DOCSLIB.ORG

Hongia Gen. Nov., a New Genus of the Order Actinomycetales

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Hongia Gen. Nov., a New Genus of the Order Actinomycetales International Journal of Systematic and Evolutionary Microbiology (2000), 50, 191–199 Printed in Great Britain Hongia gen. nov., a new genus of the order Actinomycetales Soon Dong Lee, Sa-Ouk Kang and Yung Chil Hah Author for correspondence: Yung Chil Hah. Tel: ­82 2 880 6700. Fax: ­82 2 888 4911. e-mail: hahyungc!snu.ac.kr Department of An aerobic, nocardioform actinomycete, named LM 161T, was isolated from a Microbiology, College of soil sample obtained from a gold mine in Kongiu, Republic of Korea. This Natural Sciences and Research Center for organism formed well-differentiated aerial and substrate mycelia and Molecular Microbiology, produced branched hyphae that fragmented into short or elongated rods. The Seoul National University, cell wall contains major amounts of LL-diaminopimelic acid, alanine, glycine, Seoul 151-742, Republic of Korea glutamic acid, mannose, glucose, galactose, ribose and acetyl muramic acid. The major phospholipids of this isolate are phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and the major isoprenologue is a tetrahydrogenated menaquinone with nine isoprene units. The whole-cell hydrolysate of strain LM 161T contains 12- methyltetradecanoic and 14-methylpentadecanoic acids as the predominant fatty acids, but does not contain mycolic acids. The GMC content of the DNA is 71<3 mol%. The phylogenetic position of the test strain was investigated using an almost complete 16S rDNA sequence. The isolate formed the deepest branch in the clade encompassing the members of the suborder Propionibacterineae Rainey et al. 1997. On the basis of chemical, phenotypic and genealogical data, it is proposed that this isolate be classified within a new genus as Hongia koreensis gen. nov., sp. nov. in the order Actinomycetales. The type strain is LM 161T (¯ IMSNU 50530T). Keywords: Hongia gen. nov., actinomycetes, Propionibacterineae, phylogeny INTRODUCTION Luteococcus (Tamura et al., 1994), Microlunatus (Nakamura et al., 1995), Propioniferax (Yokota et al., Phylogenetic analysis based on 16S rDNA (rDNA) 1994) and Propionibacterium (Cummins & Johnson, sequence data is currently one of the most effective 1986). The recently described genus Friedmanniella methods for the delineation of bacteria. The suborder (Schumann et al., 1997) was shown to be a new Propionibacterineae Rainey et al. (Stackebrandt et al., member of the family Propionibacteriaceae. All of the 1997) of the order Actinomycetales (Buchanan) members, except for the genus Propionibacterium Stackebrandt et al. (Stackebrandt et al., 1997) encom- (Cummins & Johnson, 1986), possess cell wall peptido- passes the type family Propionibacteriaceae (Delwiche) glycan based on -diaminopimelic acid (-DAP) as Rainey et al. (Stackebrandt et al., 1997) and the family the diagnostic diamino acid and exhibit a range of cell Nocardioidaceae (Nesterenko et al.) Rainey et al. morphology from coccus- or rod-shaped forms to (Stackebrandt et al., 1997), on the basis of 16S rDNA nocardioforms. Recently, the phylogenetic relation- studies. The family Nocardioidaceae contains the ship between members of the family Nocardioidaceae genera Aeromicrobium (Miller et al., 1991; Tamura & and related taxa was re-evaluated on the basis of 16S Yokota, 1994) and Nocardioides (Collins et al., 1989, rDNA sequence comparisons (Yoon et al., 1998). 1994; O’Donnell et al., 1982a; Prauser, 1976, 1984). The family Propionibacteriaceae contains the genera In addition, the following -DAP-containing actino- mycete genera, which belong to other phylogenetic ................................................................................................................................................. lineages (Stackebrandt et al., 1997), have been Abbreviations: LL-DAP, LL-diaminopimelic acid; ISP, International described: Streptomyces (Williams et al., 1989), Streptomyces Project. Sporichthya (Rainey et al., 1993), Kineosporia (Itoh et The EMBL accession number for the 16S rDNA sequence of strain LM 161T al., 1989), Intrasporangium (Kalakoutskii et al., 1967), is Y09159. Terrabacter (Collins et al., 1989) and Terracoccus 01146 # 2000 IUMS 191 S. D. Lee, S.