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Mahmoud H, Eapen S, Al-Bajjali F, Al-Qattan A, Jose L. Litoribacterium kuwaitense gen. nov., sp. nov., isolated from a Kuwait tidal flat. Int J Syst Evol Microbiol 2021; 71. [PMID: 33909547 PMCID: PMC8289215 DOI: 10.1099/ijsem.0.004792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, spore-forming, rod-shaped and non-motile bacterium designated strain SIJ1T was obtained from tidal flat sediment collected from the northern shore of Kuwait Bay, northwest of the Arabian Gulf. Strain SIJ1T grew optimally at 30 °C and pH 7–8 in the presence of 6 % (w/v) NaCl. The cell-wall peptidoglycan was based on meso-diaminopimelic acid and an unsaturated menaquinone with seven isoprene units (MK-7) was the predominant respiratory quinone. It contained anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0 as the major fatty acids and ribose as the major whole-cell sugar. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipid, an unidentified glycolipid, phosphoglycolipid and an unidentified lipid. Phylogenetic analysis based on 16S rRNA genes revealed that SIJ1T showed a distinct evolutionary lineage within the Firmicutes. The DNA G+C content was 43.1 mol% and the full genome analysis for strain SIJ1T showed that it had a genome size of 3 989 945 bp and contained 4085 predicted protein-encoding genes. The SIJ1T annotated genome showed more stress resistance encoding genes in comparison to its closely related strains. The amino acid identity and average nucleotide identity data for the whole genome proved that strain SIJ1T does indeed represent a novel genus. The strain was distinguishable from the phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strain SIJ1T represents a novel genus and species in the family Bacillaceae, for which the name Litoribacterium kuwaitense gen. nov., sp. nov. is proposed. The type strain is SIJ1T (=DSM 28862T=LMG 28316T).
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Affiliation(s)
- Huda Mahmoud
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
- *Correspondence: Huda Mahmoud,
| | - Susan Eapen
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
| | - Fatimah Al-Bajjali
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
| | - Anwar Al-Qattan
- Department of Earth, Ocean and Atmospheric Sciences, Faculty of Science, The University of British Columbia, Vancouver, Canada
| | - Liny Jose
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat 13060, Kuwait
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Salam N, Xian WD, Asem MD, Xiao M, Li WJ. From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:132-147. [PMID: 37073336 PMCID: PMC10077289 DOI: 10.1007/s42995-020-00064-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.
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Affiliation(s)
- Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou, 510275 China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
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3
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Kumaunang M, Sanchart C, Suyotha W, Maneerat S. Virgibacillus halodenitrificans MSK-10P, a Potential Protease-producing Starter Culture for Fermented Shrimp Paste (kapi) Production. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2019. [DOI: 10.1080/10498850.2019.1652874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Maureen Kumaunang
- Biotechnology for Bioresource Utilization Laboratory, Department of Industrial Biotechnology, Faculty of Agro‑Industry, Prince of Songkla University, HatYai, Thailand
- Department of Chemistry, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado, Indonesia
| | - Chatthaphisuth Sanchart
- Biotechnology for Bioresource Utilization Laboratory, Department of Industrial Biotechnology, Faculty of Agro‑Industry, Prince of Songkla University, HatYai, Thailand
| | - Wasana Suyotha
- Biotechnology for Bioresource Utilization Laboratory, Department of Industrial Biotechnology, Faculty of Agro‑Industry, Prince of Songkla University, HatYai, Thailand
| | - Suppasil Maneerat
- Biotechnology for Bioresource Utilization Laboratory, Department of Industrial Biotechnology, Faculty of Agro‑Industry, Prince of Songkla University, HatYai, Thailand
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Li J, Liu J, Shen Y, Ni J. Swionibacillus sediminis gen. nov., sp. nov., a member of the family Bacillaceae isolated from ocean sediment. Int J Syst Evol Microbiol 2017; 67:3440-3445. [DOI: 10.1099/ijsem.0.002133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Junfeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yulong Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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5
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Liu Y, Liang J, Zhang Z, Yu M, Wang M, Zhang XH. Aureibacillus halotolerans gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3950-3958. [PMID: 28875917 DOI: 10.1099/ijsem.0.000518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, strictly aerobic, spore-forming and rod-shaped motile bacterium with peritrichous flagellae, designated strain S1203T, was isolated from the sediment of the northern Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S1203T formed a lineage within the family Bacillaceae that was distinct from the most closely related genera Bacillus, Bhargavaea, Planomicrobium and Virgibacillus with gene sequence similarities ranging from 86.2 to 93.76 %. Optimal growth occurred in the presence of 4-8 % (w/v) NaCl, at pH 7.0-8.0 and 25-32 °C. The cell-wall peptidoglycan was based on meso-diaminopimelic acid and unsaturated menaquinone with seven isoprene units (MK-7) as the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0.The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The DNA G+C content of strain S1203T was 47.7 mol%. On the basis of polyphasic analysis, strainS1203T was considered to represent a novel species in a new genus of the family Bacillaceae, for which the name Aureibacillus halotolerans gen. nov., sp. nov. is proposed; the type strain of Aureibacillus halotolerans is S1203T ( = DSM 28697T = JCM 30067T = MCCC 1K00259T).
