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Tran TTH, Nguyen TPA, Pham TD, Nguyen TH, Nguyen TLD, Nguyen TTT, Tran TLH, Giang TK, Bui TTH, Do BC, Nguyen TT, Haltrich D, Nguyen HA. Histamine-degrading halophilic bacteria from traditional fish sauce: Characterization of Virgibacillus campisalis TT8.5 for histamine reduction. J Biotechnol 2023; 366:46-53. [PMID: 36933867 DOI: 10.1016/j.jbiotec.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/24/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
Traditionally produced fish sauce can contain significant amounts of histamine. In some instances, the histamine concentration may be well above the limit recommended by the Codex Alimentarius Commission. The aim of this study was to discover new bacterial strains capable of growing under the stressful environmental conditions of fish sauce fermentation and metabolizing histamine. In this study, 28 bacterial strains were isolated from Vietnamese fish sauce products based on their ability to grow at high salt concentrations (23% NaCl) and tested for their ability to degrade histamine. Strain TT8.5 showed the highest histamine-degradation (45.1 ± 0.2% of initially 5 mM histamine within 7 days) and was identified as Virgibacillus campisalis TT8.5. Its histamine-degrading activity was shown to be localized intracellularly and the enzyme is a putative histamine dehydrogenase. The strain exhibited optimal growth and histamine-degrading activity at 37°C, pH 7%, and 5% NaCl in halophilic archaea (HA) histamine broth. It also showed pronounced histamine-degrading activity in HA histamine broth when cultivated at temperatures of up to 40 °C as well as in the presence of up to 23% NaCl. After treatment with immobilized cells, 17.6-26.9% of the initial histamine in various fish sauce products were reduced within 24 h of incubation, while no significant changes in other parameters of fish sauce quality were observed after this treatment. Our results indicate that V. campisalis TT8.5 is of potential interest to be applied in histamine degradation of traditional fish sauce.
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Affiliation(s)
- Thi Thu Hang Tran
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Phuong Anh Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Diu Pham
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Hong Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Lam Doan Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Thanh Thuy Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Lan Huong Tran
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Trung Khoa Giang
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Thi Thu Hien Bui
- Research Institute for Marine Fisheries, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam
| | - Bien-Cuong Do
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Viet Nam
| | - Tien-Thanh Nguyen
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Viet Nam
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences Vienna, Austria.
| | - Hoang Anh Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam.
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Wei YL, Long ZJ, Ren MX. Microbial community and functional prediction during the processing of salt production in a 1000-year-old marine solar saltern of South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152014. [PMID: 34852250 DOI: 10.1016/j.scitotenv.2021.152014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
In Hainan Island, South China, a 1000-year-old marine saltern has been identified as an intangible cultural heritage due to its historical complicated salt-making techniques, whereas the knowledge about this saltern is extremely limited. Herein, DNA sequencing and biochemical technologies were applied to determine bacterial and fungal communities of this saltern and their possible functions during four stages of salt-making, i.e. seawater storage, mud solarization, brine concentrating, and solar crystallization. The results showed that both of bacterial and fungal communities were suffered from significant changes during processing of salt-making in Danzhou Ancient Saltern, whereas the richness and diversity of bacterial community dominated by Proteobacteria, Bacteroidota and Cyanobacteria was considerably greater than that of fungal community dominated by Ascomycota, Basidiomycota and Mortierellomycota. Additionally, the succession of bacterial community was closely associated with both of salt physicochemical properties (Na+, Cl-, total phosphorus, total nitrogen, Ca2+ and Mg2+) and bacteria themselves, whereas fungal community was more closely associated with physicochemical properties than fungi themselves. Importantly, Cyanobium_PCC-6307, Synechococcus_CC9902, Marinobacter, Prevotella and Halomonas as dominant bacterial genera respectively related to the metabolisms of amino acid, carbohydrate, terpenoids/polyketides, lipid and nucleotide were correlated with salt flavors. Saprophytic and saprotroph-symbiotroph fungi dominated by Aspergillus, Mortierella, Amanita, Neocucurbitaria and Tausonia also played core roles in the formation of salt flavors including umami and sweet smells. These findings revealed the highly specified microbiome community in this 1000-year-old saltern that mainly selected by brine solarization on basalt platforms, which is helpful to explore the underlying mechanisms of traditional salt-making techniques and to explore the useful microbes for nowadays food, medicine and chemical industries.
