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Barcia-Cruz R, Balboa S, Lema A, Romalde JL. Comparative genomics of Vibrio toranzoniae strains. Int Microbiol 2024:10.1007/s10123-024-00557-z. [PMID: 38995500 DOI: 10.1007/s10123-024-00557-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade that was originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at the genomic level among six strains (4 isolated from clam and 2 from seawater) and to determine their phylogeny. For this purpose, whole genomes of the six strains were sequenced by different technologies including Illumina and PacBio, and the resulting sequences were corrected. Genomes were annotated and compared using different online tools. Furthermore, the study of core- and pan-genomes were examined, and the phylogeny was inferred. The content of the core genome ranged from 2953 to 2766 genes and that of the pangenome ranged from 6278 to 6132, depending on the tool used. Although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI values higher than 97%, some differences were found related to motility, capsule synthesis, iron acquisition systems or mobile genetic elements. Phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle (commensal or free-living), but that of the pangenome indicated certain geographical isolation in the same growing area. This study led to the reclassification of some isolates formerly described as V. toranzoniae and demonstrated the importance of cured deposited sequences to proper phylogenetic assignment.
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Affiliation(s)
- Rubén Barcia-Cruz
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- French Agency for Food, Environmental and Occupational Health and Safety (Anses), 94701, Maisons-Alfort Cedex, France
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- Centro de Investigación Interdisciplinar en Tecnología Ambientales (CRETUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain
- AllGenetics & Biology SL, Oleiros, 15172, Perillo, A Coruña, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida S/N, 15782, Santiago de Compostela, Spain.
- Centro de Investigación Interdisciplinar en Tecnología Ambientales (CRETUS), Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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Barcia-Cruz R, Balboa S, Lema A, Romalde JL. Comparative genomics of Vibrio toranzoniae strains. RESEARCH SQUARE 2024:rs.3.rs-4360386. [PMID: 38826277 PMCID: PMC11142368 DOI: 10.21203/rs.3.rs-4360386/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.
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3
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Jiang C, Kasai H, Mino S, Romalde JL, Sawabe T. The pan‐genome of Splendidus clade species in the family
Vibrionaceae
: insights into evolution, adaptation, and pathogenicity. Environ Microbiol 2022; 24:4587-4606. [DOI: 10.1111/1462-2920.16209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Hisae Kasai
- Laboratory of Marine Biotechnology and 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 Spain
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
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4
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Lattos A, Bitchava K, Giantsis IA, Theodorou JA, Batargias C, Michaelidis B. The Implication of Vibrio Bacteria in the Winter Mortalities of the Critically Endangered Pinna nobilis. Microorganisms 2021; 9:922. [PMID: 33925782 PMCID: PMC8145015 DOI: 10.3390/microorganisms9050922] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/25/2023] Open
Abstract
Pinna nobilis populations, constituting the largest bivalve mollusk endemic to the Mediterranean, is characterized as critically endangered, threatened by extinction. Among the various factors proposed as etiological agents are the Haplosporidium pinnae and Mycobacterium sp. parasites. Nevertheless, devastation of the fan mussel populations is still far from clear. The current work is undertaken under a broader study aiming to evaluate the health status of Pinna nobilis population in Aegean Sea, after the mass mortalities that occurred in 2019. A significant objective was also (a) the investigation of the etiological agents of small-scale winter mortalities in the remaining populations after the devastating results of Haplosporidium pinnae and Mycobacterium sp. infections, as well as (b) the examination of the susceptibility of the identified bacterial strains in antibiotics for future laboratory experiments. Microbiological assays were used in order to detect the presence of potential bacterial pathogens in moribund animals in combination with molecular tools for their identification. Our results provide evidence that Vibrio bacterial species are directly implicated in the winter mortalities, particularly in cases where the haplosporidian parasite was absent. Additionally, this is the first report of Vibrio mediterranei and V. splendidus hosted by any bivalve on the Greek coastline.
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Affiliation(s)
- Athanasios Lattos
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Konstantina Bitchava
- Laboratory of Fish, Shellfish & Crustacean Diseases, Veterinary Research Institute of Thessaloniki ELGO-DEMETER, 570 01 Thessaloniki, Greece;
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 531 00 Florina, Greece
| | - John A. Theodorou
- Department of Animal Production Fisheries & Aquaculture, University of Patras, 232 00 Mesolonghi, Greece; (J.A.T.); (C.B.)
| | - Costas Batargias
- Department of Animal Production Fisheries & Aquaculture, University of Patras, 232 00 Mesolonghi, Greece; (J.A.T.); (C.B.)
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
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Chen X, Ye Q, Sanders CJ, Du J, Zhang J. Bacterial-derived nutrient and carbon source-sink behaviors in a sandy beach subterranean estuary. MARINE POLLUTION BULLETIN 2020; 160:111570. [PMID: 32861939 DOI: 10.1016/j.marpolbul.2020.111570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities in subterranean estuaries play important roles in the biogeochemical cycle. However, the microorganisms associated with biogeochemical behaviors in subterranean estuaries have received little attention. Here, the bacterial communities were compared between the fresh and saline groundwater in a subterranean estuary. Correlation analysis between bacterial groups and salinity indicated that different species represented different groundwater types. The key bacterial groups found along the subterranean estuaries have been shown to influence organic pollutant degradation and nitrate utilization. These species may be potential candidates for the in situ bioremediation of subterranean estuaries that are contaminated with pollutants. The utilization of nitrate and organic pollutants by bacteria in subterranean estuaries serves as a nitrate sink and inorganic carbon source. Our results show the role of bacteria in remediating pollutants through submarine groundwater discharge (SGD) to the coastal ocean, and specific species may be helpful in selecting reasonable groundwater end-members and reducing SGD uncertainties.
