Rare Actinobacteria: a Possible Solution for Antimicrobial Drug Resistance in Egypt
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Selective Isolation, Characterisation and Identification of Streptosporangia
SELECTIVE ISOLATION, CHARACTERISATION AND IDENTIFICATION OF STREPTOSPORANGIA Thesissubmitted in accordancewith the requirementsof theUniversity of Newcastleupon Tyne for the Degreeof Doctor of Philosophy by Hong-Joong Kim B. Sc. NEWCASTLE UNIVERSITY LIBRARY ____________________________ 093 51117 X ------------------------------- fn L:L, Iýý:, - L. 51-ý CJ - Departmentof Microbiology, The Medical School,University of Newcastleupon Tyne December1993 CONTENTS ACKNOWLEDGEMENTS Page Number PUBLICATIONS SUMMARY INTRODUCTION A. AIMS 1 B. AN HISTORICAL SURVEY OF THE GENUS STREPTOSPORANGIUM 5 C. NUMERICAL SYSTEMATICS 17 D. MOLECULAR SYSTEMATICS 35 E. CHARACTERISATION OF STREPTOSPORANGIA 41 F. SELECTIVE ISOLATION OF STREPTOSPORANGIA 62 MATERIALS AND METHODS A. SELECTIVE ISOLATION, ENUMERATION AND 75 CHARACTERISATION OF STREPTOSPORANGIA B. NUMERICAL IDENTIFICATION 85 C. SEQUENCING OF 5S RIBOSOMAL RNA 101 D. PYROLYSIS MASS SPECTROMETRY 103 E. RAPID ENZYME TESTS 113 RESULTS A. SELECTIVE ISOLATION, ENUMERATION AND 122 CHARACTERISATION OF STREPTOSPORANGIA B. NUMERICAL IDENTIFICATION OF STREPTOSPORANGIA 142 C. PYROLYSIS MASS SPECTROMETRY 178 D. 5S RIBOSOMAL RNA SEQUENCING 185 E. RAPID ENZYME TESTS 190 DISCUSSION A. SELECTIVE ISOLATION 197 B. CLASSIFICATION 202 C. IDENTIFICATION 208 D. FUTURE STUDIES 215 REFERENCES 220 APPENDICES A. TAXON PROGRAM 286 B. MEDIA AND REAGENTS 292 C. RAW DATA OF PRACTICAL EVALUATION 295 D. RAW DATA OF IDENTIFICATION 297 E. RAW DATA OF RAPID ENZYME TESTS 300 ACKNOWLEDGEMENTS I would like to sincerely thank my supervisor, Professor Michael Goodfellow for his assistance,guidance and patienceduring the course of this study. I am greatly indebted to Dr. Yong-Ha Park of the Genetic Engineering Research Institute in Daejon, Korea for his encouragement, for giving me the opportunity to extend my taxonomic experience and for carrying out the 5S rRNA sequencing studies. -
Downloaded from Genbank
bioRxiv preprint doi: https://doi.org/10.1101/036087; this version posted January 7, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Automating Assessment of the Undiscovered 2 Biosynthetic Potential of Actinobacteria 3 Bogdan Tokovenko1*, Yuriy Rebets1, Andriy Luzhetskyy1,2* 4 1 Actinomycetes Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research 5 Saarland, Saarbrücken, Germany 6 2 Department of Pharmaceutical Biotechnology, Faculty of Natural Sciences and Technology, University of 7 Saarland, Saarbrücken, Germany 8 * Corresponding author 9 E-mail: [email protected] (AL), [email protected] (BT) 1 bioRxiv preprint doi: https://doi.org/10.1101/036087; this version posted January 7, 2016. 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 Abstract 2 Background. Biosynthetic potential of Actinobacteria has long been the subject of theoretical estimates. 3 Such an estimate is indeed important as a test of further exploitability of a taxon or group of taxa for new 4 therapeutics. As neither a set of available genomes nor a set of bacterial cultivation methods are static, it 5 makes sense to simplify as much as possible and to improve reproducibility of biosynthetic gene clusters 6 similarity, diversity, and abundance estimations. -
Actinobacteria and Myxobacteria Isolated from Freshwater Snails and Other Uncommon Iranian Habitats, Their Taxonomy and Secondary Metabolism
Actinobacteria and Myxobacteria isolated from freshwater snails and other uncommon Iranian habitats, their taxonomy and secondary metabolism Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades einer Doktorin der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Nasim Safaei aus Teheran / Iran 1. Referent: Professor Dr. Michael Steinert 2. Referent: Privatdozent Dr. Joachim M. Wink eingereicht am: 24.02.2021 mündliche Prüfung (Disputation) am: 20.04.2021 Druckjahr 2021 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Safaei, N. Mast, Y. Steinert, M. Huber, K. Bunk, B. Wink, J. (2020). Angucycline-like aromatic polyketide from a novel Streptomyces species reveals freshwater snail Physa acuta as underexplored reservoir for antibiotic-producing actinomycetes. J Antibiotics. DOI: 10.3390/ antibiotics10010022 Safaei, N. Nouioui, I. Mast, Y. Zaburannyi, N. Rohde, M. Schumann, P. Müller, R. Wink.J (2021) Kibdelosporangium persicum sp. nov., a new member of the Actinomycetes from a hot desert in Iran. Int J Syst Evol Microbiol (IJSEM). DOI: 10.1099/ijsem.0.004625 Tagungsbeiträge Actinobacteria and myxobacteria isolated from freshwater snails (Talk in 11th Annual Retreat, HZI, 2020) Posterbeiträge Myxobacteria and Actinomycetes isolated from freshwater snails and -
Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain. -
Exploring the Potential of Antibiotic Production from Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis
fmicb-11-01540 July 27, 2020 Time: 14:51 # 1 ORIGINAL RESEARCH published: 15 July 2020 doi: 10.3389/fmicb.2020.01540 Exploring the Potential of Antibiotic Production From Rare Actinobacteria by Whole-Genome Sequencing and Guided MS/MS Analysis Dini Hu1,2, Chenghang Sun3, Tao Jin4, Guangyi Fan4, Kai Meng Mok2, Kai Li1* and Simon Ming-Yuen Lee5* 1 School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China, 2 Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China, 3 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, 4 Beijing Genomics Institute, Shenzhen, China, 5 State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China Actinobacteria are well recognized for their production of structurally diverse bioactive Edited by: secondary metabolites, but the rare actinobacterial genera have been underexploited Sukhwan Yoon, for such potential. To search for new sources of active compounds, an experiment Korea Advanced Institute of Science combining genomic analysis and tandem mass spectrometry (MS/MS) screening and Technology, South Korea was designed to isolate and characterize actinobacterial strains from a mangrove Reviewed by: Hui Li, environment in Macau. Fourteen actinobacterial strains were isolated from the collected Jinan University, China samples. Partial 16S sequences indicated that they were from six genera, including Baogang Zhang, China University of Geosciences, Brevibacterium, Curtobacterium, Kineococcus, Micromonospora, Mycobacterium, and China Streptomyces. The isolate sp.01 showing 99.28% sequence similarity with a reference *Correspondence: rare actinobacterial species Micromonospora aurantiaca ATCC 27029T was selected for Kai Li whole genome sequencing. -
Actinopolyspora Egyptensis Sp. Nov., a New Halophilic Actinomycete
African Journal of Microbiology Research Vol. 5(2) pp. 100-105, 18 January, 2011 Available online http://www.academicjournals.org/ajmr DOI: 10.5897/AJMR10.667 ISSN 1996-0808 ©2011 Academic Journals Full Length Research Paper Actinopolyspora egyptensis sp. nov., a new halophilic actinomycete Wael N. Hozzein1,2* and Michael Goodfellow3 1Chair of Advanced Proteomics and Cytomics Research, College of Science, King Saud University, Riyadh, Saudi Arabia. 2Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt. 3Division of Biology, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK. Accepted 22 December, 2010 A halophilic actinomycete, designated HT371T, was isolated from a soil sample collected from the shore of the salty Lake Qaroun, Egypt, and was the subject of a polyphasic study. Analysis of 16S rRNA indicated that the isolate belonged to the genus Actinopolyspora and constituted a separate clade in the Actinopolyspora 16S rRNA gene tree with similarity values of 96.5 and 96.2% with Actinopolyspora halophila DSM43834T and Actinopolyspora mortivallis DSM44261T, respectively. Isolate HT371T had chemotaxonomic and morphological properties consistent with its classification in the genus Actinopolyspora and could grow on agar plates at NaCl concentrations of up to 25% (w/v). The isolate was readily differentiated from the type strains of genus Actinopolyspora using a range of phenotypic characters. On the basis of polyphasic evidence, the strain HT371T represents a novel species for which the name Actinopolyspora egyptensis sp. nov. is proposed. The type strain is HT371T (=CGMCC 4.2041T). Key words: Actinopolyspora egyptensis sp. nov., halophilic isolate, polyphasic taxonomy. INTRODUCTION The genus Actinopolyspora was created by Gochnauer et taxonomic status, which showed that it merited al. -
