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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Boya BR, Kumar P, Lee JH, Lee J. Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. Microorganisms 2021; 9:microorganisms9102156. [PMID: 34683477 PMCID: PMC8537960 DOI: 10.3390/microorganisms9102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.
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Gomez-Gil B, González-Castillo A, Aguilar-Méndez MJ, López-Cortés A, Gómez-Gutiérrez J, Roque A, Lang E, Enciso-Ibarra J. Veronia nyctiphanis gen. nov., sp. nov., Isolated from the Stomach of the Euphausiid Nyctiphanes simplex (Hansen, 1911) in the Gulf of California, and Reclassification of Enterovibrio pacificus as Veronia pacifica comb. nov. Curr Microbiol 2021; 78:3782-3790. [PMID: 34410465 DOI: 10.1007/s00284-021-02627-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
The bacterial strain 42Xb2 T was isolated from a female adult krill Nyctiphanes simplex infected with the apostome parasitoid ciliate Pseudocollinia brintoni in January 2007 in the Gulf of California. The strain has the morphological, phenotypic, and molecular characteristics of the bacteria of the family Vibrionaceae. The 16S rRNA gene sequence has a similarity of 97.7% with Enterovibrio pacificus SW014 T and 96.1% similarity with Enterovibrio norvegicus LMG 19839 T. A phylogenomic and a multilocus sequence analyses placed this strain close to the genera Enterovibrio, Grimontia, and Salinivibrio, but clearly forming a separate branch from these bacterial genera. Genomic analyses presented further support this result. A novel genus Veronia gen. nov. and a species Veronia nyctiphanis sp. nov. is here described with CAIM 600 T (= DSM 24592 T = CECT 7578 T) as the type strain. Morphological, physiological, and genetic evidence presented here support the unification of Enterovibrio pacificus and Veronia nyctiphanis in the new genus Veronia. Enterovibrio pacificus is reclassified as Veronia pacifica. V. pacifica is assigned as the type species of the new genus Veronia.Genome Sequencing Data The GenBank/EMBL/DDBJ accession numbers for the genome sequence of Veronia nyctiphanis CAIM 600 T is PEIB01 and of Enterovibrio pacificus CAIM 1920 T is LYBM01. The 16S rRNA gene sequence of V. nyctiphanis CAIM 600 T is JX129353.
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Affiliation(s)
- Bruno Gomez-Gil
- CIAD, A.C. Mazatlán Unit for Aquaculture and Environmental Management, A.P. 711, 82000, Mazatlán, Sinaloa, Mexico.
| | - Adrián González-Castillo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México
| | - Mario J Aguilar-Méndez
- Laboratorio de Geomicrobiología Y Biotecnología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), 23096, La Paz, BCS, Mexico.,Instituto Politécnico Nacional (IPN), Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato (UPIIG), 36275, Silao de la Victoria, Guanajuato, Mexico
| | - Alejandro López-Cortés
- Laboratorio de Geomicrobiología Y Biotecnología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), 23096, La Paz, BCS, Mexico
| | - Jaime Gómez-Gutiérrez
- Instituto Politécnico, Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. IPN s/n, Col. Palo de Santa Rita, 23096, La Paz, BCS, Mexico
| | - Ana Roque
- Institut de Recerca I Tecnologia Agroalimentaries, Centre d'Aquicultura, Sant Carles de La Rapita, Spain
| | - Elke Lang
- Leibniz Institute DSMZ - Deutsche Sammlung Von Mikroorganismen Und Zellkulturen GmbH, Inhoffenstr. 7B, 38124, Braunschweig, Germany
| | - Julissa Enciso-Ibarra
- CIAD, A.C. Mazatlán Unit for Aquaculture and Environmental Management, A.P. 711, 82000, Mazatlán, Sinaloa, Mexico
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Wang X, Guo F, Tian P, Yu S, Xue CX, Wang W, Xiao J, Niu W. Vibrio agarilyticus sp. nov., an agar-digesting marine bacterium isolated from coastal seawater in Daya Bay (Guangdong, China). Int J Syst Evol Microbiol 2021; 71. [PMID: 33480834 DOI: 10.1099/ijsem.0.004647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-strain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacterium, designated SM6T, was isolated from surface seawater collected in Daya Bay (Guangdong, China). Phylogenetic analysis based on 16S rRNA gene sequences, multilocus sequence analysis, phylogenomic analysis of single-copy gene families and whole genome data showed that strain SM6T belonged to the genus Vibrio. The closest phylogenetic relatives of SM6T were Vibrio plantisponsor MSSRF60T (97.38 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis R-40492T (97.27 %), Vibrio aestuarianus ATCC 35048T (97.21 %) and Vibrio sagamiensis LC2-047T (97.3 %). Growth of strain SM6T occurred at 10-45 °C (optimum 30 °C), at pH 6.0-9.0 (optimum 6.0) and in the presence of 0-10 % (w/v) NaCl (optimum 3-8 %). The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1 ω7c or/and C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c). The DNA G+C content of the assembled genomic sequences was 47.37 % for strain SM6T. Average nucleotide identity values between SM6T and its reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further showed that the strains shared less than 70 % similarity. On the basis of evidence from the present polyphasic study, strain SM6T is considered to represent a novel species of the genus Vibrio, for which the name Vibrio agarilyticus sp. nov. is proposed. The type strain is SM6T (=KCTC 82076T=MCCC 1K04327 T).