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Affiliation(s)
- Yan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jing Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zenghu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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Khelaifia S, Croce O, Lagier JC, Robert C, Couderc C, Di Pinto F, Davoust B, Djossou F, Raoult D, Fournier PE. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut. New Microbes New Infect 2015; 8:78-88. [PMID: 26649181 PMCID: PMC4644261 DOI: 10.1016/j.nmni.2015.09.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 11/23/2022] Open
Abstract
Strain Vm-5(T) was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5(T) (CSUR P971 = DSM 28587).
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Affiliation(s)
- S. Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - O. Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Di Pinto
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - B. Davoust
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Djossou
- Centre Hospitalier André Rosemon, Cayenne, French Guiana
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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7
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Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut. New Microbes New Infect 2015; 8:116-26. [PMID: 26693281 PMCID: PMC4660226 DOI: 10.1016/j.nmni.2015.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Virgibacillus senegalensis SK-1(T) (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.
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Affiliation(s)
- E. Seck
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - J. Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - S. Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - O. Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Di Pinto
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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Adaptation in Haloalkaliphiles and Natronophilic Bacteria. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lee SY, Kang CH, Oh TK, Yoon JH. Virgibacillus campisalis sp. nov., from a marine solar saltern. Int J Syst Evol Microbiol 2011; 62:347-351. [PMID: 21441379 DOI: 10.1099/ijs.0.033084-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-variable, motile, endospore-forming and rod-shaped bacterial strain, IDS-20(T), was isolated from a marine solar saltern in Korea and subjected to a polyphasic taxonomic investigation. Strain IDS-20(T) grew optimally at 37 °C, at pH 7.5-8.0 and in the presence of 4-5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IDS-20(T) belongs to the genus Virgibacillus. Strain IDS-20(T) exhibited 93.4-96.6 % 16S rRNA gene sequence similarity to the type strains of species of the genus Virgibacillus. Strain IDS-20(T) had MK-7 as the predominant menaquinone and a cell-wall peptidoglycan based on meso-diaminopimelic acid. The major fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0) and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unidentified phospholipids. The DNA G+C content was 39.5 mol%. The phylogenetic distinctiveness and differential phenotypic characteristics of strain IDS-20(T) demonstrated that this strain can be distinguished from recognized species of the genus Virgibacillus. On the basis of the data presented, strain IDS-20(T) represents a novel species of the genus Virgibacillus, for which the name Virgibacillus campisalis sp. nov. is proposed. The type strain is IDS-20(T) ( = KCTC 13727(T) = CCUG 59308(T)).
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Affiliation(s)
- Soo-Young Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejon, Republic of Korea
| | - Chul-Hyung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea.,Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejon, Republic of Korea
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Kim J, Jung MJ, Roh SW, Nam YD, Shin KS, Bae JW. Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food. Int J Syst Evol Microbiol 2011; 61:2851-2855. [PMID: 21239563 DOI: 10.1099/ijs.0.028191-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-positive, rod-shaped, motile, endospore-forming, halophilic bacterial strain, J18(T), was isolated from a traditional salt-fermented seafood made of gizzard shad in Korea. Colonies were convex, cream-coloured and 1.0-2.0 mm in diameter after incubation for 3 days on marine agar. Growth occurred at pH 7.0-11.0 (optimum, pH 10.0), at 4-40 °C (optimum, 37 °C) and in the presence of 0-30% NaCl (optimum, 9-10%). On the basis of 16S rRNA gene sequence analysis, strain J18(T) was related most closely to Virgibacillus byunsanensis ISL-24(T) (96.3% similarity), Virgibacillus carmonensis LMG 20964(T) (96.2%), Virgibacillus halodenitrificans DSM 10037(T) (96.0%), Virgibacillus arcticus Hal 1(T) (95.5%) and Virgibacillus necropolis LMG 19488(T) (95.5%). The major fatty acids were anteiso-C(15:0) and anteiso-C(17:0). The DNA G+C content of strain J18(T) was 37.0 mol%. The cell-wall peptidoglycan was of the meso-diaminopimelic acid type. The major quinone was menaquinone 7 (MK-7). Based on phenotypic, chemotaxonomic and phylogenetic data, strain J18(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus alimentarius sp. nov. is proposed. The type strain is J18(T) (=KACC 14624(T) =JCM 16994(T)).