-O. Kang and Y. C. Hah (Prauser et al., 1997). The members of the suborder Catalase activity was determined by the production of Propionibacterineae are readily differentiated from bubbles after the addition of a drop of 3% (v}v) hydrogen each other and from the other -DAP-containing peroxide solution on to a slide. Growth was tested over a genera mentioned above by a combination of mor- range of temperatures (10–45 mC) and pH values (5–10). phological, physiological and chemotaxonomic Nitrate reduction, urease activity, hydrogen sulfide pro- duction, decomposition of hippurate and hydrolysis of properties (Prauser et al., 1997; Schumann et al., arbutin, casein, aesculin, gelatin and starch were tested as 1997). described by Mac Faddin (1980). Hydrolysis of the DNA During the taxonomic study of soil actinomycetes was determined using Bacto DNase test agar (Difco). T from natural environments, strain LM 161 (T ¯ type Pectinolytic activity was examined according to the method strain) was isolated from a gold-mine cave in Kongju, of Hankin et al. (1971). Acid production from carbohydrates Republic of Korea. Strain LM 161T contained - was determined by means of a colour change from green to yellow in Bacto OF basal medium (Difco). The utilization of DAP as the diagnostic diamino acid in the peptido- organic acids as carbon sources and the decomposition of glycan, and the substrate- and aerial mycelia showed adenine, hypoxanthine, -tyrosine and xanthine were a tendency to fragment. In this work, we have de- examined using previously described methods (Gordon et termined the taxonomic and phylogenetic position of al., 1974). The utilization of carbohydrates as the sole the isolate by examining its morphological, physio- carbon source was studied according to the method of logical and chemotaxonomic properties and by ana- Pridham & Gottlieb (1948). NaCl-tolerance studies were lysing its 16S rDNA. Our results indicate that the performed on nutrient agar containing NaCl at final isolate should be placed in a new species of a novel concentrations of 3, 5, 7 and 10% (w}v). Susceptibility to genus, for which the name Hongia koreensis is antibiotics and chemical inhibitors was determined as proposed. Strain LM 161T has been deposited in the described previously (Williams et al., 1983). To determine sensitivity to lysozyme, a 0±1% solution of lysozyme was Culture Collection Centre of the Institute of Micro- sterilized by membrane filtration and added to nutrient agar biology, Seoul National University (IMSNU) as strain T at a final concentration of 0±01%. Antimicrobial activity was IMSNU 50530 . tested for nine target organisms by using the overlay technique of Williams et al. (1983). METHODS Cell wall analysis. Purified cell wall peptidoglycan was Micro-organisms and culture conditions. Strain LM 161T was prepared according to the method of Yamada & Komagata isolated, using the dilution plating method, from soil (1972) and its amino acid composition was analysed by two- collected at a gold-mine cave in Kongju, Republic of Korea. dimensional, ascending TLC on cellulose plates by using the The soil suspensions were pretreated at 30 mC for 20 min solvent systems described previously (Schleifer & Kandler, before plating (Lee, 1996). The medium used for selective 1972). The molar ratio of amino acids was determined by isolation was a tap-water agar (pH 7 0) supplemented with GC of N-heptafluorobutyryl amino acid isobutyl esters " ± " 50 g cycloheximide ml− and 50 g nystatin ml− . After the (O’Donnell et al., 1982b). The isomers of diaminopimelic purity had been checked, the organism was subcultured on acid were determined according to the method of Staneck & yeast extract}malt extract agar [medium 2 of the Inter- Roberts (1974). Cell wall sugars as alditol acetates were national Streptomyces Project (ISP)] (Shirling & Gottlieb, determined by GC (Saddler et al., 1991). GC analyses were 1966) at 28 mC. The following reference strains were used performed with a Hewlett Packard model HP5890A gas to compare chemotaxonomic properties: Aeromicrobium chromatograph equipped with a flame-ionization detector erythreum DSM 8599T, Aeromicrobium fastidiosum IFO and integrator. The acyl type of the cell wall was determined 14987T, Nocardioides albus IFO 13917T, Nocardioides jensenii using the colorimetric method of Uchida & Aida (1984). T T KCTC 9134 , Nocardioides luteus IFO 14491 , Nocardioides Lipid analysis. T T Cellular fatty acid methyl esters were prepared simplex IFO 12069 , Luteococcus japonicus IFO 12422 , from cells grown on yeast extract}glucose broth at 30 mC for Microlunatus phosphovorus JCM 9379T, Propioniferax T T 3 d by alkaline methanolysis (Minnikin, 1988) and were innocua DSM 8251 and Kineosporia aurantiaca IFO 13890 . analysed with a Hewlett Packard model 5890A gas Morphological and cultural characteristics. Growth and chromatograph equipped with a SPB-1 fused silica capillary morphology were examined by using the ISP media de- column (0±25 mm¬30 m; Supelco). The column tempera- scribed by Shirling & Gottlieb (1966) and the media ture was programmed according to the manufacturer’s described by Waksman (1961). The formation of melanin instructions. The fatty acid methyl esters were identified by was investigated on peptone}yeast extract}iron agar (ISP comparison with the Bacterial Acid Methyl Ester CP MIX medium 6) and
