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Evaluation of MALDI Biotyper for Identification of Taylorella Equigenitalis and Taylorella Asinigenitalis Kristina Lantz Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis Kristina Lantz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons, and the Veterinary Medicine Commons Recommended Citation Lantz, Kristina, "Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis" (2017). Graduate Theses and Dissertations. 16520. https://lib.dr.iastate.edu/etd/16520 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis by Kristina Lantz A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Microbiology Program of Study Committee: Ronald Griffith, Major Professor Steve Carlson Matthew Erdman Timothy Frana The student author and the program of study committee are solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit -
Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: the Case of Bovine Digital Dermatitis
antibiotics Article Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis Ashenafi F. Beyi 1 , Alan Hassall 2, Gregory J. Phillips 1 and Paul J. Plummer 1,2,3,* 1 Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; [email protected] (A.F.B.); [email protected] (G.J.P.) 2 Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA; [email protected] 3 National Institute of Antimicrobial Resistance Research and Education, Ames, IA 50010, USA * Correspondence: [email protected] Abstract: Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution Citation: Beyi, A.F.; Hassall, A.; ≥ Phillips, G.J.; Plummer, P.J. Tracking using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with 80% complete Reservoirs of Antimicrobial genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring Resistance Genes in a Complex resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin Microbial Community Using were identified along with their bacterial hosts. -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. 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 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. -
Development of a PCR-Based Method for Monitoring the Status of Alcaligenes Species in the Agricultural Environment
Biocontrol Science, 2014, Vol. 19, No. 1, 23-31 Original Development of a PCR-Based Method for Monitoring the Status of Alcaligenes Species in the Agricultural Environment MIYO NAKANO1, MASUMI NIWA2, AND NORIHIRO NISHIMURA1* 1 Department of Translational Medical Science and Molecular and Cellular Pharmacology, Pharmacogenomics, and Pharmacoinformatics, Mie University Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan 2 DESIGNER FOODS. Co., Ltd. NALIC207, Chikusa 2-22-8, Chikusa-ku, Nagoya, Aichi 464-0858, Japan Received 1 April, 2013/Accepted 14 September, 2013 To analyze the status of the genus Alcaligenes in the agricultural environment, we developed a PCR method for detection of these species from vegetables and farming soil. The selected PCR primers amplified a 107-bp fragment of the 16S rRNA gene in a specific PCR assay with a detection limit of 1.06 pg of pure culture DNA, corresponding to DNA extracted from approxi- mately 23 cells of Alcaligenes faecalis. Meanwhile, PCR primers generated a detectable amount of the amplicon from 2.2×102 CFU/ml cell suspensions from the soil. Analysis of vegetable phyl- loepiphytic and farming soil microbes showed that bacterial species belonging to the genus Alcaligenes were present in the range from 0.9×100 CFU per gram( or cm2)( Japanese radish: Raphanus sativus var. longipinnatus) to more than 1.1×104 CFU/g( broccoli flowers: Brassica oleracea var. italic), while 2.4×102 to 4.4×103 CFU/g were detected from all soil samples. These results indicated that Alcaligenes species are present in the phytosphere at levels 10–1000 times lower than those in soil. -
Middle Ear Microbiome Differences in Indigenous Filipinos with Chronic Otitis Media Due to a Duplication in the A2ML1 Gene Regie Lyn P
Santos-Cortez et al. Infectious Diseases of Poverty (2016) 5:97 DOI 10.1186/s40249-016-0189-7 SHORT REPORT Open Access Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene Regie Lyn P. Santos-Cortez1,9*, Diane S. Hutchinson2, Nadim J. Ajami2, Ma. Rina T. Reyes-Quintos3,4, Ma. Leah C. Tantoco3, Patrick John Labra4, Sheryl Mae Lagrana3, Melquiadesa Pedro3,ErasmoGonzalod.V.Llanes3,4, Teresa Luisa Gloria-Cruz3,4, Abner L. Chan3,4,EvaMariaCutiongco-delaPaz5,6, John W. Belmont7,10, Tasnee Chonmaitree8, Generoso T. Abes3,4, Joseph F. Petrosino2, Suzanne M. Leal1 and Charlotte M. Chiong3,4 Abstract Background: Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access. Methods: Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the A2ML1 duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing. Results: Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus Fusobacterium were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including Oligella that was reported only once in the middle ear. -
Using Culture Independent Approaches to Gain Insights Into Human Urinary Tract Microbiome in Healthy Male and Female Individuals