Streptosporangium Roseum Type Strain (NI 9100T)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Permalink https://escholarship.org/uc/item/7g79w47k Journal Standards in genomic sciences, 2(1) ISSN 1944-3277 Authors Nolan, Matt Sikorski, Johannes Jando, Marlen et al. Publication Date 2010-01-28 DOI 10.4056/sigs.631049 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:29-37 DOI:10.4056/sigs.631049 Complete genome sequence of Streptosporangium T roseum type strain (NI 9100 ) Matt Nolan1, Johannes Sikorski2, Marlen Jando2, Susan Lucas1, Alla Lapidus1, Tijana Glavina Del Rio1, Feng Chen1, Hope Tice1, Sam Pitluck1, Jan-Fang Cheng1, Olga Chertkov1,3, David Sims1,3, Linda Meincke1,3, Thomas Brettin1,3, Cliff Han1,3, John C. Detter1,3, David Bruce1,3, Lynne Goodwin1,3, Miriam Land1,4, Loren Hauser1,4, Yun-Juan Chang1,4, Cynthia D. Jeffries1,4, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amy Chen5, Krishna Pala- niappan5, Patrick Chain1,3, Manfred Rohde6, Markus Göker2, Jim Bristow1, Jonathan A. Ei- sen1,7, Victor Markowitz5, Philip Hugenholtz1, Nikos C. Kyrpides1, and Hans-Peter Klenk2* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: sporangia, vegetative and aerial mycelia, aerobic, non-motile, non-motile spores, Gram-positive, Streptosporangiaceae, S. -
Actinomycetospora Chiangmaiensis Gen. Nov., Sp. Nov., a New Member of the Family Pseudonocardiaceae
International Journal of Systematic and Evolutionary Microbiology (2008), 58, 408–413 DOI 10.1099/ijs.0.64976-0 Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae Yi Jiang,1,2 Jutta Wiese,1 Shu-Kun Tang,2 Li-Hua Xu,2 Johannes F. Imhoff1 and Cheng-Lin Jiang2 Correspondence 1Leibniz-Institut fu¨r Meereswissenschaften, IFM-GEOMAR, Du¨sternbrooker Weg 20, Johannes F. Imhoff D-24105 Kiel, Germany [email protected] 2Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China Li-Hua Xu [email protected] A novel actinomycete strain, YIM 0006T, was isolated from soil of a tropical rainforest in northern Thailand. The isolate displayed the following characteristics: aerial mycelium is absent, short spore chains are formed directly on the substrate mycelium, contains meso-diaminopimelic acid, arabinose and galactose (cell-wall chemotype IV), the diagnostic phospholipid is phosphatidylcholine, MK-9(H4) is the predominant menaquinone and the G+C content of the genomic DNA is 69.0 mol%. Phylogenetic analysis and phenotypic characteristics showed that strain YIM 0006T belongs to the family Pseudonocardiaceae but can be distinguished from representatives of all genera classified in the family. The novel genus and species Actinomycetospora chiangmaiensis gen. nov., sp. nov. are proposed, with strain YIM 0006T (5CCTCC AA 205017T 5DSM 45062T) as the type strain of Actinomycetospora chiangmaiensis. The first description of the family Pseudonocardiaceae was the strain were determined after growth at 28 uC for given by Embley et al. (1988), and the description was 2 weeks by methods used in the International Streptomyces emended by Stackebrandt et al. -
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. -
Complete Genome Sequence of the Actinomycete Actinoalloteichus
Schaffert et al. Standards in Genomic Sciences (2016) 11:91 DOI 10.1186/s40793-016-0213-3 SHORT GENOME REPORT Open Access Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge Lena Schaffert1, Andreas Albersmeier1, Anika Winkler1, Jörn Kalinowski1, Sergey B. Zotchev2 and Christian Rückert1,3* Abstract Actinoalloteichus hymeniacidonis HPA 177T is a Gram-positive, strictly aerobic, black pigment producing and spore- forming actinomycete, which forms branching vegetative hyphae and was isolated from the marine sponge Hymeniacidon perlevis. Actinomycete bacteria are prolific producers of secondary metabolites, some of which have been developed into anti-microbial, anti-tumor and immunosuppressive drugs currently used in human therapy. Considering this and the growing interest in natural products as sources of new drugs, actinomycete bacteria from the hitherto poorly explored marine environments may represent promising sources for drug discovery. As A. hymeniacidonis, isolated from the marine sponge, is a type strain of the recently described and rare genus Actinoalloteichus, knowledge of the complete genome sequence enables genome analyses to identify genetic loci for novel bioactive