Load more

Recommended publications
  • Aestuariimicrobium Ganziense Sp. Nov., a New Gram-Positive Bacterium Isolated from Soil in the Ganzi Tibetan Autonomous Prefecture, China
    Aestuariimicrobium ganziense sp. nov., a new Gram-positive bacterium isolated from soil in the Ganzi Tibetan Autonomous Prefecture, China Yu Geng Yunnan University Jiang-Yuan Zhao Yunnan University Hui-Ren Yuan Yunnan University Le-Le Li Yunnan University Meng-Liang Wen yunnan university Ming-Gang Li yunnan university Shu-Kun Tang ( [email protected] ) Yunnan Institute of Microbiology, Yunnan University https://orcid.org/0000-0001-9141-6244 Research Article Keywords: Aestuariimicrobium ganziense sp. nov., Chemotaxonomy, 16S rRNA sequence analysis Posted Date: February 11th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-215613/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Archives of Microbiology on March 12th, 2021. See the published version at https://doi.org/10.1007/s00203-021-02261-2. Page 1/11 Abstract A novel Gram-stain positive, oval shaped and non-agellated bacterium, designated YIM S02566T, was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23–35°C (optimum, 30°C) in the presence of 0.5-4 % (w/v) NaCl (optimum, 1%) and at pH 7.0–8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27T and Aestuariimicrobium soli D6T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566T contained LL-diaminopimelic acid in the cell wall.
    [Show full text]
  • Polyamine Profiles Within Genera of the Class Actinobacteria with U-Diaminopimelic Acid in the Peptidoglycan
    International Journal of Systematic Bacteriology (1 999), 49, 179-1 84 Printed in Great Britain Polyamine profiles within genera of the class NOTE Actinobacteria with u-diaminopimelic acid in the peptidoglycan Hans-Jurgen Busse't and Peter Schumann2 Author for correspondence: Hans-Jurgen Busse. Tel: +43 1 25077 2128. Fax: +43 1 25077 2190. e-mail : Hans-Juergen. Busse @vu-wien.ac.at 1 Institute of Microbiology Polyamine patterns of coryne- and nocardioform representatives of the class and Genetics, University of Actinobacteria with u-diaminopimelic acid in the peptidoglycan, comprising Vienna, A-1030 Vienna, Austria strains of the genera A eromicrobium, Nocardioides, In trasporangium, Terrabacter, Terracoccus, Propioniferax, Friedmanniella, Microlunatus, * DSMZ-German Collection of Microorganisms and Luteococcus and Sporichthya, were analysed. The different polyamine patterns Cell Cultures GmbH, were in good agreement with the phylogenetic heterogeneity within this D-07745 Jena, Germany group of actinomycetes. Strains of the closely related genera Nocardioides and Aeromicrobium were characterized by the presence of cadaverine. The second cluster, consisting of the type strains of the species Friedmanniella antarctica, Propioniferax innocua, Microlunatus phosphovorus and Luteococcus japonicus, displayed as a common feature the presence of the two predominant compounds spermidine and spermine. The presence of putrescine was common to the type strains of the species Intrasporangium calvum, Terrabacter tumescens and Terracoccus luteus. Sporichthyapolymotpha,
    [Show full text]
  • International Code of Nomenclature of Prokaryotes
    2019, volume 69, issue 1A, pages S1–S111 International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision) Charles T. Parker1, Brian J. Tindall2 and George M. Garrity3 (Editors) 1NamesforLife, LLC (East Lansing, Michigan, United States) 2Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) 3Michigan State University (East Lansing, Michigan, United States) Corresponding Author: George M. Garrity ([email protected]) Table of Contents 1. Foreword to the First Edition S1–S1 2. Preface to the First Edition S2–S2 3. Preface to the 1975 Edition S3–S4 4. Preface to the 1990 Edition S5–S6 5. Preface to the Current Edition S7–S8 6. Memorial to Professor R. E. Buchanan S9–S12 7. Chapter 1. General Considerations S13–S14 8. Chapter 2. Principles S15–S16 9. Chapter 