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Liu BT, Sun XK, Wang C, Du ZJ, Chen GJ. Hyunsoonleella flava sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2020; 70:240-245. [DOI: 10.1099/ijsem.0.003746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Bang-Tao Liu
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Xun-Ke Sun
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Chong Wang
- Marine College, Shandong University, Weihai, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Guan-Jun Chen
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- Marine College, Shandong University, Weihai, 264209, PR China
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Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat. J Microbiol 2019; 57:569-574. [DOI: 10.1007/s12275-019-8666-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 01/30/2023]
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Caputo A, Fournier PE, Raoult D. Genome and pan-genome analysis to classify emerging bacteria. Biol Direct 2019; 14:5. [PMID: 30808378 PMCID: PMC6390601 DOI: 10.1186/s13062-019-0234-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy. Reviewers This article was reviewed by William Martin, Eric Bapteste and James Mcinerney. Open peer review Reviewed by William Martin, Eric Bapteste and James Mcinerney.
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Affiliation(s)
- Aurélia Caputo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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Hollensteiner J, Poehlein A, Spröer C, Bunk B, Sheppard AE, Rosentstiel P, Schulenburg H, Liesegang H. Complete Genome sequence of the nematicidal Bacillus thuringiensis MYBT18246. Stand Genomic Sci 2017; 12:48. [PMID: 28852435 PMCID: PMC5569534 DOI: 10.1186/s40793-017-0259-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/08/2017] [Indexed: 01/22/2023] Open
Abstract
10.1601/nm.5000 is a rod-shaped facultative anaerobic spore forming bacterium of the genus 10.1601/nm.4857. The defining feature of the species is the ability to produce parasporal crystal inclusion bodies, consisting of δ-endotoxins, encoded by cry-genes. Here we present the complete annotated genome sequence of the nematicidal 10.1601/nm.5000 strain MYBT18246. The genome comprises one 5,867,749 bp chromosome and 11 plasmids which vary in size from 6330 bp to 150,790 bp. The chromosome contains 6092 protein-coding and 150 RNA genes, including 36 rRNA genes. The plasmids encode 997 proteins and 4 t-RNA's. Analysis of the genome revealed a large number of mobile elements involved in genome plasticity including 11 plasmids and 16 chromosomal prophages. Three different nematicidal toxin genes were identified and classified according to the Cry toxin naming committee as cry13Aa2, cry13Ba1, and cry13Ab1. Strikingly, these genes are located on the chromosome in close proximity to three separate prophages. Moreover, four putative toxin genes of different toxin classes were identified on the plasmids p120510 (Vip-like toxin), p120416 (Cry-like toxin) and p109822 (two Bin-like toxins). A comparative genome analysis of 10.1601/nm.5000 MYBT18246 with three closely related 10.1601/nm.5000 strains enabled determination of the pan-genome of 10.1601/nm.5000 MYBT18246, revealing a large number of singletons, mostly represented by phage genes, morons and cryptic genes.
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Affiliation(s)
- Jacqueline Hollensteiner
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna E. Sheppard
- Present address: Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Philip Rosentstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S. Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1205258. [PMID: 28819625 PMCID: PMC5551467 DOI: 10.1155/2017/1205258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/18/2017] [Indexed: 02/07/2023]
Abstract
This study has focused on the isolation of twenty-three halophilic actinomycetes from two ponds of different salinity and the evaluation of their ability to exert an antimicrobial activity against both their competitors and several other pathogens. From the 23 isolates, 18 strains showed antagonistic activity, while 19 showed activities against one or more of the seven pathogen strains tested. Six strains exhibited consistent antibacterial activity against Gram-negative and Gram-positive pathogens characterized at the physiological and molecular levels. These strains shared only 94-95% 16S rRNA sequence identity with the closely related species of the Thermoactinomycetaceae family. Among them, the potent strain SMBg3 was further characterized and assigned to a new genus in the family for which the name Paludifilum halophilum (DSM 102817T) is proposed. Sequential extraction of the antimicrobial compounds with ethyl acetate revealed that the crude extract from SMBg3 strain had inhibitory effect on the growth of the plant pathogen Agrobacterium tumefaciens and the human pathogens Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa. Based on the HRESI-MS spectral data, the cyclic lipopeptide Gramicidin S and four cyclic dipeptides (CDPs) named cyclo(L-4-OH-Pro-L-Leu), cyclo(L-Tyr-L-Pro), cyclo(L-Phe-L-Pro), and cyclo(L-Leu-L-Pro) were detected in the fermentation broth of Paludifilum halophilum. To our knowledge, this is the first report on the isolation of these compounds from members of the Thermoactinomycetaceae family.
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Affiliation(s)
- Donyez Frikha Dammak
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Ziad Zarai
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, BPW, 1173 Sfax, Tunisia
| | - Soumaya Najah
- Institut de Biologie Integrative, UMR 9198, Université Paris-Sud, Bat 400, 91405 Orsay Cedex, France
| | - Rayed Abdennabi
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Mostafa E. Rateb
- School of Science & Sport, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Hafedh Mejdoub
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, FSS, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Sami Maalej
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
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Munson E, Carroll KC. What's in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015. J Clin Microbiol 2017; 55:24-42. [PMID: 27795334 PMCID: PMC5228236 DOI: 10.1128/jcm.01379-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Singh N, Goel G, Raghav M. Insights into virulence factors determining the pathogenicity of Cronobacter sakazakii. Virulence 2015; 6:433-40. [PMID: 25950947 PMCID: PMC4601314 DOI: 10.1080/21505594.2015.1036217] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 02/07/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen associated with outbreaks of life-threatening necrotizing enterocolitis, meningitis and sepsis in neonates and infants. The pathogen possesses an array of virulence factors which aid in tissue adhesion, invasion and host cell injury. Although the identification and validation of C. sakazakii virulence factors has been hindered by availability of suitable neonatal animal model, various studies has reported outer membrane protein A (ompA) as a potential virulence marker. Various other plasmid associated genes such as filamentous hemagglutinin (fhaBC), Cronobacter plasminogen activator (cpa) and genes responsible for iron acquisition (eitCBAD and iucABD/iutA) have been reported in different strains of C. sakazakii. Besides these proposed virulence factors, several biophysical growth factors such as formation of biofilms and resistance to various environmental stresses also contributes to the pathogenic potential of this pathogen. This review provides an update on virulence determinants associated with the pathogenesis of C. sakazakii. The potential reservoirs of the pathogen, mode of transmission and epidemiology are also discussed.
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Affiliation(s)
- Niharika Singh
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
| | - Mamta Raghav
- Department of Biotechnology and Bioinformatics; Jaypee University of Information Technology; Waknaghat, Solan, India
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Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy TBK, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Göker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 2015; 10:8. [PMID: 26203325 PMCID: PMC4511580 DOI: 10.1186/1944-3277-10-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/24/2014] [Indexed: 12/21/2022] Open
Abstract
Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1(T) along with its complete genome sequence and annotation from a culture of DSM 17521(T). The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
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Affiliation(s)
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - TBK Reddy
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | | | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Brian J Tindall
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
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