seien sie sich gewiss, dass auf Sturm immer ruhiges Wasserfolgt. Wertrauen sie auf ihr größtes Gut — ihre Freunde und Familie. Nutgen sie ihre Schwächen, um neue Stärken gu finden. Soll Zuversicht ihr Kompass sein! Summary In the oceans, microbial mats formed by chemosynthetic sulfide-oxidizing bacteria are mostly found in so-called ‘reduced habitats’ that are characterized by chemoclines where energy-rich, reduced substances, like hydrogen sulfide, are transported into oxic or suboxic zones. There, these organisms often thrive in narrow zones or gradients of their electron donor (sulfide) and their electron acceptor (mostly oxygen or nitrate). Through the build up of large biomasses, mat-forming sulfide oxidizers may significantly contribute to primary production in their habitats and dense mats represent efficient benthic filters against the toxic gas hydrogen sulfide. As gradient organisms, these mat-forming sulfide oxidizers seem to be adapted to very defined ecological niches with respect to oxygen (or nitrate) and sulfide gradients. However, many aspects regarding their diversity as well as their geological drivers in marine sulfidic habitats required further investigation. -
Biodegradation of Aromatic Hydrocarbons by Methanogenic Consortia and Groundwater-Associated Microbial Communities
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2021-01-08 Biodegradation of Aromatic Hydrocarbons by Methanogenic Consortia and Groundwater-Associated Microbial Communities Taylor, Nicole Taylor, N. (2021). Biodegradation of Aromatic Hydrocarbons by Methanogenic Consortia and Groundwater-Associated Microbial Communities (Unpublished master's thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/112987 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Biodegradation of Aromatic Hydrocarbons by Methanogenic Consortia and Groundwater- Associated Microbial Communities by Nicole Taylor A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JANUARY, 2021 © Nicole Taylor 2021 Abstract The biodegradation of hydrocarbons is an important environmental process responsible for in situ remediation of crude oil and gas components. Microorganisms of many lineages and redox conditions have been characterized to degrade numerous types of -
Dissertação Mestrado Ana Carreira.Pdf
Caracterização de isolados de Campylobacter jejuni e Campylobacter coli obtidos de cecos de frangos, em Portugal, no âmbito de um estudo comunitário de prevalência Genotipagem e elucidação dos determinantes associados ao crescimento em biofilme RESUMO A Campilobacteriose é a zoonose mais notificada em países desenvolvidos, sendo Campylobacter jejuni o agente etiológico mais frequente e o consumo da carne de aves um importante factor de risco. A análise dos polimorfismos dos fragmentos de restrição do gene flaA de 112 isolados de C. coli e 67 de C. jejuni, obtidos de frangos de abate, em Portugal, durante o estudo nacional de prevalência de Campylobacter (Decisão da Comissão 2007/516/EC), gerou 11 perfis de restrição com HinfI (índice de diversidade Simpson; D=0,62) e 48 perfis com DdeI (D=0,89), evidenciando elevada variabilidade genética e ampla distribuição geográfica dos genótipos prevalentes. A comparação dos biofilmes formados por isolados de C. jejuni e C. coli em poliestireno, vidro e aço inoxidável, sugeriu, ainda, que o crescimento em biofilme poderá promover a sobrevivência destas bactérias em diferentes superfícies e condições de stresse ambiental, favorecendo a persistência ao longo da cadeia de processamento alimentar. i Characterization of Campylobacter jejuni and Campylobacter coli isolates obtained from broilers caeca, in Portugal, in the framework of a prevalence community study Genotyping and elucidation of biofilm growth associated determinants ABSTRACT Campylobacteriosis is the most notified zoonosis in developed countries, Campylobacter jejuni being the most frequent etiological agent and poultry meat consumption representing an important risk factor. Restriction fragment length polymorphism analysis of the flaA gene (flaA-RFLP) of 112 C. -