3. Rules of Nomenclature with Recommendations S17–S40 10. Chapter 4. Advisory Notes S41–S42 11. References S43–S44 12. Appendix 1. Codes of Nomenclature S45–S48 13. Appendix 2. Approved Lists of Bacterial Names S49–S49 14. Appendix 3. Published Sources for Names of Prokaryotic, Algal, Protozoal, Fungal, and Viral Taxa S50–S51 15. Appendix 4. Conserved and Rejected Names of Prokaryotic Taxa S52–S57 16. Appendix 5. Opinions Relating to the Nomenclature of Prokaryotes S58–S77 17. Appendix 6. Published Sources for Recommended Minimal Descriptions S78–S78 18. Appendix 7. Publication of a New Name S79–S80 19. Appendix 8. Preparation of a Request for an Opinion S81–S81 20. Appendix 9. Orthography S82–S89 21. Appendix 10. Infrasubspecific Subdivisions S90–S91 22. Appendix 11. The Provisional Status of Candidatus S92–S93 23.
    [Show full text]
  • .~
    .6 I ï ,32 CJx University Free State 1111111111111111111111 ~I~~I~I!~I~~~~II!~JI~~II~111111111111111111 Universiteit Vrystaat GFE ()', "\ !DIGHEDE LJ'T IlIF -_.~------------RfRUOTé.U U<\vYDER WO o I'tJl£ A TAXONOMIC RE-EVALUATION OF 66 Propionibacterium coccoides" by JANINE VAN NIEUWHOL TZ Submitted in fulfilment of the requirements for the degree of MASTER OF SCIENCE in the Department of Microbiology and Biochemistry, Faculty of Natural Science University of the Orange Free State Bloemfontein, South Africa Promotor: Dr. K-H.J. Riedel Co-promotor: Prof. Dr. B.D. Wingfield November 1998 To my parents, especially my mother OTE K "It is, however, important to realise that species are entities created by man to group organisms into, and that these groupings are based on hypotheses which are subject to continual re-evaluation" K-H.J. Riedel (1996) Acknowledgements I wish to express my sincere gratitude and appreciation to the following persons for their contributions to the successful completion of this study: Or. K-I-I.J. Riedel, Department of Microbiology and Biochemistry, University of the Orange Free State, for his adequate guidance, continual patience and for his valuable and constructive criticism of the manuscript; Prof. B.D. Wingfield, Department of Genetics, University of Pretoria, for her advice and for granting a post-graduate bursary through the Foundation of Research Development; Prof. L.I. Vorobjeva, Department of Microbiology, Moscow State University, Russia, for the two "Propionibacterium coccoides" strains and sincere interest throughout this study; Prof. LP. van der Walt, Department of Microbiology and Biochemistry, University of the Orange Free State, for his invaluable assistance in the nomenclature of the two "P.
    [Show full text]
  • Abstract Tracing Hydrocarbon
    ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.
    [Show full text]
  • Systematic Research on Actinomycetes Selected According
    Systematic Research on Actinomycetes Selected according to Biological Activities Dissertation Submitted in fulfillment of the requirements for the award of the Doctor (Ph.D.) degree of the Math.-Nat. Fakultät of the Christian-Albrechts-Universität in Kiel By MSci. - Biol. Yi Jiang Leibniz-Institut für Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Düsternbrooker Weg 20, D-24105 Kiel, Germany Supervised by Prof. Dr. Johannes F. Imhoff Kiel 2009 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: ______________________ Tag der mündlichen Prüfung: Kiel, ____________ Zum Druck genehmigt: Kiel, _____________ Summary Content Chapter 1 Introduction 1 Chapter 2 Habitats, Isolation and Identification 24 Chapter 3 Streptomyces hainanensis sp. nov., a new member of the genus Streptomyces 38 Chapter 4 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae 52 Chapter 5 A new member of the family Micromonosporaceae, Planosporangium flavogriseum gen nov., sp. nov. 67 Chapter 6 Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea 87 Chapter 7 Discussion 99 Appendix a Resume, Publication list and Patent 115 Appendix b Medium list 122 Appendix c Abbreviations 126 Appendix d Poster (2007 VAAM, Germany) 127 Appendix e List of research strains 128 Acknowledgements 134 Erklärung 136 Summary Actinomycetes (Actinobacteria) are the group of bacteria producing most of the bioactive metabolites. Approx. 100 out of 150 antibiotics used in human therapy and agriculture are produced by actinomycetes. Finding novel leader compounds from actinomycetes is still one of the promising approaches to develop new pharmaceuticals. The aim of this study was to find new species and genera of actinomycetes as the basis for the discovery of new leader compounds for pharmaceuticals.