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Affiliation(s)
- Xiaolei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Feng Guo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Peng Tian
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Shuangen Yu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Wei Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Jiaguang Xiao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
| | - Wentao Niu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Xiamen 361005, PR China
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Kurakin GF, Samoukina AM, Potapova NA. Bacterial and Protozoan Lipoxygenases Could be Involved in Cell-to-Cell Signaling and Immune Response Suppression. Biochemistry (Mosc) 2020; 85:1048-1071. [PMID: 33050851 DOI: 10.1134/s0006297920090059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipoxygenases are found in animals, plants, and fungi, where they are involved in a wide range of cell-to-cell signaling processes. The presence of lipoxygenases in a number of bacteria and protozoa has been also established, but their biological significance remains poorly understood. Several hypothetical functions of lipoxygenases in bacteria and protozoa have been suggested without experimental validation. The objective of our study was evaluating the functions of bacterial and protozoan lipoxygenases by evolutionary and taxonomic analysis using bioinformatics tools. Lipoxygenase sequences were identified and examined using BLAST, followed by analysis of constructed phylogenetic trees and networks. Our results support the theory on the involvement of lipoxygenases in the formation of multicellular structures by microorganisms and their possible evolutionary significance in the emergence of multicellularity. Furthermore, we observed association of lipoxygenases with the suppression of host immune response by parasitic and symbiotic bacteria including dangerous opportunistic pathogens.
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Affiliation(s)
- G F Kurakin
- Department of Biochemistry and Laboratory Medicine, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia.
| | - A M Samoukina
- Department of Microbiology, Virology, and Immunology, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia
| | - N A Potapova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B. Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes. Appl Environ Microbiol 2020; 86:e02788-19. [PMID: 31953333 DOI: 10.1128/AEM.02788-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation. The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.
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Li Y, Liang J, Liu R, Xue CX, Zhou S, He X, Li B, Wang X, Zhang XH. Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:889-896. [DOI: 10.1099/ijsem.0.003842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Yuying Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Ronghua Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Shun Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xinxin He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Bei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiaolei 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
- 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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Azevedo GPR, Mattsson HK, Appolinario LR, Calegario G, Leomil L, Walter JM, Campeão M, Tonon LAC, Moreira APB, Vidal L, Vieira VV, Otsuki K, Tschoeke DA, Swings J, Thompson FL, Thompson CC. Enterovibrio baiacu sp. nov. Curr Microbiol 2020; 77:154-7. [PMID: 31620811 DOI: 10.1007/s00284-019-01785-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
We report here the novel species to encompass the isolate A649T (=CBAS 716T = CBRVS P1061T) obtained from viscera of the healthy pufferfish Sphoeroides spengleri (Family Tetraodontidae). Genomic taxonomy analysis demonstrates that the novel strain A649T had < 95% average amino acid identity/average nucleotide identity (AAI/ANI) and < 70% similarity of genome-to-genome distance (GGDH) towards its closest neighbors which places A649T into a new Enterovibrio species (Enterovibrio baiacu sp nov.). In silico phenotyping disclosed several features that may be used to differentiate related Enterovibrio species. The nearly complete genome assembly of strain A649T consisted of 5.4 Mbp and 4826 coding genes.
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Meng YC, Liu HC, Zhou YG, Cai M, Kang Y. Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen. Int J Syst Evol Microbiol 2018; 68:1969-1974. [DOI: 10.1099/ijsem.0.002779] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yu-Chen Meng
- Department of Microbiology, Key Laboratory of Environmental Pollution Monitoring/Disease Control, Ministry of Education and Key Laboratory of Medical Microbiology and Parasitology, Guizhou Medical University, Guiyang 550025, PR China
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Man Cai
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yingqian Kang
- Department of Microbiology, Key Laboratory of Environmental Pollution Monitoring/Disease Control, Ministry of Education and Key Laboratory of Medical Microbiology and Parasitology, Guizhou Medical University, Guiyang 550025, PR China
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Doi H, Osawa I, Adachi H, Kawada M. Vibrio japonicus sp. nov., a novel member of the Nereis clade in the genus Vibrio isolated from the coast of Japan. PLoS One 2017; 12:e0172164. [PMID: 28231272 PMCID: PMC5322892 DOI: 10.1371/journal.pone.0172164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/30/2017] [Indexed: 11/20/2022] Open
Abstract
A novel Vibrio strain, JCM 31412T, was isolated from seawater collected from the Inland Sea (Setonaikai), Japan, and characterized as a Gram-negative, oxidase-positive, catalase-negative, facultatively anaerobic, motile, ovoid-shaped bacterium with one polar flagellum. Based on 16S rDNA gene identity, strain JCM 31412T showed a close relationship with type strains of Vibrio brasiliensis (LMG 20546T, 98.2% identity), V. harveyi (NBRC 15634T, 98.2%), V. caribbeanicus (ATCC BAA-2122T, 97.8%) and V. proteolyticus (NBRC 13287T, 97.8%). The G+C content of strain JCM 31412T DNA was 46.8%. Multi-locus sequence analysis (MLSA) of eight loci (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA; 5535bp) further clustered strain JCM 31412T in the Nereis clade, genus Vibrio. Phenotypically, strain JCM 31412T differed from the closest related Vibrio species in its utilization of melibiose and raffinose, and its lack of casein and gelatin hydrolysis. It was further differentiated based on its fatty acid composition, specifically properties of C12:03OH and summed features, which were significantly different from those of V. brasiliensis, V. nigripulchritudo and V. caribbeanicus type strains. Overall, the results of DNA-DNA hybridization, and physiological and biochemical analysis differentiated strain JCM 31412T from other described species of the genus Vibrio. Based on these polyphasic taxonomic findings, it was therefore concluded that JCM 31412T was a novel Vibrio species, for which the name Vibrio japonicus sp. nov. was proposed, with JCM 31412T (= LMG 29636T = ATCC TSD-62T) as the type strain.
