DOCSLIB.ORG

Phd Thesis Final

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

THE ROLES OF OXYGEN AND DISULFIDE REDUCTASES IN THE PHYSIOLOGY OF CAMPYLOBACTERALES Nadeem O Kaakoush A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy School of Medical Sciences Faculty of Medicine The University of New South Wales Sydney, Australia 2008 “Science is a wonderful thing if one does not have to earn one's living at it.” - Albert Einstein ACKNOWLEDGEMENTS This thesis would not have been possible without the contributions of many people who have helped and supported me throughout the various stages of this candidature. I must thank my supervisor, Prof. George L Mendz, for giving me the opportunity to carry out my PhD degree in his laboratory at UNSW, and for his support throughout the years. I hope this quest was as rewarding for you as it was for me. You have taught me many valuable “tricks of the trade”; I hope we can continue to pursue not only a scientific collaboration together but also a good friendship. I’d like to thank Prof. Hazel Mitchell for providing support, especially the necessary lab space, during the final stages of my candidature. To Edward, Megan, Arinze, Phil, Justin, Bernice, Zsuzsanna, Johnny, Alfred and Sophie fellow warriors of science, thank you for your friendship and support throughout the years, and best of luck in the future. To A/Prof. Hilde De Reuse at the Institut Pasteur, thank you for allowing me to join your team and work in your lab for four months during my candidacy. To Damien Leduc, for your help and support in the lab and your countless translations of French to English; and to the rest of the group, especially Kristine and Marie for making me feel like I was part of the team. On a more personal note, thank you to Ali in Orlando, Adeline in Sydney, Amer and Ziad in Beirut, and Hussein and Jana in Dubai for staying in touch all this time and for their concern about my well-being. Finally, a special thank you to my sisters Nina and Nada, my Mum and Dad– you know how much you mean to me. ABSTRACT This work has studied several aspects of the physiology of the animal-colonizing species Campylobacter jejuni, Helicobacter pylori, Wolinella succinogenes and Arcobacter butzleri. C. jejuni and H. pylori were found to be obligate microaerophiles and W. succinogenes an anaerobe. A. butzleri was found to be an aerobe able to grow anaerobically. Comparative analyses of the responses of C. jejuni, H. pylori and W. succinogenes to various oxygen concentrations were investigated using transcriptomics and genes differentially expressed at higher oxygen concentrations were identified. At the time of this study no microarrays were available for A. butzleri. These comparative studies provided a better understanding of bacterial adaptation to and interaction with their environment. Several enzymes involved in oxireduction processes, including disulfide reductases, were upregulated under oxidative stress. Disulfide reductases of host-colonizing bacteria are involved in the expression of virulence factors, resistance to drugs, and elimination of toxic compounds. CXXC and CXXC-derived motifs are present in the active sites of disulfide reductases and are essential for the catalysis of these redox reactions. Large-scale genome analyses of 281 prokaryotes identified CXXC and CXXC-derived motifs in each microorganism. The total number of these motifs showed correlations with genome size and oxygen tolerance of the prokaryotes. Specific bioinformatic analyses served to identify putative disulfide reductases in the four Campylobacterales species. The project investigated the involvement of these enzymes in resistance to the antibiotic metronidazole, cadmium detoxication and pathogenesis. The activities of disulfide reductases were modulated by the presence of metronidazole, and its reduction was inhibited by the presence of disulfide reductase substrates. In addition, proteins involved in oxireduction of the low redox potential ferredoxin were downregulated in metronidazole resistant strains, suggesting that ferredoxin is involved in the resistant phenotype. Cellular processes and pathways regulated under cadmium stress included fatty acid biosynthesis, protein biosynthesis, chemotaxis and mobility, the tricarboxylic acid cycle, protein modification, redox processes and heat shock response. Notably, the data provided evidence for a role of oxireduction processes in the development of metronidazole resistance and the detoxication of cadmium. Furthermore, a method was developed to identify thiol disulfide oxidoreductases in the four Campylobacterales. The results suggested that H. pylori contained a novel disulfide bond formation system. Investigation of their potential involvement in