Microorganisms Overwinter Within the Ice Column of a Coastal Antarctic Lake
RESEARCH ARTICLE When a habitat freezes solid: microorganisms over-winter within the ice column ofa coastal Antarctic lake Christine M. Foreman1, Markus Dieser1, Mark Greenwood2, Rose M. Cory3, Johanna Laybourn-Parry4, John T. Lisle5, Christopher Jaros3, Penney L. Miller6, Yu-Ping Chin7 & Diane M. McKnight3 1Department of Land Resources and Environmental Sciences, Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; 2Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA; 3INSTAAR, University of Colorado, Boulder, CO, USA; 4Bristol Glaciology Centre, University of Bristol, Bristol, UK; 5USGS, Center for Coastal and Watershed Studies, St. Petersburg, FL, USA; 6Department of 7 Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN, USA; and 285 Mendenhall Laboratory, the Ohio State University, School of Earth Downloaded from https://academic.oup.com/femsec/article/76/3/401/486873 by guest on 27 September 2021 Sciences, Columbus, OH, USA Correspondence: Christine M. Foreman, Abstract Department of Land Resources and Environmental Sciences, Center for Biofilm A major impediment to understanding the biology of microorganisms inhabiting Engineering, Montana State University, 366 Antarctic environments is the logistical constraint of conducting field work EPS Building, Bozeman, MT 59717, USA. primarily during the summer season. However, organisms that persist throughout Tel.: 11 406 994 7361; fax: 11 406 994 the year encounter severe environmental changes between seasons. In an attempt 6098; e-mail: [email protected] to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the Present address: Rose M. -
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order from the Chaos
fmicb-09-02077 September 1, 2018 Time: 10:25 # 1 ORIGINAL RESEARCH published: 04 September 2018 doi: 10.3389/fmicb.2018.02077 Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos Alba Pérez-Cataluña1, Nuria Salas-Massó1, Ana L. Diéguez2, Sabela Balboa2, Alberto Lema2, Jesús L. Romalde2* and Maria J. Figueras1* 1 Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain, 2 Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. Edited by: The objective of the present study was to reassess the taxonomy of the genus Martha E. Trujillo, Arcobacter using information derived from the core genome (286 genes), a Multilocus Universidad de Salamanca, Spain Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic Reviewed by: John Phillip Bowman, indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), University of Tasmania, Australia Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Javier Pascual, Deutsche Sammlung von Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains Mikroorganismen und Zellkulturen that represent all the 27 species included in the genus Arcobacter together with 13 (DSMZ), Germany strains that are potentially new species, and the analysis of 57 genomes. -
APORTACIONES a LA EPIDEMIOLOGÍA DE Arcobacter Y Helicobacter Spp.: APLICACIÓN DE MÉTODOS MOLECULARES a SU DETECCIÓN E IDENTIFICACIÓN EN ALIMENTOS
Universidad Politécnica de Valencia Departamento de Biotecnología APORTACIONES A LA EPIDEMIOLOGÍA DE Arcobacter Y Helicobacter spp.: APLICACIÓN DE MÉTODOS MOLECULARES A SU DETECCIÓN E IDENTIFICACIÓN EN ALIMENTOS Tesis Doctoral Autor: Isidro Favian Bayas Morejón Directoras: Dra. Ma Antonia Ferrús Pérez Dra. Ana González Pellicer Valencia, Octubre de 2016 DEDICATORIA Este trabajo realizado con mucho esfuerzo lo dedico a mi hijo Anthony Fabián, el cual ha sido la fuerza principal que me impulsó día a día para seguir adelante; a mi amada esposa Rosa Angélica, que de manera incondicional y pese a la distancia me ha apoyado, y me ha dado fuerzas para continuar. A mi querida madre Laura Judith, que sé que desde el cielo me ha estado iluminando en este largo camino. A mí apreciado padre Elías Alberto, a mis queridas hermanas; Rocío, Maritza y Rosario que aunque a la distancia me supieron apoyar. ¡Los quiero mucho! AGRADECIMIENTOS Agradezco a DIOS por brindarme siempre nuevas oportunidades en los caminos de la vida para así aprender