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Affiliation(s)
- Hiroyasu Doi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Numazu-shi, Shizuoka, Japan
- * E-mail:
| | - Ikuko Osawa
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa, Tokyo, Japan
| | - Hayamitsu Adachi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Numazu-shi, Shizuoka, Japan
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Numazu-shi, Shizuoka, Japan
- Institute of Microbial Chemistry (BIKAKEN), Shinagawa, Tokyo, Japan
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Adin DM, Visick KL, Stabb EV. Identification of a cellobiose utilization gene cluster with cryptic beta-galactosidase activity in Vibrio fischeri. Appl Environ Microbiol 2008; 74:4059-69. [PMID: 18487409 DOI: 10.1128/AEM.00190-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellobiose utilization is a variable trait that is often used to differentiate members of the family Vibrionaceae. We investigated how Vibrio fischeri ES114 utilizes cellobiose and found a cluster of genes required for growth on this beta-1,4-linked glucose disaccharide. This cluster includes genes annotated as a phosphotransferase system II (celA, celB, and celC), a glucokinase (celK), and a glucosidase (celG). Directly downstream of celCBGKA is celI, which encodes a LacI family regulator that represses cel transcription in the absence of cellobiose. When the celCBGKAI gene cluster was transferred to cellobiose-negative strains of Vibrio and Photobacterium, the cluster conferred the ability to utilize cellobiose. Genomic analyses of naturally cellobiose-positive Vibrio species revealed that V. salmonicida has a homolog of the celCBGKAI cluster, but V. vulnificus does not. Moreover, bioinformatic analyses revealed that CelG and CelK share the greatest homology with glucosidases and glucokinases in the phylum Firmicutes. These observations suggest that distinct genes for cellobiose utilization have been acquired by different lineages within the family Vibrionaceae. In addition, the loss of the celI regulator, but not the structural genes, attenuated the ability of V. fischeri to compete for colonization of its natural host, Euprymna scolopes, suggesting that repression of the cel gene cluster is important in this symbiosis. Finally, we show that the V. fischeri cellobioase (CelG) preferentially cleaves beta-d-glucose linkages but also cleaves beta-d-galactose-linked substrates such as 5-bromo-4-chloro-3-indolyl-beta-d-galactoside (X-gal), a finding that has important implications for the use of lacZ as a marker or reporter gene in V. fischeri.
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Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, Hoste B, Munn CB, Swings J. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 2005; 71:5107-15. [PMID: 16151093 PMCID: PMC1214639 DOI: 10.1128/aem.71.9.5107-5115.2005] [Citation(s) in RCA: 311] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.
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Affiliation(s)
- F L Thompson
- Microbial Resources Division and Brazilian Collection of Environmental and Industrial Micro-Organisms (CBMAI), CPQBA, UNICAMP, CP 6171, 13081-970 Campinas, Brazil.
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Abstract
Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.
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Affiliation(s)
- Fabiano L Thompson
- Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium.
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Abstract
We describe the polyphasic characterization of four Vibrio isolates which formed a tight AFLP group in a former study. The group was closely related to V. cyclitrophicus, V. lentus and V. splendidus (98.2-98.9% similarity) on the basis of the 16S rDNA sequence analysis, but by DNA-DNA hybridisation experiments it had at maximum 61% DNA similarity towards V. splendidus. Thus, we propose that the isolates represent a new Vibrio species i.e. V. tasmaniensis (LMG 20012T; EMBL under the accession numbers AJ316192; mol% G+C of DNA of the type strain is 44.7). Useful phenotypical features for discrimination of V. tasmaniensis from other Vibrio species include gelatinase and beta-galactosidase activity, fatty acid composition (particularly 14:0), utilisation and fermentation of different compounds (e.g. sucrose, melibiose and D-galactose) as sole carbon source.
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Affiliation(s)
- F L Thompson
- Laboratory for Microbiology, Ghent University, K.L. Ghent, Belgium.
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