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Zhang P, Wang X, Liu R, Zhu X, Zhao W, Zhang XH. Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748487 DOI: 10.1099/ijsem.0.005674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26T and ZSDZ34T within the genus Vibrio, family Vibrionaceae, class Gammaproteobacteria. Strain ZSDE26T was most closely related to Vibrio gallaecicus VB 8.9T with 97.3 % sequence similarity, whereas ZSDZ34T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723T with 97.8 % sequence similarity. Strain ZSDE26T grew with 1-5 % (w/v) NaCl (optimum, 4 %), at 16-28 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Growth of strain ZSDZ34T occurred with 1-6 % (w/v) NaCl (optimum, 3 %), at 16-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. Additionally, strain ZSDZ34T contained a higher proportion of iso-C16 : 0. The DNA G+C contents of strains ZSDE26T and ZSDZ34T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26T and ZSDZ34T are considered to represent novel species within the genus Vibrio, for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26T=KCTC 82890T=MCCC 1K06290T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34T=KCTC 82888T=MCCC 1K06292T) are proposed, respectively.
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Affiliation(s)
- Pingping Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Xiaolei Wang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Ronghua Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Xiaoyu Zhu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Wenbin Zhao
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 5 Yushan Road, Qingdao 266003, PR China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
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Kim YO, Park IS, Kim DG, Park S, Han SH, Yoon JH. Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748413 DOI: 10.1099/ijsem.0.005593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, flagellated and coccoid, ovoid or rod-shaped bacterial strain, NIFS-20-8T, was isolated from the intestine of an olive flounder (Paralichthys olivaceus) from the East Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain NIFS-20-8T fell within the clade comprising the type strains of Enterovibrio species. Strain NIFS-20-8T exhibited 16S rRNA gene sequence similarities of 97.2 and 97.1 % to the type strains of Enterovibrio nigricans and Enterovibrio norvegicus, respectively, and of 96.6-97.0 % to the type strains of the other Enterovibrio species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequence of strain NIFS-20-8T and those of the type strains of four Enterovibrio species were 73.8-75.0 and 19.8-21.1 %, respectively. The DNA G+C content of strain NIFS-20-8T from genomic sequence data was 50.55 mol%. Strain NIFS-20-8T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C18 : 1 ω7c as the major fatty acids. The major polar lipids detected in stain NIFS-20-8T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain NIFS-20-8T is separated from recognized Enterovibrio species. On the basis of the data presented here, strain NIFS-20-8T is considered to represent a novel species of the genus Enterovibrio, for which the name Enterovibrio paralichthyis sp. nov. is proposed. The type strain is NIFS-20-8T (= KCTC 82873T=NBRC 115237T).
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Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - In-Suk Park
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sung Hoon Han
- Sungkyun Biotech Co., Ltd, Suwon 16419, Gwonseon-gu, Suwon 16648, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, Republic of Korea
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González-Castillo A, Carballo JL, Bautista-Guerrero E. Genomics, Phylogeny, and in Silico Phenotyping of Nitrosopumilus Genus. Curr Microbiol 2022; 80:3. [PMID: 36427110 DOI: 10.1007/s00284-022-03121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
The present study reports the first genome of Nitrosopumilus extracted from the marine sponge Thoosa mismalolli. The genomic study of Nitrosopumilus genus using seven genomes type strains (N. maritimus, N. piranensis, N. zosterae, N. ureiphilus, N. adriaticus, N. oxyclinae and N. cobalaminigenes), four genomes Candidatus species (Ca. N. koreensis, Ca. N. sp. AR2, Ca. N. salaria BD31, and SZUA-335), and six reference genomes (SI075, SI0036, SI0060, SI0034, SI0048, and bin36o) isolated from marine sponge, a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, near-surface sediment, and MAG N. sp NMAG03 isolated from Thoosa mismalolli was performed. These genomes were characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA) of 139 single-copy genes (SCG), core-pangenome, ANI, and in silico phenotypic characterization. We found that the genomes of the Nitrosopumilus genus formed three separate clusters (A, B, and C) based in 139 SCG sequence similarity. The genomes showed values between 75.2 and 99.5% for ANI, the core genome consisted of 168 gene families and the pangenome of 6,011 gene families. Based on the genomic analyses performed, the cluster A may contain a potential new species (NMAG03), and the cluster C could be represented by three new species of the genus. Finally, based on the results shown in this polyphasic approach, we support the use of the integrated approach for genomic analysis of poorly studied genera.
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Affiliation(s)
- Adrián González-Castillo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.
| | - José Luis Carballo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.,Departamento de Zoología, Laboratorio de Biología Marina, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012, Seville, Spain
| | - Eric Bautista-Guerrero
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de La Costa, Universidad de Guadalajara, Puerto Vallarta, México
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Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203. Int J Syst Evol Microbiol 2022; 72. [PMID: 35108178 DOI: 10.1099/ijsem.0.005167] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 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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Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL, Thompson FL, Gomez-Gil B, Sawabe T. Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach. Curr Microbiol 2021; 79:10. [PMID: 34905112 DOI: 10.1007/s00284-021-02725-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
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Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayo Nishikawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, España
| | - Fabiano L Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC, Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, México
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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