    [Show full text]
  • Summary - Bacterial Systematics
    Bacterial Systematics (bact-sys) 1 Summary - Bacterial Systematics Bacterial Phylogeny - Genotypic Characteristics of Bacteria: Nucleic acids are universally distributed (RNA and chromosomal DNA) and they alone can be used as standards for wide-ranging comparisons. DNA-Analysis: DNA is far more stable than RNA (RNAase rapidly decomposes RNA). • Base Composition (G-C Ratio): Among prokaryotic DNA the ratio of the nucleotide bases adenine (A) plus thiamine (T) to guanine (G) and cytosine (C) varies within the range of 23-78 [mol%]; __[C+G]__ expressed in [mol%]; G+C ratios w/ differences >20-30% among species samples seem less ⋅ 100 [A+T+G+C] closely related; determination of C-G ratio is required in order to establish new taxa. Samples showing 10% - 20% differences should be assigned to the same genus, 5% is the maximum range permissible for same species. A >G+C ratio requires a > temperature to break the DNA-double helix into single strands; G+C is held by 3 H-bonds, whereas A+T has only 2 H-bonds (see genetics). • DNA-Fingerprinting: Via Restriction Fragment Length Polymerization (requires little DNA), the genetic probe is broken by endonucleases into certain fragments. The number and locations of these units / cuts are unique for each genome (includes pattern / groups of these fragments of different size). The cleaved DNA-fragments are amplified via Polymerase Chain Reaction, purified, separated by gel- electrophoresis (larger units by Pulse Field Gel Electrophoresis), and compared with already existing patterns. ERIC-PCR: selected primers are used to amplify specific DNA sequences. RAPD (Random Amplified Polymorphic DNA): Randomly selected primers are used to specify for its existence, and if present, to amplify that particular sequence to be analyzed in gel-electrophoresis.
    [Show full text]
  • These De Doctorat De
    2018 - 14 THESE DE DOCTORAT DE AGROCAMPUS OUEST COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 600 Ecole doctorale Ecologie, Géosciences, Agronomie et Alimentation Spécialité : Biochimie, biologie moléculaire et cellulaire Par Fillipe Luiz ROSA DO CARMO La protéine de couche de surface SlpB assure la médiation de l’immunomodulation et de l’adhésion chez le probiotique Propionibacterium freudenreichii CIRM-BIA 129 Thèse présentée et soutenue à AGROCAMPUS OUEST campus de Rennes, le 6 septembre 2018 Unité de recherche : UMR INRA AGROCAMPUS OUEST Science et Technologie du lait et de l’œuf (STLO) Thèse en Cotutelle : Université Fédérale du Minas Gerais Thèse N° : 2018-14 _ B-315 Rapporteurs avant soutenance : Aristóteles Góes Neto Professeur Université fédérale du Minas Gerais, Brésil. Muriel Thomas Directrice de recherche INRA UMR1319 Micalis, Jouy en Josas. Composition du Jury : Président : Françoise Nau Professeur AGROCAMPUS OUEST-Rennes Examinateurs : Nathalie Desmasures Professeur Université de Caen Normandie, Caen Benoit Foligné Université du Droit et de la Santé Lille 2, Lille Dir. de thèse : Gwénaël Jan Directeur de recherche UMR STLO INRA, Rennes Dir. de thèse : Vasco Azevedo Professeur Université fédérale du Minas Gerais, Brésil. Invité(s) Yves Le Loir Directeur de l’UMR STLO INRA, Rennes Gwennola Ermel Professeur Université de Rennes 1,Rennes UNIVERSIDADE FEDERAL DE MINAS GERAIS INSTITUTO DE CIÊNCIAS BIOLÓGICAS DEPARTAMENTO DE BIOLOGIA GERAL PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA Tese de Doutorado Papel da proteína de superfície SlpB na imunomodulação e adesão da linhagem probiótica Propionibacterium freudenreichii CIRM-BIA 129. Orientado: Fillipe Luiz Rosa do Carmo Orientadores: Prof./Dr. Vasco Ariston de Carvalho Azevedo Dr.