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Affiliation(s)
- Ya-Li Wei
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China
| | - Zi-Jie Long
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China
| | - Ming-Xun Ren
- Ministry of Education Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Hainan University, Haikou 570228, PR China; Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, PR China.
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Khalilova EA, Kotenko ST, Islammagomedova EA, Abakarova AA, Chernyh NА, Aliverdiyeva DA. Halophilic bacteria of salt lakes and saline soils of the Peri-Caspian lowland (Republic of Daghestan) and their biotechnological potential. Vavilovskii Zhurnal Genet Selektsii 2021; 25:224-233. [PMID: 34901720 PMCID: PMC8627887 DOI: 10.18699/vj21.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/02/2022] Open
Abstract
The article presents the results of studying the biodiversity and biotechnological potential of halophilic
microorganisms from the thermal highly mineralized Berikey Lake, the salty Lake Tarumovskoye and saline soils of
the Peri-Caspian Lowland (Republic of Daghestan). Denitrifying halophilic bacteria of the genus Halomonas and
Virgibacillus were identified using microbiological methods and 16S rRNA gene analysis. A new species Halomonas sp. G2 (MW386470) with a similarity of the nucleotide sequences of the 16S rRNA genes is 95 %. Strain G2 is
an extreme halophile capable of growing in the range of 5–25 % NaCl (optimum 25 %) and forming a carotenoid
pigment. Mesophil, 30–37 °С (optimum 30 °С); neutrophil, pH 6–8 (optimum 7.2–7.4). Strain G2 chemolithotroph;
reduces nitrate or nitrite as electron donors; catalase-, amylase-, protease- and β-galactosidase-positive; lipase-,
oxidase- and urease-negative. Not able to hydrolyze inositol, indole; produces lysine, gelatin, ectoine; uses citrate
and sodium malate as a source of carbon and energy; does not produce ornitin, H2S or acid from d-mannose, sucrose, glycerol, cellobiose, except for lactose and d-glucose. Susceptible to trimethoprim, ciprofloxacin, ofloxacin,
kanamycin, vancomycin, rifampicin, cefuroxime, ampicillin, ceftazidime, fosfomycin, clarithromycin, cefepime, cefaclor. The G+C content in DNA is 67.3 %. A distinctive characteristic of the isolate was the production of industrially significant hydrolytic enzymes such as amylase, protease, β-galactosidase, and oxidoreductase (catalase) at a
NaCl concentration of 25 % in the medium. Habitat: saline soils on the territory of the Tersko-Kumskaya lowland
(Republic of Daghestan, Russia). The rest of the halophilic isolates of H. ventosae G1 (MW386469), H. elongata G3
(MW386471), V. salinarius B2 (MW386472), and V. salinarius B3 (MW386473) had a high degree of similarity (100 %)
with the type strains of H. elongata DSM 2581Т
and V. salarius DSM 18441Т
; the content of G+C in DNA was 65.8,
66.5, 42.8 and 37.3 %, respectively. The strains had a high biotechnological potential at NaCl concentrations of 5 and
25 % in the medium. The data obtained expanded the understanding of the diversity and ecological significance
of denitrifying bacteria in the functioning of arid ecosystems and make it possible to identify strains producing
enzymes of industrial importance.
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Affiliation(s)
- E A Khalilova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - S T Kotenko
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - E A Islammagomedova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - A A Abakarova
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
| | - N А Chernyh
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - D A Aliverdiyeva
- Precaspian Institute of Biological Resources of the Daghestan Federal Research Center of the Russian Academy of Sciences, Makhachkala, Daghestan, Russia
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Wang HT, Xu L, Sun JQ. Aquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011. Int J Syst Evol Microbiol 2021; 71. [PMID: 34617881 DOI: 10.1099/ijsem.0.005030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-14.0 % NaCl (optimum, 5.0-8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain HU2P27T with A. koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.
