Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline
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Bradymonabacteria, a Novel Bacterial Predator Group with Versatile
Mu et al. Microbiome (2020) 8:126 https://doi.org/10.1186/s40168-020-00902-0 RESEARCH Open Access Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments Da-Shuai Mu1,2, Shuo Wang2, Qi-Yun Liang2, Zhao-Zhong Du2, Renmao Tian3, Yang Ouyang3, Xin-Peng Wang2, Aifen Zhou3, Ya Gong1,2, Guan-Jun Chen1,2, Joy Van Nostrand3, Yunfeng Yang4, Jizhong Zhou3,4 and Zong-Jun Du1,2* Abstract Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. -
New 16S Rrna Primers to Uncover Bdellovibrio and Like Organisms Diversity and Abundance Jade Ezzedine, Cécile Chardon, Stéphan Jacquet
New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance Jade Ezzedine, Cécile Chardon, Stéphan Jacquet To cite this version: Jade Ezzedine, Cécile Chardon, Stéphan Jacquet. New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance. Journal of Microbiological Methods, Elsevier, 2020, 10.1016/j.mimet.2020.105996. hal-02935301 HAL Id: hal-02935301 https://hal.inrae.fr/hal-02935301 Submitted on 10 Sep 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Journal of Microbiological Methods 175 (2020) 105996 Contents lists available at ScienceDirect Journal of Microbiological Methods journal homepage: www.elsevier.com/locate/jmicmeth New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity T and abundance ⁎ Jade A. Ezzedine, Cécile Chardon, Stéphan Jacquet Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France ARTICLE INFO ABSTRACT Keywords: Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups Bdellovibrio and like organisms of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of Primer design other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. -
Imperialibacter Roseus Gen. Nov., Sp. Nov., a Novel Bacterium of the Family Flammeovirgaceae Isolated from Permian Groundwater
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4136–4140 DOI 10.1099/ijs.0.052662-0 Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater Hui Wang,1,2,3 Junde Li,1 Tianling Zheng,2 Russell T. Hill3 and Xiaoke Hu1 Correspondence 1Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Xiaoke Hu 2Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, [email protected] Xiamen University, Xiamen 361005, China 3Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1v6c/C16 : 1v7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycoli- pids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T (5CICC 10659T5KCTC 32399T). Bacteria affiliated with the family Flammeovirgaceae of the staining was performed according to the method described phylum Bacteroidetes are widely distributed in various by Gerhardt et al. -
Characterization of the First Highly Predatory Bdellovibrio
Iranian Journal of Basic Medical Sciences ijbms.mums.ac.ir Bdellovibrio bacteriovorus from Iran and its potential lytic activity against Characterizationprincipal pathogenic of Enterobacteriaceaethe first highly predatory Salman Odooli 1, Rasoul Roghanian 1*, Giti Emtiazi 1, Milad Mohkam 2, Younes Ghasemi 2, 3 1 Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran 2 Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran 3 Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran -A R T I C L E I N F O A B S T R A C T Article type: Objective(s): Bdellovibrio-and-like organisms (BALOs) are predatory prokaryotes that attack and Original article kill other Gram-negative bacteria for growth and reproduction. This study describes the isolation, Bdellovibrio bacteriovorus Article history: with a broad prey range from Iran. Received: Sep 15, 2019 Accepted: Aug 11, 2020 identification,Materials and biologicalMethods: properties,One BALO and strain bacteriolytic with high activity predatory of the potency first was isolated from the rhizosphere soil using Enteropathogenic Escherichia coli Keywords: Bdellovibrio bacteriovorus strain SOIR-1 through plaque assays, transmission electron microscopy (TEM), Bdellovibrio as prey. It was identified and designated as Bacteriolytic activity and analysis of bacteriolytic activity were also performed. 16SBdellovibrio rRNA Analysis Results: TEM and Bdellovibrio-specific PCRs, and 16S rRNA gene sequence analysis. Biological characterization Enterobacteriaceae Bdellovibrio Iran strains of Bdellovibrio bacteriovorus-specific. The PCRs strain confirmed SOIR-1 grew that within the strain the temperature SOIR-1 belongs range to of the 25–37 genus °C Isolation and the pH range. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Neuroprotective Natural Products Neuroprotective Natural Products
Neuroprotective Natural Products Neuroprotective Natural Products Clinical Aspects and Mode of Action Edited by Goutam Brahmachari Editor All books published by Wiley-VCH are carefully produced. Nevertheless, authors, Dr. Goutam Brahmachari editors, and publisher do not warrant the Visva-Bharati (a Central University) information contained in these books, including Department of Chemistry, Laboratory this book, to be free of errors. Readers are of Natural Products and Organic Synthesis, advised to keep in mind that statements, data, Santiniketan illustrations, procedural details or other items West Bengal 731 235 may inadvertently be inaccurate. India Cover Library of Congress Card No.: applied for Neurons: © fotolia_ktsdesign British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http:// dnb.d-nb.de. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are -
Analysis of 1000 Type-Strain Genomes Improves
Lawrence Berkeley National Laboratory Recent Work Title Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Permalink https://escholarship.org/uc/item/5pg6w486 Authors García-López, Marina Meier-Kolthoff, Jan P Tindall, Brian J et al. Publication Date 2019 DOI 10.3389/fmicb.2019.02083 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 23 September 2019 doi: 10.3389/fmicb.2019.02083 Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes Marina García-López 1, Jan P. Meier-Kolthoff 1, Brian J. Tindall 1, Sabine Gronow 1, Tanja Woyke 2, Nikos C. Kyrpides 2, Richard L. Hahnke 1 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Edited by: Although considerable progress has been made in recent years regarding the Martin G. Klotz, classification of bacteria assigned to the phylum Bacteroidetes, there remains a Washington State University, United States need to further clarify taxonomic relationships within a diverse assemblage that Reviewed by: includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes Maria Chuvochina, classification has proved to be difficult, not least when taxonomic decisions rested University of Queensland, Australia Vera Thiel, heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number Tokyo Metropolitan University, Japan of phenotypic features. Here, draft genome sequences of a greatly enlarged collection David W. Ussery, of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used University of Arkansas for Medical Sciences, United States to infer phylogenetic trees from genome-scale data using the principles drawn from Ilya V. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
Diversity of Marine Gliding Bacteria in Thailand and Their Cytotoxicity
Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.12 No.3, Issue of July 15, 2009 © 2009 by Pontificia Universidad Católica de Valparaíso -- Chile Received October 7, 2008 / Accepted March 29, 2009 DOI: 10.2225/vol12-issue3-fulltext-13 RESEARCH ARTICLE Diversity of marine gliding bacteria in Thailand and their cytotoxicity Yutthapong Sangnoi Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Pornpoj Srisukchayakul Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Vullapa Arunpairojana Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Akkharawit Kanjana-Opas* Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Tel: 66 74286373 Fax: 66 74212889 E-mail: [email protected] Financial support: Thailand Research Fund (MRG4880153) and a Biodiversity Research and Training Grant (BRTR_149011). Scholarship for YS from the Graduate School, Prince of Songkla University. Keywords: Aureispira marina, Aureispira maritime, Fulvivirga kasyanovii, human cell lines, Rapidithrix thailandica, Tenacibaculum mesophilum. Abbreviations: CFB: Cytophaga-Flavobacterium-Bacteriodes HeLa: cervical cancer HT-29: colon cancer KB: oral cancer MCF-7: breast adenocarcinoma PCR: polymerase chain reaction SK: skim milk medium SRB: sulphorodamine B Eighty-four marine gliding bacteria were isolated from thailandica, Aureispira marina and Aureispira maritima specimens collected in the Gulf of Thailand and the respectively. The isolates were cultivated in four Andaman Sea. All exhibited gliding motility and swarm different cultivation media (Vy/2, RL 1, CY and SK) colonies on cultivation plates and they were purified by and the crude extracts were submitted to screen subculturing and micromanipulator techniques. -