    [Show full text]
  • Computer Assisted Classification and Identification of Actinomycetes
    Computer Assisted Classification and Identification of Actinomycetes Jongsik Chun (B.Sc. Microbiology, Seoul National University, Seoul, Korea) NEWCASTLE UNIVERSITY LIERARY 094 52496 3 Thesis submitted in accordance with the requirements of the University of Newcastle upon Tyne for the Degree of Doctor of Philosophy Department of Microbiology The Medical School Newcastle upon Tyne England-UK July 1995 ABSTRACT Three computer software packages were written in the C++ language for the analysis of numerical phenetic, 16S rRNA sequence and pyrolysis mass spectrometric data. The X program, which provides routines for editing binary data, for calculating test error, for estimating cluster overlap and for selecting diagnostic and selective tests, was evaluated using phenotypic data held on streptomycetes. The AL16S program has routines for editing 16S rRNA sequences, for determining secondary structure, for finding signature nucleotides and for comparative sequence analysis; it was used to analyse 16S rRNA sequences of mycolic acid-containing actinomycetes. The ANN program was used to generate backpropagation-artificial neural networks using pyrolysis mass spectra as input data. Almost complete 1 6S rDNA sequences of the type strains of all of the validly described species of the genera Nocardia and Tsukamurel!a were determined following isolation and cloning of the amplified genes. The resultant nucleotide sequences were aligned with those of representatives of the genera Corynebacterium, Gordona, Mycobacterium, Rhodococcus and Turicella and phylogenetic trees inferred by using the neighbor-joining, least squares, maximum likelihood and maximum parsimony methods. The mycolic acid-containing actinomycetes formed a monophyletic line within the evolutionary radiation encompassing actinomycetes. The "mycolic acid" lineage was divided into two clades which were equated with the families Coiynebacteriaceae and Mycobacteriaceae.
    [Show full text]
  • View Was Conducted in Terms of Cheese Quality and Safety Issues
    The Application of Culture-Independent Methods in Microbial Assessment of Quality and Safety Risk Factors in Swiss Cheese and Oysters Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Qianying Yao, B.S. Graduate Program in Food Science and Technology The Ohio State University 2016 Dissertation Committee: Dr. Hua Wang, advisor Dr. Lynn Knipe Dr. Melvin Pascall Dr. Zhongtang Yu Copyright by Qianying Yao 2016 Abstract Unwanted microorganisms greatly affect the quality and safety of the final food products. For instance, besides foodborne pathogens, quality defects in Swiss cheese ranging from unusual eyes, splits, off-flavors, to off-odors result in an estimated $24 million economic loss annually to the industry. Ohio has the largest Swiss cheese industry in the U.S., and to reveal microbial causative agents in Swiss cheese with quality defects has become a critical need to solve the problem for the industry. While conventional approaches were insufficient to identify the risk factors promptly and accurately, recent advancements in molecular techniques enabled in-depth investigation of potential causative agents and the development of rapid detection method for safety and quality control. To properly assess the split defect associated bacteria in Swiss cheese, a rapid detection platform for propionibacteria in dairy matrices was developed, and the microbial profiles of Swiss cheese with and without split defect were successfully evaluated. Results of these studies contributed to a comprehensive understanding of the microbial cause of split defect in Swiss cheese, enabled culture-independent methods in ii microbial assessment for dairy products, and illustrated the power of 16S metagenomics in improving fundamental understanding of the microbiology in Swiss cheese.
