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Draft Genome Sequences of the Kocuria subflava Type Strain KCTC 39547 and
Kocuria
sp. Strain JC486, a Newly Isolated Strain from a Wild Ass Sanctuary in Gujarat, India. Microbiol Resour Announc 2022; 11:e0053522. [DOI: 10.1128/mra.00535-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report a 2.86-Mbp genome sequence of
Kocuria
sp. strain JC486, which was isolated from a salt marsh, and a 3.03-Mbp sequence of the type strain
Kocuria subflava
KCTC 39547. Prediction from their genomes indicates that both strains are nonpathogenic.
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Palyzová A, Řezanka T. Separation and identification of diacylglycerols containing branched chain fatty acids by liquid chromatography-mass spectrometry. J Chromatogr A 2020; 1635:461708. [PMID: 33223151 DOI: 10.1016/j.chroma.2020.461708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/08/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
A combination of two chromatographic and two enzymatic methods was used for the analysis of molecular species of lipids from Gram-positive bacteria of the genus Kocuria. Gram-positive bacteria contain a majority of branched fatty acids (FAs), especially iso- and/or anteiso-FAs. Two strains K. rhizophila were cultivated at three different temperatures (20, 28, and 37°C) and the majority phospholipid, i.e., the mixture of molecular species of phosphatidylglycerols (PGs) was separated by means of hydrophilic interaction liquid chromatography (HILIC). After enzymatic hydrolysis of PGs by phospholipase C and derivatization of the free OH group, the sn-1,2-diacyl-3-acetyl triacylglycerols (AcTAGs) were separated by reversed phase HPLC. Molecular species such as i-15:0/i-15:0/2:0, ai-15:0/ai-15:0/2:0, and 15:0/15:0/2:0 (straight chains) were identified by liquid chromatography-positive electrospray ionization mass spectrometry. The tandem mass spectra of both standards and natural compounds containing iso, anteiso and straight chain FAs with the same carbons were identical. Therefore, for identification of the ratio of two regioisomers, i.e. i-15:0/ai-15:0/2:0 vs. ai-15:0/i-15:0/2:0, they were cleavage by pancreatic lipase. The mixture of free fatty acids (FFAs) and 2-monoacylglycerols (2-MAGs) was obtained. After their separation by TLC and esterification and/or transesterification, the fatty acid methyl esters were quantified by GC-MS and thus the ratio of regioisomers was determined. It has been shown that the ratio of PG (containing as majority i-15: 0 / i-15: 0, i-15: 0 / ai-15: 0 and / or ai-15: 0 / i-15: 0 and ai-15: 0 / ai-15: 0 molecular species) significantly affected the membrane flow of bacterial cells cultured at different temperatures.
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Affiliation(s)
- Andrea Palyzová
- Institute of Microbiology, the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Tomáš Řezanka
- Institute of Microbiology, the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
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Li J, Zhang S. Kocuria coralli sp. nov., a novel actinobacterium isolated from coral reef seawater. Int J Syst Evol Microbiol 2020; 70:785-789. [PMID: 31671054 DOI: 10.1099/ijsem.0.003825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinobacterial strain, SCSIO 13007T, was isolated from seawater collected from the Luhuitou fringing reef at a depth of 4.2 m. Phylogenetic and phenotypic properties of the organism supported the hypothesis that it represented a member of the genus Kocuria. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between SCSIO 13007T and type strains of other recognized members of the genus Kocuria were lower than 96.99 %. Growth in the presence of up to 15 % (w/v) NaCl was a distinctive characteristic of SCSIO 13007T. Other biochemical and physiological properties and the major fatty acids also differentiated the isolate from its phylogenetically closest relative Kocuria subflava YIM 13062T. The menaquinone types were MK-7(H2) and MK-8(H2). Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified lipid and an unidentified aminolipid. The DNA G+C content was 73.7 mol%. The combined genotypic and phenotypic data indicated that strain SCSIO 13007T represents a novel species of the genus Kocuria, for which the name Kocuria coralli sp. nov. is proposed; the type strain is SCSIO 13007T (=DSM 27811T=NBRC 109942T).
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
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Tuo L, Li FN, Bao YX, Yan XR, Sun CH. Kocuria soli sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2019; 69:2064-2068. [DOI: 10.1099/ijsem.0.003438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Li Tuo
- 1Research Center for Medicine & Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Fei-Na Li
- 2Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Xin Bao
- 1Research Center for Medicine & Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Rui Yan
- 1Research Center for Medicine & Biology, Zunyi Medical University, Zunyi 563006, PR China
| | - Cheng-Hang Sun
- 2Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
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Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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Řezanka T, Gharwalová L, Nováková G, Kolouchová I, Uhlík O, Sigler K. KocuriaBacterial Isolates from Radioactive Springs of Jáchymov spa (Joachimsthal) as Sources of Polyunsaturated Fatty Acids. Lipids 2019; 54:177-187. [DOI: 10.1002/lipd.12136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Tomáš Řezanka
- Institute of MicrobiologyThe Czech Academy of Sciences Vídeňská 1083, 142 20, Prague Czech Republic
| | - Lucia Gharwalová
- Department of Biotechnology, Faculty of Food and Biochemical TechnologyUniversity of Chemistry and Technology Prague Technická 5, 166 28, Prague Czech Republic
| | - Gabriela Nováková
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical TechnologyUniversity of Chemistry and Technology Prague Technická 5, 166 28, Prague Czech Republic
| | - Irena Kolouchová
- Department of Biotechnology, Faculty of Food and Biochemical TechnologyUniversity of Chemistry and Technology Prague Technická 5, 166 28, Prague Czech Republic
| | - Ondřej Uhlík
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical TechnologyUniversity of Chemistry and Technology Prague Technická 5, 166 28, Prague Czech Republic
| | - Karel Sigler
- Institute of MicrobiologyThe Czech Academy of Sciences Vídeňská 1083, 142 20, Prague Czech Republic
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Sun W, Liu C, Zhang F, Zhao M, Li Z. Comparative Genomics Provides Insights Into the Marine Adaptation in Sponge-Derived Kocuriaflava S43. Front Microbiol 2018; 9:1257. [PMID: 29937765 PMCID: PMC6002675 DOI: 10.3389/fmicb.2018.01257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Sponge-derived actinomycetes represent a significant component of marine actinomycetes. Members of the genus Kocuria are distributed in various habitats such as soil, rhizosphere, clinical specimens, marine sediments, and sponges, however, to date, little is known about the mechanism of their environmental adaptation. Kocuria flava S43 was isolated from a coastal sponge. Phylogenetic analysis revealed that it was closely related to the terrestrial airborne K. flava HO-9041. In this study, to gain insights into the marine adaptation in K. flava S43 we sequenced the draft genome for K. flava S43 by third generation sequencing (TGS) and compared it with those of K. flava HO-9041 and some other Kocuria relatives. Comparative genomics and phylogenetic analyses revealed that K. flava S43 might adapt to the marine environment mainly by increasing the number of the genes linked to potassium homeostasis, resistance to heavy metals and phosphate metabolism, and acquiring the genes associated with electron transport and the genes encoding ATP-binding cassette (ABC) transporter, aquaporin, and thiol/disulfide interchange protein. Notably, gene acquisition was probably a primary mechanism of environmental adaptation in K. flava S43. Furthermore, this study also indicated that the Kocuria isolates from various marine and hyperosmotic environments possessed common genetic basis for environmental adaptation.
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Affiliation(s)
- Wei Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changrong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengli Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingzhu Zhao
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:2463-2466. [DOI: 10.1099/ijsem.0.001149] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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