virulence or colonization indicated that the putative thiol disulfide oxidoreductases HP0231 and HP0595 are related to the colonization efficiency of H. pylori. Finally, the only known disulfide reduction system in Campylobacterales, the thioredoxin system, was investigated in more detail. Phylogenetic analyses of the thioredoxin reductases TrxB1 and TrxB2 of the four bacteria were performed. The phylogenetic features of the TrxB2 suggested a special role for this enzyme in the physiology of these bacteria; thus, the enzyme was investigated further in H. pylori. TrxB2 was found to be an NADPH reductase, possibly involved in important oxireduction processes within the cell. CERTIFICATE OF ORIGINALITY I hereby declare that this submission is my own work, and to the best of my knowledge materials previously published or written by another person have been properly acknowledged. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work to the extent that assistance from others in the project’s design and conception or in style, presentation and linguistic expression is acknowledged. Nadeem O Kaakoush PUBLICATIONS JOURNAL ARTICLES N. O. Kaakoush and G. L. Mendz (2005) Helicobacter pylori Disulphide Reductases: Role in Metronidazole Reduction. FEMS Immunology and Medical Microbiology 44: 137-142. N. O. Kaakoush and G. L. Mendz (2006) Involvement of disulphide reductases in the response of Campylobacter jejuni to cadmium stress. Metal Ions in Biology and Medicine (Eds. Collery P., Morais P. V., Alpoim M. C.) Vol. 9 John Libbey & Co., Montrouge, France. S. Bury-Moné, N. O. Kaakoush, C. Asencio, F. Mégraud, A. Labigne, H. De Reuse and G. L. Mendz (2006) Is Helicobacter pylori a true microaerophile? Helicobacter 11: 296- 303. N. O. Kaakoush, Z. Kovach and G. L. Mendz (2007) Potential Role of Thiol:disulfide Oxidoreductases in the Pathogenesis of Helicobacter pylori. FEMS Immunology and Medical Microbiology 50: 177-183. N. O. Kaakoush, T. Sterzenbach, W. G. Miller, S. Suerbaum and G. L. Mendz (2007) Identification of Disulphide Reductases in Campylobacterales: a bioinformatics investigation. Antonie van Leeuwenhoek 92: 429-441. N. O. Kaakoush, W. G. Miller, H. De Reuse, G. L. Mendz (2007) The oxygen requirement and tolerance of Campylobacter jejuni. Research in Microbiology 158: 644- 650. N. O. Kaakoush and G. L. Mendz (2008) Responses of four Campylobacterales to cadmium stress. Metal Ions in Biology and Medicine (Eds. Collery P., Morais P. V., Alpoim M. C.) Vol. 10 John Libbey & Co., Montrouge, France. N. O. Kaakoush, M. Raftery and G. L. Mendz (2008) Molecular responses of Campylobacter jejuni to cadmium stress. FEBS Journal. (Accepted). JOURNAL ARTICLES IN PREPARATION N. O. Kaakoush, C. Baar, E. M. Fox, J. MacKichan, S. C. Schuster and G. L. Mendz (2008) Comparative analysis of the response of three Campylobacterales species to different oxygen tensions. International Journal of Biochemistry and Cell Biology. N. O. Kaakoush, C. Asencio, M. Raftery, F. Mégraud and G. L. Mendz (2008) A redox basis for metronidazole resistance in Helicobacter pylori. Antimicrobial Agents and Chemotherapy. N. O. Kaakoush and G. L. Mendz (2008) Inhibition of disulfide reductases as a therapeutic strategy. Current Enzyme Inhibition. CONFERENCE PROCEEDINGS N. O. Kaakoush and G. L. Mendz (2008) Responses of four Campylobacterales to cadmium stress. Metal Ions in Biology and Medicine 10th International Symposium. Corsica, France. Oral Presentation. N. O. Kaakoush (2007) Molecular responses of Campylobacter jejuni to cadmium stress. UMR INRA/ENV SECALIM, l'Ecole Nationale Veterinaire de NANTES. Nantes, France. Invited talk. N. O. Kaakoush, C. Asencio, F. Mégraud and G. L. Mendz (2007) A redox basis for metronidazole resistance in Helicobacter pylori. European Helicobacter Study Group XX International Workshop. Istanbul, Turkey. Oral Presentation. N. O. Kaakoush, M. Raftery and G. L. Mendz (2007) Molecular responses of Campylobacter jejuni to cadmium stress. 14th International Workshop on Campylobacter, Helicobacter and Related Organisms. Rotterdam, The Netherlands. (ESCMID grant winner). N. O. Kaakoush, E. M. Fox, J. MacKichan and G. L. Mendz (2006) Molecular responses of Helicobacter pylori to changes in oxygen tension. European Helicobacter Study Group XIX International Workshop. Wroclaw, Poland. Oral presentation. N. O. Kaakoush and G. L. Mendz (2006) Involvement of disulphide reductases in the response of Campylobacter jejuni to cadmium stress. Metal Ions in Biology and Medicine 9th International Symposium. Lisbon, Portugal. Oral presentation. N. O. Kaakoush and G. L. Mendz (2005) Disulphide reductases of Campylobacterales: Are they involved
Recommended publications
  • Identification of 16S Rrna and Virulence-Associated Genes Of