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Affiliation(s)
- Hai-Tao Wang
- Lab for Microbial Resources, Inner Mongolia Key Lab of Environmental Pollution Prevention and Waste Resource Recycle and Ministry of Education Key Lab of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Lab for Microbial Resources, Inner Mongolia Key Lab of Environmental Pollution Prevention and Waste Resource Recycle and Ministry of Education Key Lab of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
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5
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Xu B, Hu B, Wang J, Lan Y, Zhu Y, Dai X, Huang L, Huang Y, Du W. Virgibacillus indicus sp. nov. and Virgibacillus profundi sp. nov, two moderately halophilic bacteria isolated from marine sediment by using microfluidic streak plates. Int J Syst Evol Microbiol 2018; 68:2015-2023. [DOI: 10.1099/ijsem.0.002782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bingxue Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yaxin Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wenbin Du
- Savaid Medical School, University of 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
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6
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Oh YJ, Jang JY, Lim SK, Kwon MS, Lee J, Kim N, Shin MY, Park HK, Seo MJ, Choi HJ. Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2017; 55:933-938. [PMID: 29214493 DOI: 10.1007/s12275-017-7386-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/13/2017] [Indexed: 11/27/2022]
Abstract
A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1T (96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius SA-Vb1T (96.7%). The isolate grew at pH 6.5-10.0 (optimum, pH 8.5-9.0), 0.0-25.0% (w/v) NaCl (optimum, 10-15% NaCl), and 15-50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C14:0, anteisio-C15:0, iso- C15:0, and iso-C16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2T was 42.5 mol%. On the basis of these findings, strain NKC1-2T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404T =JCM 32284T). The type strain of Virgibacillus kimchii is NKC1-2T.
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Affiliation(s)
- Young Joon Oh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Ja-Young Jang
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seul Ki Lim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Min-Sung Kwon
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jieun Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - NamHee Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Mi-Young Shin
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
- Division of Animal Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyo Kyeong Park
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
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7
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Zhang DC, Schumann P, Wu J, França L, Neuner K, Margesin R. Virgibacillus flavescens sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:1138-1143. [DOI: 10.1099/ijsem.0.000846] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- De-Chao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, PRChina
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jiang Wu
- College of Agronomy & Resources and Environment, Tianjin Agricultural University, 300384, Tianjin, PRChina
| | - Luís França
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Kathrin Neuner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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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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9
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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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10
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Nioella nitratireducens gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from Azorean Island. Antonie van Leeuwenhoek 2014; 107:589-95. [PMID: 25500750 DOI: 10.1007/s10482-014-0355-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
A novel Gram-negative, non-spore forming, rod-shaped aerobic bacterium, designated SSW136(T), was isolated from a surface seawater sample collected at Espalamaca (in Faial Island), Azores. Growth was found to occur from 10 to 37 °C, pH 6.0-8.0, and with 2-11 % of NaCl. 16S rRNA gene sequence indicated that the strain SSW136(T) belongs to the family Rhodobacteraceae. Strain SSW136(T) exhibited 96.3, 95.9, 95.7 and 95.5 sequence similarity to the type strains Oceanicola litoreus M-M22(T), Roseovarius aestuarii SMK-122(T), Marivita geojedonensis DPG-138(T), and Pseudoruegeria aquimaris SW-255(T) respectively. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSW136(T) was affiliated to the family Rhodobacteraceae and formed a separate branch. The G+C content was 63.5 mol%. The major respiratory quinone was found to be Q-10. The polar lipids of strain SSW136(T) consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and three unidentified phospholipids. The major fatty acids were C18:1 ω7c (46.5 %), Cyclo-C19:0 ω8c (16.0 %) and C16:0 (12.8 %). On the basis of the morphological, genotypic, chemotaxonomic characteristics and low DNA-DNA relatedness, strain SSW136(T) is proposed to represent a novel genus and novel species, Nioella nitratireducens gen. nov., sp. nov., in the family Rhodobacteraceae. The type strain is SSW136(T) (=KCTC 32417(T) = NCIM 5499(T)).