compounds. This project, describing the 6.31 Mbp long chromosome, with its 5346 protein- coding and 73 RNA genes, will aid the Genomic Encyclopedia of Bacteria and Archaea project. Keywords: Actinoalloteichus, Strictly aerobic, Non-motile, Gram-positive, Non-acid-fast, Branching vegetative hyphae, Spore forming, Secondary metabolite biosynthesis gene clusters Introduction actinomycetes became a focus of research since they Strain HPA 177T is the type strain of the species Acti- have evolved the greatest genomic and metabolic diver- noalloteichus hymeniacidonis, it was isolated from the sity and are auspicious sources of novel secondary me- marine sponge Hymeniacidon perlevis at the intertidal tabolites and enzymes [5, 7–9]. -
A New Micromonospora Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge
marine drugs Article A New Micromonospora Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge Catherine R. Back 1,* , Henry L. Stennett 1 , Sam E. Williams 1 , Luoyi Wang 2 , Jorge Ojeda Gomez 1, Omar M. Abdulle 3, Thomas Duffy 3, Christopher Neal 4, Judith Mantell 4, Mark A. Jepson 4, Katharine R. Hendry 5 , David Powell 3, James E. M. Stach 6 , Angela E. Essex-Lopresti 7, Christine L. Willis 2, Paul Curnow 1 and Paul R. Race 1,* 1 School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK; [email protected] (H.L.S.); [email protected] (S.E.W.); [email protected] (J.O.G.); [email protected] (P.C.) 2 School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK; [email protected] (L.W.); [email protected] (C.L.W.) 3 Summit Therapeutics, Merrifield Centre, Rosemary Lane, Cambridge CB1 3LQ, UK; [email protected] (O.M.A.); [email protected] (T.D.); [email protected] (D.P.) 4 Woolfson Bioimaging Facility, University of Bristol, University Walk, Bristol BS8 1TD, UK; [email protected] (C.N.); [email protected] (J.M.); [email protected] (M.A.J.) 5 School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK; [email protected] 6 School of Natural and Environmental Sciences, Newcastle University, King’s Road, Newcastle upon Tyne NE1 7RU, UK; [email protected] Citation: Back, C.R.; Stennett, H.L.; 7 Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK; Williams, S.E.; Wang, L.; Ojeda [email protected] Gomez, J.; Abdulle, O.M.; Duffy, T.; * Correspondence: [email protected] (C.R.B.); [email protected] (P.R.R.) Neal, C.; Mantell, J.; Jepson, M.A.; et al. -
Kibdelosporangium Philippinense Sp. Nov. Isolated from Soil
INTERNATIONAL JOURNAL OF SYSTEMATICBACTERIOLOGY, July 1988, p. 282-286 Vol. 38, No. 3 0020-7713/88/030282-05$02.OO/O Copyright 0 1988, International Union of Microbiological Societies Kibdelosporangium philippinense sp. nov. Isolated from Soil FREDERICK P. MERTZ* AND RAYMOND C. YAO The Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285 A new species of Kibdelosporungium is described. This organism is characterized by white aerial hyphae bearing long chains of smooth-walled spores and abundant sporangiumlike structures. The new species contains meso-diaminopimelic acid, arabinose, and galactose (type IV cell walls, type A whole-cell sugar pattern), phosphatidylethanolamine (type PI1 phospholipid pattern), and no mycolic acids. The single soil isolate has chemical and morphological properties consistent with the genus Kibdelosporungium. A comparison with previously described species of the genus Kibdelosporungium in which we used standard techniques, fatty acid profiles, and polypeptide banding fingerprints indicated that this strain is a new species. The name proposed for this new species is Kibdelosporungium philippinense. The type strain is strain A80407 (= NRRL 18198). Taxonomy of the Actinomycetales is constantly changing Media. Cells were grown for 72 h at 30°C in medium iis new genera are discovered and as workers develop new containing 30 g of tryptic soy broth, 3 g of yeast extract, 2 g techniques which challenge existing classifications. Isolates of MgSO, . 7H,O, 5 g of glucose, and 4 g of maltose in 1,000 ?with type IV cell walls (10) (i.e., meso-diaminopimelic acid ml of deionized water. After incubation on a rotary shaker, plus arabinose and galactose in whole-cell hydrolysates) and the cells were harvested by centrifugation, washed twice llacking mycolic acids have recently undergone a major with sterile water, and then used as inocula.