día a día lo maravilloso que es vivir. Al finalizar esta tesis es muy satisfactorio expresar mi agradecimiento a mis directoras, Mª Antonia Ferrús y Ana González. Gracias por ofrecerme la oportunidad de trabajar con vosotras, por vuestra dirección, y por supuesto, por haberme guiado con buena voluntad, paciencia, amplio conocimiento y experiencia a lo largo de este trabajo. También quiero agradecer a todos quienes conforman el Departamento de Biotecnología: A Manuel Hernández, Jorge García, Rosa Montes y Ma Ángeles Castillo, gracias por brindarme vuestra confianza y valiosos consejos. A Ana Jiménez y Salut Botella, gracias por haberme permitido compartir con vosotras esa bonita experiencia de impartir y aprender a través de la docencia en prácticas. -
Molecular Detection and Study of Campylobacter and Related
Molecular detection and study of Campylobacter and related microorganisms Nisreen Hoosain A thesis submitted in partial fulfillment of the requirements for the degree of Doctor Philosophiae in the Department of Biotechnology, University of the Western Cape. Supervisor: Professor Pieter Andries Gouws Co-supervisor: Professor Albert Joseph Lastovica November 2010 i DECLARATION I declare that “Molecular detection and study of Campylobacter and related microorganisms” is my own work, that it has not been submitted before for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged as complete references. Nisreen Hoosain November 2010 Signed:………………………. ii ACKNOWLEDGEMENTS First and foremost, I wish to thank Allah for giving me the strength, wisdom and guidance during my PhD and allowing me to obtain my PhD degree. I would like to thank my supervisor, Prof. P.A. Gouws, and my co-supervisor, Prof. A.J. Lastovica for their support, guidance, encouragement and advice. A special thanks to my colleagues in the laboratory as well as all staff in the Biotechnology Department at the University of the Western Cape. Thank you for your friendship, advice and making my stay an enjoyable one. To my beloved parents, brother, sister in-law, niece, nephew and other family members: thank you for your prayers, love, understanding, encouragement and support through the years. It is greatly appreciated, I am truly blessed! In addition, I would like to extend my sincere gratitude to my financial assistants: Department of Biotechnology at the University of the Western Cape, the National Research Foundation (NRF) of South Africa, Muslim Hands of South Africa and the South African National Zakah Fund (SANZAF). -
Regulation of Respiratory Pathways in Campylobacterota: a Review
REVIEW published: 30 July 2019 doi: 10.3389/fmicb.2019.01719 Regulation of Respiratory Pathways in Campylobacterota: A Review Anne-Xander van der Stel† and Marc M. S. M. Wösten* Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands The Campylobacterota, previously known as Epsilonproteobacteria, are a large group of Gram-negative mainly, spiral-shaped motile bacteria. Some members like the Sulfurospirillum spp. are free-living, while others such as Helicobacter spp. can only persist in strict association with a host organism as commensal or as pathogen. Species of this phylum colonize diverse habitats ranging from deep-sea thermal vents to the human stomach wall. Despite their divergent environments, they share common energy conservation mechanisms. The Campylobacterota have a large and remarkable repertoire of electron Edited by: Martin G. Klotz, transport chain enzymes, given their small genomes. Although members of recognized Washington State University, families of transcriptional regulators are found in these genomes, sofar no orthologs known United States to be important for energy or redox metabolism such as ArcA, FNR or NarP are encoded Reviewed by: James Hemp, in the genomes of the Campylobacterota. In this review, we discuss the strategies that California Institute of Technology, members of Campylobacterota utilize to conserve energy and the corresponding regulatory United States mechanisms that regulate the branched electron transport chains in these bacteria. Thomas E. Hanson, University