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Affiliation(s)
- Jandi Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Mi-Ja Jung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Young-Do Nam
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Kee-Sun Shin
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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Phrommao E, Rodtong S, Yongsawatdigul J. Identification of novel halotolerant bacillopeptidase F-like proteinases from a moderately halophilic bacterium, Virgibacillus sp. SK37. J Appl Microbiol 2010; 110:191-201. [DOI: 10.1111/j.1365-2672.2010.04871.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bioprospecting microbial natural product libraries from the marine environment for drug discovery. J Antibiot (Tokyo) 2010; 63:415-22. [PMID: 20606699 DOI: 10.1038/ja.2010.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future.
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Kämpfer P, Arun AB, Busse HJ, Langer S, Young CC, Chen WM, Syed AA, Rekha PD. Virgibacillus soli sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2010; 61:275-280. [PMID: 20228217 DOI: 10.1099/ijs.0.020974-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive bacterium (strain CC-YMP-6(T)) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6(T) clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6(T) were iso-C(15 : 0) and anteiso-C(15 : 0). The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6(T) from all recognized species of the genus Virgibacillus. Strain CC-YMP-6(T) is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6(T) (=DSM 22952(T)=CCM 7714(T)).
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Affiliation(s)
- P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - A B Arun
- Yenepoya Research Centre, Yenepoya University, University Rd, Deralakatee, Mangalore, Karnataka State, India
| | - H-J Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - S Langer
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - C-C Young
- College of Agriculture and Natural Resources, Department of Soil & Environmental Sciences, National Chung Hsing University, Taichung, 402, Taiwan, ROC
| | - W-M Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung, Taiwan, ROC
| | - A A Syed
- Yenepoya Research Centre, Yenepoya University, University Rd, Deralakatee, Mangalore, Karnataka State, India
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya University, University Rd, Deralakatee, Mangalore, Karnataka State, India
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Liu W, Jiang L, Guo C, Yang SS. Terribacillus aidingensis sp. nov., a moderately halophilic bacterium. Int J Syst Evol Microbiol 2010; 60:2940-2945. [PMID: 20118295 DOI: 10.1099/ijs.0.017228-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-positive, moderately halophilic bacteria, designated YI7-61(T), IA7 and DB2, were isolated from sediments of Aiding salt lake in the Xinjiang region of China. Cells of the strains were rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Colonies were pale yellow in colour. The strains grew optimally at 30-37 °C, pH 6-7 and 3-7 % (w/v) NaCl. The diamino acid in the murein was meso-diaminopimelic acid and the major quinone system was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 44.6-45.0 mol%. 16S rRNA gene sequence analysis revealed that strains YI7-61(T), IA7 and DB2 were closely related to members of the genus Terribacillus and showed 96.8-97.6, 96.4-97.2 and 95.4-95.5 % 16S rRNA gene sequence similarity with Terribacillus halophilus 002-051(T), Terribacillus saccharophilus RB589 and Terribacillus goriensis CL-GR16(T), respectively. DNA-DNA relatedness among the isolates was 88-92 % and strain YI7-61(T) shared 24, 18 and 18 % DNA-DNA relatedness with T. halophilus JCM 21760(T), T. saccharophilus JCM 21759(T) and T. goriensis DSM 18252(T), respectively. On the basis of phenotypic and phylogenetic distinctiveness, the three isolates should be placed in the genus Terribacillus as representatives of a novel species, for which the name Terribacillus aidingensis sp. nov. is proposed. The type strain is YI7-61(T) (=CGMCC 1.8913(T) =NBRC 105790(T)).