    [Show full text]
  • Bergeys-Manual-Of-Systematic-Bacteriology.-Volume-Five-The
    Gontents ix . .' Prefacetovolume5. xYil Contributors nil On using the Manual Part A I Road map of the phylum Actinobacteria ' ' æ the phylum Actinobacteria ' ' Taxonomic outline of 33 phyl' nov' Phylum XXYI. Actinobacteria 34 . - - Class l. Actinobacteria 35 Order l. ActinomYcetales' ' 36 l. ActinomYcetaceae Family 4i2 Genus l. ActinomYces 1(p Genus ll. Actinobaculum . 1t4 Genus lll. Arcanobacterium 16 lY. Mobiluncus. Genus 139 Genus Y. Varibaculum ord. nov' ldl Order ll. Actinopolysporales 169 Family l. ActinoPolYsPoraceae r63 l. ActinoPolYsPora . Genus ' ' 1?to Order lll. Bifidobacteriales lTl L Bifidobacteriaceae Family 171 Genus L Bifidobacterium . âË Genus ll. Aeriscardovia - - - Nf Genus lll. Alloscardovia . - - N Genus lY. Gardnerella ' ' - tll Genus Y. Metascardovia' . - ztg Genus YL Parascardovia 211 Genus Yll. Scardovia zË Order lV. Catenulisporales ord. nov' 26 Family l. CatenulisPoraceae z6 Genus L CatenulisPora- - - - Ên Family ll. ActinosPicaceae - ap, Genus l. ActinosPica É6 OrderV. Corynebacterialesord' nov' ' ' 2tu Family l. Corynebacteriaceae - 2Æ Genus l. CorYnebacterium æ Genus ll.Turicella. 3tl Family ll. Dietziaceae - - - . fln Dietzia Genus L 312 Family lll. MYcobacteriaceae 3t2 Genus l. MYcobacterium . d xtl CONTENTS Family lY. Nocardiaceae. 376 Genus L Nocardia. 376 Genus ll. Gordonia 419 Genus lll. Millisia 435 Genus lY. Rhodococcus. 437 Genus Y. Skermania 464 Genus Y L S maragdicoccus 467 Genus Yll. Williamsia. 470 Family V. Segniliparaceae. 497 Genus l. Segniliparus 497 Family Y L Tsu kamu rellaceae 500 Genus L Tsukamurella. 500 Order Vl. Frankiales ord. nov 509 Family L Frankiaceae . 512 Genus L Frankia 512 Family ll. Acidothermaceae 520 Genus l. Acidothermus. 520 Family lll. Cryptosporangiaceae 522 Genus L Cryptosporangium 522 Genus lncertae sedis l.
    [Show full text]
  • New Primers for the Class Actinobacteria: Application to Marine and Terrestrial Environments
    Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology1462-2920Blackwell Publishing Ltd, 2003510828841Original ArticlePCR primers for the class ActinobacteriaJ. E. M. Stach et al . Environmental Microbiology (2003) 5(10), 828–841 doi:10.1046/j.1462-2920.2003.00483.x New primers for the class Actinobacteria: application to marine and terrestrial environments James E. M. Stach,1* Luis A. Maldonado,2 cytosine and form a distinct phyletic line in the 16S rDNA Alan C. Ward,2 Michael Goodfellow2 and Alan T. Bull1 tree (Embley and Stackebrandt, 1994; Stackebrandt et al., 1Research School of Biosciences, University of Kent, 1997). Members of the taxon are of interest primarily Canterbury, Kent CT2 7NJ, UK. because of their importance in agriculture, ecology, indus- 2School of Biology, University of Newcastle, Newcastle try and medicine (McNeill and Brown, 1994; Strohl, 2003). upon Tyne NE1 7RU, UK. Actinobacteria are widely distributed in terrestrial (McVeigh et al., 1996; Heuer et al., 1997; Hayakawa et al., 2000), freshwater (Goodfellow et al., 1990; Wohl and Summary McArthur, 1998) and marine (Goodfellow and Haynes, In this study, we redesigned and evaluated primers for 1984; Takizawa et al., 1993; Colquhoun et al., 1998) hab- the class Actinobacteria. In silico testing showed that itats where they are involved in the turnover of organic the primers had a perfect match with 82% of genera matter (McCarthy, 1987; Schrempf, 2001) and xenobiotic in the class Actinobacteria, representing a 26–213% compounds (Kastner et al., 1994; Bunch, 1998; De Schr- improvement over previously reported primers. Only ijver and De Mot, 1999). Some actinobacteria are serious 4% of genera that displayed mismatches did so in the pathogens of animals, including humans, and plants terminal three bases of the 3¢¢¢ end, which is most (Locci, 1994; McNeill and Brown, 1994; Trujillo and critical for polymerase chain reaction success.
    [Show full text]