    Identification of 16S Rrna and Virulence-Associated Genes Of

    pathogens Article Identification of 16S rRNA and Virulence-Associated Genes of Arcobacter in Water Samples in the Kathmandu Valley, Nepal Rajani Ghaju Shrestha 1,2 , Yasuhiro Tanaka 3, Jeevan B. Sherchand 4 and Eiji Haramoto 2,* 1 Division of Sustainable Energy and Environmental Engineering, Osaka University, Suita, Osaka 565-0871, Japan 2 Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 3 Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan 4 Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 1524, Nepal * Correspondence: [email protected]; Tel.: +81-55-220-8725 Received: 8 July 2019; Accepted: 25 July 2019; Published: 26 July 2019 Abstract: This study aimed to determine the prevalence of Arcobacter and five associated virulence genes (cadF, ciaB, mviN, pldA, and tlyA) in water samples in the Kathmandu Valley, Nepal. A total of 286 samples were collected from deep tube wells (n = 30), rivers (n = 14), a pond (n = 1), shallow dug wells (n = 166), shallow tube wells (n = 33), springs (n = 21), and stone spouts (n = 21) in February and March (dry season) and August (wet season), 2016. Bacterial DNA was extracted from the water samples and subjected to SYBR Green-based quantitative PCR for 16S rRNA and virulence genes of Arcobacter. The 16S rRNA gene of Arcobacter was detected in 36% (40/112) of samples collected in the dry season, at concentrations ranging from 5.7 to 10.2 log copies/100 mL, and 34% (59/174) of samples collected in the wet season, at concentrations of 5.4–10.8 log copies/100 mL.
  • Prevalence and Characteristics of Arcobacter Butzleri

    Prevalence and Characteristics of Arcobacter Butzleri

    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2005 Prevalence and characteristics of Arcobacter butzleri: a potential food borne pathogen - in fecal samples, on carcasses and in retail meat of cattle, pig and poultry in Switzerland Keller, Sibille ; Räber, Sibylle Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-163301 Dissertation Published Version Originally published at: Keller, Sibille; Räber, Sibylle. Prevalence and characteristics of Arcobacter butzleri: a potential food borne pathogen - in fecal samples, on carcasses and in retail meat of cattle, pig and poultry in Switzerland. 2005, University of Zurich, Vetsuisse Faculty. Institut für Lebensmittelsicherheit und -hygiene der Vetsuisse-Fakultät Universität Zürich Direktor: Prof. Dr. Roger Stephan Prevalence and characteristics of Arcobacter butzleri - a potential food borne pathogen - in fecal samples, on carcasses and in retail meat of cattle, pig and poultry in Switzerland Inaugural-Dissertation zur Erlangung der Doktorwürde der Vetsuisse-Fakultät Universität Zürich vorgelegt von Sibille Keller Sibylle Räber Tierärztin Tierärztin von Meggen LU von Benzenschwil AG genehmigt auf Antrag von Prof. Dr. Roger Stephan, Referent Prof. Dr. Kurt Houf, Korreferent Zürich 2005 Sibille Keller Sibylle Räber Für meine Eltern Für meine Eltern Margrith und Peter Kathrin und Roland Content page 1 Summary 3 2 Introduction 4 3 Arcobacter, a potential foodborne
  • 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 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.
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
  • Arcobacter Butzleri – Lessons from a Meta- Analysis of Murine Infection Studies