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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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12
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Seiler H, Wenning M. Virgibacillus
halotolerans sp. nov., isolated from a dairy product. Int J Syst Evol Microbiol 2013; 63:3358-3363. [DOI: 10.1099/ijs.0.051565-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, rod-shaped and weakly motile bacterium, designated WS 4627T, was isolated from a dairy product sample collected in southern Germany. Spherical to slightly ellipsoidal endospores were formed centrally or subterminally in sometimes slightly swollen sporangia. The isolate was able to grow at 8–35 °C, at pH 6.5–8.5 and with 0.5–16.5 % (w/v) NaCl. The diamino acid of the cell wall was meso-diaminopimelic acid (peptidoglycan type A1γ) and the genomic DNA G+C content was 39.1 mol%. The major menaquinone was MK-7, the cellular fatty acid profile contained major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Strain WS 4627T was most closely related to ‘
Virgibacillus
natachei’ FarD (96.5 % 16S rRNA gene sequence similarity) and ‘
Virgibacillus
zhanjiangensis’ JSM 079157 (96.0 %). Based on the data presented, strain WS 4627T represents a novel species of the genus
Virgibacillus
, for which the name
Virgibacillus
halotolerans sp. nov. is proposed. The type strain is WS 4627T ( = DSM 25060T = LMG 26644T).
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Affiliation(s)
- Herbert Seiler
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
| | - Mareike Wenning
- Department of Microbiology (ZIEL), Technische Universität München, Weihenstephaner Berg 3, D-85350 Freising, Germany
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13
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Amziane M, Metiaz F, Darenfed-Bouanane A, Djenane Z, Selama O, Abderrahmani A, Cayol JL, Fardeau ML. Virgibacillus natechei sp. nov., a moderately halophilic bacterium isolated from sediment of a saline lake in southwest of Algeria. Curr Microbiol 2013; 66:462-6. [PMID: 23306353 DOI: 10.1007/s00284-012-0300-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 12/23/2012] [Indexed: 10/27/2022]
Abstract
A novel, Gram-positive, moderately halophilic bacterium, oxidase- and catalase-positive designated FarD(T) was isolated from sediments of a saline lake located in Taghit, 93 km from Bechar, southwest of Algeria. Cells were rod-shaped, endospore forming, and motile. Growth occurred at 15-40 °C (optimum, 35 °C), pH 6.0-12.0 (optimum, 7.0) and in the presence of 1-20 % NaCl (optimum, 10 %). Strain FarD(T) used glucose, mannitol, melibiose, D-mannose, and 5 ketogluconate. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and three phospholipids; MK-7 is the predominant menaquinone. The predominant cellular fatty acids were anteiso C15:0, anteiso C17:0, C20:0, and anteiso C19:0. The DNA G+C content was 42.1 mol%. Phylogenetic analysis of the small-subunit ribosomal RNA gene sequence indicated that strain FarD(T) had as its closest relative Virgibacillus salinus (similarity of 96.3 %). Based on phenotypic, phylogenetic, and taxonomic characteristics, strain FarD(T) is proposed as a novel species of the genus Virgibacillus within the order Clostridiales, for which the name V. natechei is proposed. The type strain is FarD(T) (=DSM 25609(T) = CCUG 62224(T)).
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Affiliation(s)
- Meriam Amziane
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria
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Virgibacillus albus sp. nov., a novel moderately halophilic bacterium isolated from Lop Nur salt lake in Xinjiang province, China. Antonie van Leeuwenhoek 2012; 102:553-60. [PMID: 22622623 DOI: 10.1007/s10482-012-9750-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/05/2012] [Indexed: 10/28/2022]
Abstract
A Gram-positive, moderately halophilic, strictly aerobic bacterium, designated YIM 93624(T), was isolated from a salt lake in Xinjiang province of China and subjected to a polyphasic taxonomic study. Strain YIM 93624(T) grew at 15-45 °C (optimum 25-30 °C), 1-17% (w/v) NaCl (optimum 5-10 %, w/v) and pH 4.0-9.0 (optimum pH 7.0). The predominant menaquinone was found to be MK-7. The major fatty acids were anteiso-C(15:0) and C(16:0). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93624(T) was a member of the genus Virgibacillus and exhibited the highest similarity of 97.0 % to Virgibacillus koreensis KCTC 3823(T). However, the level of DNA-DNA relatedness between strain YIM 93624(T) and V. koreensis KCTC 3823(T) was 32.5 %. On the basis of phylogenetic, physiological and chemotaxonomic analysis data, the isolate is concluded to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus albus sp. nov., is proposed, with type strain of YIM 93624(T) (=DSM 23711(T) = JCM 17364(T)).
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