The American University in Cairo School of Sciences and Engineering Using Culture Independent Approaches to Gain Insights Into Human Urinary Tract Microbiome in Healthy Male and Female individuals A Thesis Submitted to Biotechnology graduate program In partial fulfilment of the requirements for the degree of Master of Science By Sarah Hussein El-Alawi Under the supervision of Dr. Hamza El-Dorry January / 2012 The American University in Cairo Using Culture Independent Approaches to Gain Insights into Human Urinary Tract Microbiome in Healthy Male and Female individuals A Thesis Submitted by Sarah Hussein El-Alawi To the Biotechnology Graduate Program January / 2012 In partial fulfilment of the requirements for The degree of Master of Science Has been approved by Thesis Committee Supervisor/Chair _______________________________________________ Affiliation ____________________________________________________________________ Thesis Committee Reader/Examiner ______________________________________________ Affiliation ____________________________________________________________________ Thesis Committee Reader/Examiner ______________________________________________ Affiliation ____________________________________________________________________ Thesis Committee Reader/External Examiner _______________________________________ Affiliation ____________________________________________________________________ ____________________ _____________ ___________________ _______________ Director Date Dean Date ii DEDICATION This work is dedicated to my parents -
S1. the Genomes of the Order Burkholderiales (Taxid:80840) in The
S1. The genomes of the order Burkholderiales (taxid:80840) in the NCBI Genome List (http://www.ncbi.nlm.nih.gov/genome/browse/) 05-09-2014 N Organism/Name Kingdom Group SubGroup Size (Mb) Chr Plasmids Assemblies 1. Burkholderiales bacterium JGI 0001003-L21 Bacteria Proteobacteria Betaproteobacteria 0,070281 - - 1 2. Comamonadaceae bacterium JGI 0001003-E14 Bacteria Proteobacteria Betaproteobacteria 0,113075 - - 1 3. Candidatus Zinderia insecticola Bacteria Proteobacteria Betaproteobacteria 0,208564 1 - 1 4. Comamonadaceae bacterium JGI 0001013-A16 Bacteria Proteobacteria Betaproteobacteria 0,295955 - - 1 5. Oxalobacteraceae bacterium JGI 0001004-J12 Bacteria Proteobacteria Betaproteobacteria 0,301938 - - 1 6. Oxalobacteraceae bacterium JGI 0001002-K6 Bacteria Proteobacteria Betaproteobacteria 0,368093 - - 1 7. Burkholderiales bacterium JGI 0001003-J08 Bacteria Proteobacteria Betaproteobacteria 0,394907 - - 1 8. Burkholderiales bacterium JGI 0001002-H06 Bacteria Proteobacteria Betaproteobacteria 0,415398 - - 1 9. Pelomonas Bacteria Proteobacteria Betaproteobacteria 0,507844 - - 2 10. Leptothrix ochracea Bacteria Proteobacteria Betaproteobacteria 0,510792 - - 1 11. Oxalobacteraceae bacterium JGI 0001012-C15 Bacteria Proteobacteria Betaproteobacteria 0,640975 - - 1 12. Burkholderiales bacterium JGI 0001003-A5 Bacteria Proteobacteria Betaproteobacteria 0,686115 - - 1 13. Oxalobacteraceae bacterium JGI 001010-B17 Bacteria Proteobacteria Betaproteobacteria 0,825556 - - 1 14. Rhizobacter Bacteria Proteobacteria Betaproteobacteria 1,05799 - - -
Design and Implementation of Degenerate Qpcr/Qrt-PCR Primers to Detect Microbial Nitrogen Metabolism in Wastewater and Wastewater-Related Samples
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School August 2019 Design and Implementation of Degenerate qPCR/qRT-PCR Primers to Detect Microbial Nitrogen Metabolism in Wastewater and Wastewater-Related Samples Ryan F. Keeley University of South Florida Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Ecology and Evolutionary Biology Commons, Environmental Sciences Commons, and the Microbiology Commons Scholar Commons Citation Keeley, Ryan F., "Design and Implementation of Degenerate qPCR/qRT-PCR Primers to Detect Microbial Nitrogen Metabolism in Wastewater and Wastewater-Related Samples" (2019). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/7826 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Design and Implementation of Degenerate qPCR/qRT-PCR Primers to Detect Microbial Nitrogen Metabolism in Wastewater and Wastewater-Related Samples by Ryan F. Keeley A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology with a concentration in Environmental and Ecological Microbiology Department of Integrative Biology College of Arts and Sciences University of South Florida Major Professor: Kathleen Scott, Ph. D. Sarina Ergas, Ph. D. Valerie Harwood, Ph. D. Date of Approval: June 24, 2019 Keywords: Degenerate Primer, amoA, nxrB, nosZ, nitrification, denitrification, Photo- sequencing batch reactor, qPCR, qRT-PCR Copyright © 2019, Ryan F. Keeley TABLE OF CONTENTS List of Tables ................................................................................................................................. iv List of Figures ................................................................................................................................ -
Oligella Urethralis Comb