    Arcobacter Butzleri – Lessons from a Meta- Analysis of Murine Infection Studies

    RESEARCH ARTICLE The Immunopathogenic Potential of Arcobacter butzleri – Lessons from a Meta- Analysis of Murine Infection Studies Greta Gölz1*, Thomas Alter1, Stefan Bereswill2, Markus M. Heimesaat2 1 Institute of Food Hygiene, Freie Universität Berlin, Berlin, Germany, 2 Department of Microbiology and Hygiene, Charité - University Medicine Berlin, Berlin, Germany * [email protected] Abstract a11111 Background Only limited information is available about the immunopathogenic properties of Arcobacter infection in vivo. Therefore, we performed a meta-analysis of published data in murine infection models to compare the pathogenic potential of Arcobacter butzleri with Campylobacter jejuni and commensal Escherichia coli as pathogenic and harmless reference bacteria, respectively. OPEN ACCESS Citation: Gölz G, Alter T, Bereswill S, Heimesaat MM Methodology / Principal Findings (2016) The Immunopathogenic Potential of -/- Arcobacter butzleri – Lessons from a Meta-Analysis Gnotobiotic IL-10 mice generated by broad-spectrum antibiotic compounds were perorally of Murine Infection Studies. PLoS ONE 11(7): infected with A. butzleri (strains CCUG 30485 or C1), C. jejuni (strain 81-176) or a commensal e0159685. doi:10.1371/journal.pone.0159685 intestinal E. coli strain. Either strain stably colonized the murine intestines upon infection. At Editor: Sergei Grivennikov, Fox Chase Cancer day 6 postinfection (p.i.), C. jejuni infected mice only displayed severe clinical sequelae such Center, UNITED STATES as wasting bloody diarrhea. Gross disease was accompanied by increased numbers of Received: March 10, 2016 colonic apoptotic cells and distinct immune cell populations including macrophages and Accepted: July 5, 2016 monocytes, T and B cells as well as regulatory T cells upon pathogenic infection. Whereas A.
  • Toll-Like Receptor-4 Dependent Small Intestinal Immune Responses Following Murine Arcobacter Butzleri Infection

    Toll-Like Receptor-4 Dependent Small Intestinal Immune Responses Following Murine Arcobacter Butzleri Infection

    European Journal of Microbiology and Immunology 5 (2015) 4, pp. 333–342 Original article DOI: 10.1556/1886.2015.00042 TOLL-LIKE RECEPTOR-4 DEPENDENT SMALL INTESTINAL IMMUNE RESPONSES FOLLOWING MURINE ARCOBACTER BUTZLERI INFECTION Markus M. Heimesaat1,*, Gül Karadas2, André Fischer1, Ulf B. Göbel1, Thomas Alter2, Stefan Bereswill1, Greta Gölz2 1 Department of Microbiology and Hygiene, Charité – University Medicine Berlin, Berlin, Germany 2 Institute of Food Hygiene, Freie Universität Berlin, Berlin, Germany Received: October 27, 2015; Accepted: November 3, 2015 Sporadic cases of gastroenteritis have been attributed to Arcobacter butzleri infection, but information about the underlying im- munopathological mechanisms is scarce. We have recently shown that experimental A. butzleri infection induces intestinal, ex- traintestinal and systemic immune responses in gnotobiotic IL-10−/− mice. The aim of the present study was to investigate the immunopathological role of Toll-like Receptor-4, the receptor for lipopolysaccharide and lipooligosaccharide of Gram-negative bacteria, during murine A. butzleri infection. To address this, gnotobiotic IL-10−/− mice lacking TLR-4 were generated by broad- spectrum antibiotic treatment and perorally infected with two different A. butzleri strains isolated from a patient (CCUG 30485) or fresh chicken meat (C1), respectively. Bacteria of either strain stably colonized the ilea of mice irrespective of their genotype at days 6 and 16 postinfection. As compared to IL-10−/− control animals, TLR-4−/− IL-10−/− mice were protected from A. butzleri-induced ileal apoptosis, from ileal influx of adaptive immune cells including T lymphocytes, regulatory T-cells and B lymphocytes, and from increased ileal IFN-γ secretion. Given that TLR-4-signaling is essential for A.
  • 1 Microbial Transformations of Organic Chemicals in Produced Fluid From