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Affiliation(s)
- Wenyan Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, Beijing 100088, PR China.,College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
| | - Linlin Jiang
- Northeast Agricultural University, Haerbin 150030, PR China
| | - Chunjing Guo
- Northeast Agricultural University, Haerbin 150030, PR China
| | - Su Sheng Yang
- Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Key Laboratory for Agro-Microbial Resource and Application, Ministry of Agriculture, Beijing 100193, PR China
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16
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Wang X, Xue Y, Ma Y. Virgibacillus subterraneus sp. nov., a moderately halophilic Gram-positive bacterium isolated from subsurface saline soil. Int J Syst Evol Microbiol 2010; 60:2763-2767. [PMID: 20061492 DOI: 10.1099/ijs.0.019554-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram reaction-positive, moderately halophilic bacterium, designated H57B72(T), was isolated from subsurface saline soil of Qaidam basin in the Qinghai province, China. Cells were rod-shaped, strictly aerobic, spore-forming and motile. The isolate grew optimally at 9 % (w/v) NaCl, pH7.5 and 30°C. The cell-wall peptidoglycan of strain H57B72(T) contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) (59.97 %) and anteiso-C(17 : 0) (17.14 %). Phosphatidylglycerol, diphosphatidylglycerol and a glycolipid were found to be the predominant polar lipids. The genomic DNA G+C content of strain H57B72(T) was 37.1mol%. 16S rRNA gene sequence analysis showed that strain H57B72(T) was a member of the genus Virgibacillus and was most closely related to Virgibacillus salinus DSM 21756(T) (98.3 % gene sequence similarity). The level of DNA-DNA relatedness between strain H57B72(T) and V. salinus DSM 21756(T) was 8.5 %. Based on the phenotypic, genotypic and phylogenetic data presented, strain H57B72(T) represents a novel species, for which the name Virgibacillus subterraneus sp. nov. is proposed. The type strain is H57B72(T) (=DSM 22441(T) =CGMCC 1.7734(T)).
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Affiliation(s)
- Xiaowei Wang
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Peng QZ, Chen J, Zhang YQ, Chen QH, Peng DJ, Cui XL, Li WJ, Chen YG. Virgibacillus zhanjiangensis sp. nov., a marine bacterium isolated from sea water. Antonie van Leeuwenhoek 2009; 96:645-52. [PMID: 19774482 DOI: 10.1007/s10482-009-9381-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
A Gram-positive, endospore-forming, catalase- and oxidase-positive, motile, rod-shaped, aerobic bacterium, designated strain JSM 079157(T), was isolated from surface seawater off the coastline of Naozhou Island in South China Sea. The organism was able to grow with 1-15% (w/v) total salts (optimum, 4-7%), and at pH 6.0-10.0 (optimum, pH 7.5) and 10-45 degrees C (optimum, 30 degrees C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7, and the polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were anteiso-C(15:0) (45.1%) and anteiso-C(17:0) (16.2%), and the DNA G + C content was 39.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 079157(T) should be assigned to the genus Virgibacillus, being related most closely to the type strains of Virgibacillus litoralis (97.4% sequence similarity), Virgibacillus necropolis (97.3%) and Virgibacillus carmonensis (97.1%). These four strains formed a distinct subcluster in the phylogenetic tree. The levels of DNA-DNA relatedness between the new isolate and the type strains of V. litoralis, V. necropolis and V. carmonensis were 30.4, 19.3 and 12.6%, respectively. The results of the phylogenetic analysis, combined with DNA-DNA relatedness data, phenotypic characteristics and chemotaxonomic information, support the suggestion that strain JSM 079157(T) represents a new species of the genus Virgibacillus, for which the name Virgibacillus zhanjiangensis sp. nov. is proposed. The type strain is JSM 079157(T) (=DSM 21084(T) = KCTC 13227(T)).
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Affiliation(s)
- Qing-Zhong Peng
- College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, People's Republic of China
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Yoon JH, Kang SJ, Jung YT, Lee KC, Oh HW, Oh TK. Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2009; 60:291-295. [PMID: 19651717 DOI: 10.1099/ijs.0.009837-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-variable, motile, endospore-forming and rod-shaped bacterial strain, ISL-24(T), was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by a polyphasic study. Strain ISL-24(T) grew optimally at pH 7.0-8.0, at 30-37 degrees C and in the presence of 8 % (w/v) NaCl. It contained MK-7 as the predominant menaquinone and anteiso-C(15 : 0) as the predominant fatty acid. The DNA G+C content was 37.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-24(T) fell within the genus Virgibacillus, clustering with Virgibacillus carmonensis LMG 20964(T) and Virgibacillus necropolis LMG 19488(T), with a bootstrap resampling value of 92.3 %, and exhibiting 97.3 and 97.4 % 16S rRNA gene sequence similarity, respectively, to these strains. Strain ISL-24(T) exhibited 94.8-96.8 % 16S rRNA gene sequence similarity to the type strains of the other Virgibacillus species. Mean DNA-DNA relatedness values between strain ISL-24(T) and V. carmonensis DSM 14868(T) and V. necropolis DSM 14866(T) were 11 and 19 %, respectively. Differential phenotypic properties of strain ISL-24(T), together with the phylogenetic and genetic distinctiveness, revealed that this strain is different from recognized Virgibacillus species. On the basis of phenotypic, phylogenetic and genetic data, strain ISL-24(T) represents a novel species of the genus Virgibacillus, for which the name Virgibacillus byunsanensis sp. nov. is proposed. The type strain is ISL-24(T) (=KCTC 13259(T) =CCUG 56754(T)).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Yong-Taek Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Keun Chul Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Hyun Woo Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
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