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1987, p. 198-210 Vol. 37, No. 3 0020-7713/87/030198-13$02 .OO/O Copyright 0 1987, International Union of Microbiological Societies Oligella, a New Genus Including Oligella urethralis comb. nov. (Formerly Moraxella urethralis) and Oligella ureolytica sp. nov. (Formerly CDC Group IVe): Relationship to Taylorella equigenitalis and Related Taxa R. ROSSAU,l K. KERSTERS,l E. FALSEN,* E. JANTZEN,3 P. SEGERS,l A. UNION,l L. NEHLS,2 AND J. DE LEY1* Laboratorium voor Microbiologie en Microbiele Genetica, Rijksuniversiteit, B-9000, Ghent, Belgium’; Culture Collection, Department of Clinical Bacteriology, University of Goteborg, S-41346 Giiteborg, Sweden2; and Department of Methodology, National Institute of Public Health, Oslo, Norway3 The taxonomic relationships of Moraxella urethralis, the Centers for Disease Control (CDC) group IVe, Tayldrellu equigenitalis, and other grambnegative bacteria were studied by deoxyribonucleic acid (DNA)-DNA polyacrylamide gel electrophoresis of cellular proteins, and serological, biochemical, and auxanographic anrilyses. A high relationship was detected between M. urethralis and the CDC group IVe strains. However, no relationship of M. urethralis and CDC group IVe with genuine Moraxella species was obsek-ved. We describe a new genus, Oligella, containing two species: Oligella urethralis (to accommodate Moraxella urethralis) and Oligella ureolytica (to accommodate CDC group IVe strains). The type species is Oligella urethralis, with type strain ATCC 17960T. The type strain of Oligella ureolytica is CDC C379 (ATCC 43534, CCUG 1465, LMG 6519). Oligella is a member of rRNA superfamily 111, containing, e.g., the Pseudomonas acidovorans and Pseudomonas solandcearum complexes and Chromdbacterium, Janthisobacterium, and Neisseria species. The closest relatives of Oligella species are Taylorella equigenitalis and the Alcaligenaceae family. -
Purple Bacteria and Their Relatives”
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1988, p. 321-325 Vol. 38, No. 3 0020-7713/88/03032 1-05$02.OOtO Copyright 0 1988, International Union of Microbiological Societies Proteobacteria classis nov. a Name for the Phylogenetic Taxon That Includes the “Purple Bacteria and Their Relatives” E. STACKEBRANDT,l R. G. E. MURRAY,2* AND H. G. TRUPER3 Lehrstuhl fur Allgemeine Mikrobiologie, Biologiezentrum, Christian-Albrechts Universitat, 2300 Kid, Federal Republic of Germany’; Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C12; and Institut fur Mikrobiulogie, Universitat Bonn, 5300 Bonn I, Federal Republic of Germany3 Proteobacteria classis nov. is suggested as the name for a new higher taxon to circumscribe the a, p, y, and 6 groups that are included among the phylogenetic relatives of the purple photosynthetic bacteria and as a suitable collective name for reference to that group. The group names (alpha, etc.) remain as vernacular terms at the level of subclass pending further studies and nomenclatural proposals. Phylogenetic interpretations derived from the study of the interim while the phylogenetic data are being integrated ribosomal ribonucleic acid (rRNA) sequences and oligonu- into formal bacterial taxonomy. It does not appear to be cleotide catalogs provide an important factual base for inappropriate or confusing to use the protean prefix because arrangements of higher taxa of bacteria (25, 26). A recent of the genus Proteus among the Proteobacteria; the reasons workshop organized by the International Committee on for use are clear enough. Systematic Bacteriology recognized that a particularly di- This new class is so far only definable in phylogenetic verse but related group of gram-negative bacteria, including terms. -
ID 11 | Issue No: 3 | Issue Date: 03.02.15 | Page: 1 of 28 © Crown Copyright 2015 Identification of Moraxella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Moraxella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 11 | Issue no: 3 | Issue date: 03.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Moraxella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 11 | Issue no: 3 | Issue date: 03.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Moraxella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Bacteria Recovered from Aquaculture in Oman, With
BACTERIA RECOVERED FROM AQUACULTURE IN OMAN, WITH EMPHASIS ON AEROMONAS SPP. THESIS SUMITTED TO THE UNIVERSITY OF STIRLING FOR THE DEGREE OF DOCTOR OF PHILOSOPHY BY ALYA SALIM AL-GHABSHI APRIL 2015 INSTITUTE OF AQUACULTURE DECLARATION I hereby declare that the work and results presented in this thesis were conducted by me at the Institute of Aquaculture, University of Stirling, Scotland. The work presented in this thesis has not been previously submitted for any other degree or qualification. The litera- ture consulted has been cited and where appropriate, collaborative assistance has been acknowledged. Signature: ________________________________________ Signature of Principal Supervisor: ________________________________________ Signature of Supervisor: ________________________________________ Date: ________________________________________ I In loving memory of my mother To my husband Hamood Al-Ghabshi and My lovely sons Yousuf and Mohammed II Acknowledgements ACKNOWLEDGEMENTS First of all, I would like to thank the almighty Allah for helping me to finish my study successfully. I would like to express my warmest gratitude to my supervisor’s and mentors Professor Brian Austin and Dr. Mags Crumlish, who has introduced me to the world of science. Their support and guidance gave me to find out the way to continue my research in the field and laboratory. During writing up this thesis, their valuable comments, suggestions, excellent proofreading skills and encouragement helped me to complete this work with the incredible optimism. I am also extremely grateful for the assistance and guidance from Dr. Ponnerassery S. Sudheesh and from staff members at the Institute of Aquaculture (stirling) particularly, Mrs. Debbie Faichney, Mrs. Jan Seggie, Dr. John Taggart, Mrs. Jacquie Ireland, Mr.