    1 Microbial Transformations of Organic Chemicals in Produced Fluid From

    Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem.
  • Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter

    Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter

    182 ORIGINAL ARTICLE Identification by 16S ribosomal RNA gene sequencing of Mol Path: first published as 10.1136/mp.55.3.182 on 1 June 2002. Downloaded from Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis SKPLau,PCYWoo,JLLTeng, K W Leung, K Y Yuen ............................................................................................................................. J Clin Pathol: Mol Pathol 2002;55:182–185 Aims: To identify a strain of Gram negative facultative anaerobic curved bacillus, concomitantly iso- lated with Escherichia coli and Streptococcus milleri, from the blood culture of a 69 year old woman with acute gangrenous appendicitis. The literature on arcobacter bacteraemia and arcobacter infections associated with appendicitis was reviewed. Methods: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR prod- uct was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence align- ment. Literature review was performed by MEDLINE search (1966–2000). Results: The bacterium grew on blood agar, chocolate agar, and MacConkey agar to sizes of 1 mm in diameter after 24 hours of incubation at 37°C in 5% CO2. It grew at 15°C, 25°C, and 37°C; it also grew in a microaerophilic environment, and was cytochrome oxidase positive and motile, typically a member of the genus arcobacter. Furthermore, phenotypic testing showed that the biochemical profile See end of article for of the isolate did not fit into the pattern of any of the known arcobacter species.
  • Complete Genome Sequence of Arcobacter Nitrofigilis Type Strain (CIT)

    Complete Genome Sequence of Arcobacter Nitrofigilis Type Strain (CIT)

    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Permalink https://escholarship.org/uc/item/4kk473v4 Journal Standards in genomic sciences, 2(3) ISSN 1944-3277 Authors Pati, Amrita Gronow, Sabine Lapidus, Alla et al. Publication Date 2010-06-15 DOI 10.4056/sigs.912121 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:300-308 DOI:10.4056/sigs.912121 Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) Amrita Pati1, Sabine Gronow3, Alla Lapidus1, Alex Copeland1, Tijana Glavina Del Rio1, Matt Nolan1, Susan Lucas1, Hope Tice1, Jan-Fang Cheng1, Cliff Han1,2, Olga Chertkov1,2, David Bruce1,2, Roxanne Tapia1,2, Lynne Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1,2, Manfred Rohde6, Markus Göker3, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Hans-Peter Klenk3, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. Kyrpides Keywords: symbiotic, Spartina alterniflora Loisel, nitrogen fixation, micro-anaerophilic, mo- tile, Campylobacteraceae, GEBA Arcobacter nitrofigilis (McClung et al.
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

    The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
  • Aliarcobacter Butzleri from Water Poultry: Insights Into Antimicrobial Resistance, Virulence and Heavy Metal Resistance

    Aliarcobacter Butzleri from Water Poultry: Insights Into Antimicrobial Resistance, Virulence and Heavy Metal Resistance

    G C A T T A C G G C A T genes Article Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance Eva Müller, Mostafa Y. Abdel-Glil * , Helmut Hotzel, Ingrid Hänel and Herbert Tomaso Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 07743 Jena, Germany; Eva.Mueller@fli.de (E.M.); Helmut.Hotzel@fli.de (H.H.); [email protected] (I.H.); Herbert.Tomaso@fli.de (H.T.) * Correspondence: Mostafa.AbdelGlil@fli.de Received: 28 July 2020; Accepted: 16 September 2020; Published: 21 September 2020 Abstract: Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases.