Taxonomy Annotation and Guide Tree Errors in 16S Rrna Databases
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The Use of Purple Nonsulfur Photosynthetic Bacteria to Maintain Water Quality, Sources of Single Cell Protein and Bioactive Compounds for Shrimp Cultivation
The Use of Purple Nonsulfur Photosynthetic Bacteria to Maintain Water Quality, Sources of Single Cell Protein and Bioactive Compounds for Shrimp Cultivation Supaporn Chumpol A Thesis Submitted in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Microbiology Prince of Songkla University 2017 Copyright of Prince of Songkla University i The Use of Purple Nonsulfur Photosynthetic Bacteria to Maintain Water Quality, Sources of Single Cell Protein and Bioactive Compounds for Shrimp Cultivation Supaporn Chumpol A Thesis Submitted in Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Microbiology Prince of Songkla University 2017 Copyright of Prince of Songkla University ii Thesis Title The Use of Purple Nonsulfur Photosynthetic Bacteria to Maintain Water Quality, Sources of Single Cell Protein and Bioactive Compounds for Shrimp Cultivation Author Miss Supaporn Chumpol Major Program Microbiology Major Advisor Examining Committee: ........................................................ ..........................................Chairperson (Prof. Dr. Duangporn Kantachote) (Dr. Ampaitip Sukhoom) Co-advisor ............................................Committee (Prof. Dr. Duangporn Kantachote) ........................................................ (Prof. Dr. Hiroshi Kanzaki) ............................................Committee (Prof. Dr. Hiroshi Kanzaki) ........................................................ (Assoc. Prof. Dr. Teruhiko Nitoda) ............................................Committee -
Genomic Signatures of Predatory Bacteria
The ISME Journal (2013) 7, 756–769 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE By their genes ye shall know them: genomic signatures of predatory bacteria Zohar Pasternak1, Shmuel Pietrokovski2, Or Rotem1, Uri Gophna3, Mor N Lurie-Weinberger3 and Edouard Jurkevitch1 1Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel; 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel and 3Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,’ that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. -
Metagenomic Insights Into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Lawrence Berkeley National Laboratory Recent Work Title Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Permalink https://escholarship.org/uc/item/9xc5s0v5 Journal Frontiers in microbiology, 7(FEB) ISSN 1664-302X Authors Vavourakis, Charlotte D Ghai, Rohit Rodriguez-Valera, Francisco et al. Publication Date 2016 DOI 10.3389/fmicb.2016.00211 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 25 February 2016 doi: 10.3389/fmicb.2016.00211 Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines Charlotte D. Vavourakis 1, Rohit Ghai 2, 3, Francisco Rodriguez-Valera 2, Dimitry Y. Sorokin 4, 5, Susannah G. Tringe 6, Philip Hugenholtz 7 and Gerard Muyzer 1* 1 Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands, 2 Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain, 3 Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Ceskéˇ Budejovice,ˇ Czech Republic, 4 Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia, 5 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 6 The Department of Energy Joint Genome Institute, Walnut Creek, CA, USA, 7 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration Edited by: of sodium carbonates in the absence of major divalent cations. -
Horizontal Gene Flow Into Geobacillus Is Constrained by the Chromosomal Organization of Growth and Sporulation
bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. 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 4.0 International license. Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation Alexander Esin1,2, Tom Ellis3,4, Tobias Warnecke1,2* 1Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom 2Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom 3Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom 4Department of Bioengineering, Imperial College London, London, United Kingdom *corresponding author ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. 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 4.0 International license. Abstract Horizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment. -
Prokaryotic Biodiversity of Halophilic Microorganisms Isolated from Sehline Sebkha Salt Lake (Tunisia)
Vol. 8(4), pp. 355-367, 22 January, 2014 DOI: 10.5897/AJMR12.1087 ISSN 1996-0808 ©2014 Academic Journals African Journal of Microbiology Research http://www.academicjournals.org/AJMR Full Length Research Paper Prokaryotic biodiversity of halophilic microorganisms isolated from Sehline Sebkha Salt Lake (Tunisia) Abdeljabbar HEDI1,2*, Badiaa ESSGHAIER1, Jean-Luc CAYOL2, Marie-Laure FARDEAU2 and Najla SADFI1 1Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar 2092, Tunisie. 2Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR180, IRD, Université de Provence et de la Méditerranée, ESIL case 925, 13288 Marseille cedex 9, France. Accepted 7 February, 2013 North of Tunisia consists of numerous ecosystems including extreme hypersaline environments in which the microbial diversity has been poorly studied. The Sehline Sebkha is an important source of salt for food. Due to its economical importance with regards to its salt value, a microbial survey has been conducted. The purpose of this research was to examine the phenotypic features as well as the physiological and biochemical characteristics of the microbial diversity of this extreme ecosystem, with the aim of screening for metabolites of industrial interest. Four samples were obtained from 4 saline sites for physico-chemical and microbiological analyses. All samples studied were hypersaline (NaCl concentration ranging from 150 to 260 g/L). A specific halophilic microbial community was recovered from each site and initial characterization of isolated microorganisms was performed by using both phenotypic and phylogenetic approaches. The 16S rRNA genes from 77 bacterial strains and two archaeal strains were isolated and phylogenetically analyzed and belonged to two phyla Firmicutes and gamma-proteobacteria of the domain Bacteria. -
Nor Hawani Salikin
Characterisation of a novel antinematode agent produced by the marine epiphytic bacterium Pseudoalteromonas tunicata and its impact on Caenorhabditis elegans Nor Hawani Salikin A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biological, Earth and Environmental Sciences Faculty of Science August 2020 Thesis/Dissertation Sheet Surname/Family Name : Salikin Given Name/s : Nor Hawani Abbreviation for degree as give in the University : Ph.D. calendar Faculty : UNSW Faculty of Science School : School of Biological, Earth and Environmental Sciences Characterisation of a novel antinematode agent produced Thesis Title : by the marine epiphytic bacterium Pseudoalteromonas tunicata and its impact on Caenorhabditis elegans Abstract 350 words maximum: (PLEASE TYPE) Drug resistance among parasitic nematodes has resulted in an urgent need for the development of new therapies. However, the high re-discovery rate of antinematode compounds from terrestrial environments necessitates a new repository for future drug research. Marine epiphytic bacteria are hypothesised to produce nematicidal compounds as a defence against bacterivorous predators, thus representing a promising, yet underexplored source for antinematode drug discovery. The marine epiphytic bacterium Pseudoalteromonas tunicata is known to produce a number of bioactive compounds. Screening genomic libraries of P. tunicata against the nematode Caenorhabditis elegans identified a clone (HG8) showing fast-killing activity. However, the molecular, chemical and biological properties of HG8 remain undetermined. A novel Nematode killing protein-1 (Nkp-1) encoded by an uncharacterised gene of HG8 annotated as hp1 was successfully discovered through this project. The Nkp-1 toxicity appears to be nematode-specific, with the protein being highly toxic to nematode larvae but having no impact on nematode eggs. -
Isolation of Lactic-Acid Related Bacteria from the Pig Mucosal P
Aus dem Institut für Tierernährung des Fachbereichs Veterinärmedizin der Freien Universität Berlin Isolation of lactic acid-related bacteria from the pig mucosal proximal gastrointestinal tract, including Olsenella umbonata sp. nov. and Veillonella magna sp. nov. Inaugural-Dissertation zur Erlangung des Grades eines Doktors der Veterinärmedizin an der Freien Universität Berlin vorgelegt von Mareike Kraatz Tierärztin aus Berlin Berlin 2011 Journal-Nr.: 3431 Gedruckt mit Genehmigung des Fachbereichs Veterinärmedizin der Freien Universität Berlin Dekan: Univ.-Prof. Dr. Leo Brunnberg Erster Gutachter: Univ.-Prof. a. D. Dr. Ortwin Simon Zweiter Gutachter: Univ.-Prof. Dr. Lothar H. Wieler Dritter Gutachter: Univ.-Prof. em. Dr. Dr. h. c. Gerhard Reuter Deskriptoren (nach CAB-Thesaurus): anaerobes; Bacteria; catalase; culture media; digestive tract; digestive tract mucosa; food chains; hydrogen peroxide; intestinal microorganisms; isolation; isolation techniques; jejunum; lactic acid; lactic acid bacteria; Lactobacillus; Lactobacillus plantarum subsp. plantarum; microbial ecology; microbial flora; mucins; mucosa; mucus; new species; Olsenella; Olsenella profusa; Olsenella uli; oxygen; pigs; propionic acid; propionic acid bacteria; species composition; stomach; symbiosis; taxonomy; Veillonella; Veillonella ratti Tag der Promotion: 21. Januar 2011 Diese Dissertation ist als Buch (ISBN 978-3-8325-2789-1) über den Buchhandel oder online beim Logos Verlag Berlin (http://www.logos-verlag.de) erhältlich. This thesis is available as a book (ISBN 978-3-8325-2789-1) -
Phylogeny of the Family Halomonadaceae Based on 23S and 16S Rdna Sequence Analyses
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 241–249 Printed in Great Britain Phylogeny of the family Halomonadaceae based on 23S and 16S rDNA sequence analyses 1 Lehrstuhl fu$ r David R. Arahal,1,2 Wolfgang Ludwig,1 Karl H. Schleifer1 Mikrobiologie, Technische 2 Universita$ tMu$ nchen, and Antonio Ventosa 85350 Freising, Germany 2 Departamento de Author for correspondence: Antonio Ventosa. Tel: j34 954556765. Fax: j34 954628162. Microbiologı!ay e-mail: ventosa!us.es Parasitologı!a, Facultad de Farmacia, Universidad de Sevilla, 41012 Seville, Spain In this study, we have evaluated the phylogenetic status of the family Halomonadaceae, which consists of the genera Halomonas, Chromohalobacter and Zymobacter, by comparative 23S and 16S rDNA analyses. The genus Halomonas illustrates very well a situation that occurs often in bacterial taxonomy. The use of phylogenetic tools has permitted the grouping of several genera and species believed to be unrelated according to conventional taxonomic techniques. In addition, the number of species of the genus Halomonas has increased as a consequence of new descriptions, particularly during the last few years, but their features are too heterogeneous to justify their placement in the same genus and, therefore, a re-evaluation seems necessary. We have determined the complete sequences (about 2900 bases) of the 23S rDNA of 18 species of the genera Halomonas and Chromohalobacter and resequenced the complete 16S rDNA sequences of seven species of Halomonas. The results of our analysis show that two phylogenetic groups (respectively containing five and seven species) can be distinguished within the genus Halomonas. Six other species cannot be assigned to either of the above-mentioned groups. -
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment. -
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. -
The Correlation Between Morphological and Phylogenetic Classification of Myxobacteria
International Journal of Systematic Bacteriology (1 999), 49, 1255-1 262 Printed in Great Britain The correlation between morphological and phylogenetic classification of myxobacteria Cathrin Sproer,’ Hans Reichenbach’ and Erko Stackebrandtl Author for correspondence: Erko Stackebrandt.Tel: +49 531 2616 352. Fax: +49 531 2616 418. e-mail : [email protected] DSMZ-Deutsche Sammlung In order to determine whether morphological criteria are suitable to affiliate von Mikroorganismen und myxobacterial strains to species, a phylogenetic analysis of 16s rDNAs was Zellkulturen GmbH1 and G BF-Gesel Isc haft fur performed on 54 myxobacterial strains that represented morphologically 21 Biotechnologische species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Forschung mbH*, 381 24 Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species Braunschweig, Germany and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of Corallococcus’, previously ‘Chondrococcus’,within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium (‘Sorangium’) cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria (‘Polyangium thaxteri’ PI t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947Tand Angiococcus disciformis An dl), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material. -
Isolation and Diversity of Sediment Bacteria in The
bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. 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 4.0 International license. 1 Isolation and Diversity of Sediment Bacteria in the 2 Hypersaline Aiding Lake, China 3 4 Tong-Wei Guan, Yi-Jin Lin, Meng-Ying Ou, Ke-Bao Chen 5 6 7 Institute of Microbiology, Xihua University, Chengdu 610039, P. R. China. 8 9 Author for correspondence: 10 Tong-Wei Guan 11 Tel/Fax: +86 028 87720552 12 E-mail: [email protected] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. 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 4.0 International license. 29 Abstract A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using 30 nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered 31 from the different media significantly varied, indicating the need to optimize the isolation conditions. 32 The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, 33 Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, 34 Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, 35 Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and 36 Streptosporangiales), including 17 families, 41 genera, and 71 species.