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Affiliation(s)
- Xiaogang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; School of Engineering, Westlake University, Hangzhou 310024, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Christian J Sanders
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW 2450, Australia
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Institute of Eco-Chongming (IEC), Shanghai 202162, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
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Thode SK, Rojek E, Kozlowski M, Ahmad R, Haugen P. Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives. PLoS One 2018; 13:e0191860. [PMID: 29444108 PMCID: PMC5812596 DOI: 10.1371/journal.pone.0191860] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/13/2018] [Indexed: 11/19/2022] Open
Abstract
Siderophores are small molecules synthesized and secreted by bacteria and fungi to scavenge iron. Extracellular ferri-siderohores are recognized by cognate receptors on the cell surface for transport over membranes. Several siderophore systems from Vibrionaceae representatives are known and well understood, e.g., the molecular structure of the siderophore, the biosynthesis gene cluster and pathway, and the gene expression pattern. Less is known about how these systems are distributed among the ~140 Vibrionaceae species, and which evolutionary processes contributed to the present-day distribution. In this work, we compiled existing knowledge on siderophore biosynthesis systems and siderophore receptors from Vibrionaceae and used phylogenetic analyses to investigate their organization, distribution, origin and evolution. Through literature searches, we identified nine different siderophore biosynthesis systems and thirteen siderophore receptors in Vibrionaceae. Homologs were identified by BLAST searches, and the results were mapped onto a Vibrionaceae phylogeny. We identified 81 biosynthetic systems distributed in 45 Vibrionaceae species and 16 unclassified Vibrionaceae strains, and 409 receptors in 89 Vibrionaceae species and 49 unclassified Vibrionaceae strains. The majority of taxa are associated with at least one type of siderophore biosynthesis system, some (e.g., aerobactin and vibrioferrin) of which are widely distributed in the family, whereas others (i.e., bisucaberin and vibriobactin) are found in one lineage. Cognate receptors are found more widespread. Phylogenetic analysis of three siderophore systems (piscibactin, vibrioferrin and aerobactin) show that their present-day distribution can be explained by an old insertion into Vibrionaceae, followed mainly by stable vertical evolution and extensive loss, and some cases of horizontal gene transfers. The present work provides an up to date overview of the distribution of siderophore-based iron acquisition systems in Vibrionaceae, and presents phylogenetic analysis of these systems. Our results suggest that the present-day distribution is a result of several evolutionary processes, such as old and new gene acquisitions, gene loss, and both vertical and horizontal gene transfers.
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Affiliation(s)
- Sunniva Katharina Thode
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
| | - Ewelina Rojek
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Mikolaj Kozlowski
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Natural Sciences and Technology, Faculty of Education and Natural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway
- * E-mail: (PH); (RA)
| | - Peik Haugen
- Department of Chemistry and Center for Bioinformatics (SfB), Faculty of Science and Technology, UiT − The Arctic University of Norway, Tromsø, Norway
- * E-mail: (PH); (RA)
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7
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Fang Y, Chen A, Dai H, Huang Y, Kan B, Wang D. Vibrio fujianensis sp. nov., isolated from aquaculture water. Int J Syst Evol Microbiol 2018; 68:1146-1152. [PMID: 29458501 DOI: 10.1099/ijsem.0.002642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A Gram-stain-negative, facultatively anaerobic strain, designated FJ201301T, was isolated from aquaculture water collected from Fujian province, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain FJ201301T belonged to the genus Vibrio, formed a distinct cluster with Vibriocincinnatiensis ATCC 35912T and shared the highest similarity with Vibriosalilacus CGMCC 1.12427T. A 15 bp insertion found in the 16S rRNA gene was a significant marker that distinguished strain FJ201301T from several phylogenetic neighbours (e.g. V. cincinnatiensis). Multilocus sequence analysis of eight genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA; concatenated 4135 bp sequence) showed that, forming a long and independent phylogenetic branch, strain FJ201301T clustered with V. cincinnatiensis ATCC 35912T, Vibrioinjenensis KCTC 32233T and Vibriometschnikovii CIP 69.14T clearly separated from V. salilacus CGMCC 1.12427T. Furthermore, the highest in silico DNA-DNA hybridization and average nucleotide identity values between strain FJ201301T and the closest related species were 26.3 and 83.1 % with V. cincinnatiensis ATCC 35912T, less than the proposed cutoff levels for species delineation, i.e. 70 and 95 %, respectively. Biochemical, sequence and genomic analysis suggested the designation of strain FJ201301T representing a novel species of the genus Vibrio, for which the name Vibrio fujianensis sp. nov. is proposed. The type strain is FJ201301T (=DSM 104687T=CGMCC 1.16099T).
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Affiliation(s)
- Yujie Fang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, PR China.,Center for Human Pathogen Collection, China CDC, Beijing 102206, PR China
| | - Aiping Chen
- Center for Disease Control and Prevention of Fujian Province, Fuzhou 350001, PR China
| | - Hang Dai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, PR China.,Center for Human Pathogen Collection, China CDC, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, PR China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, PR China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, PR China.,Center for Human Pathogen Collection, China CDC, Beijing 102206, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, PR China
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8
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Poli A, Romano I, Mastascusa V, Buono L, Orlando P, Nicolaus B, Leone L, Hong KW, Chan KG, Goh KM, Pascual J. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy. Antonie van Leeuwenhoek 2018; 111:1105-1115. [PMID: 29299771 DOI: 10.1007/s10482-017-1013-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022]
Abstract
Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).
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Affiliation(s)
- Annarita Poli
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Ida Romano
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Vincenza Mastascusa
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Lorena Buono
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Pierangelo Orlando
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Applied Science and Intelligent Systems (I.S.A.S.I.-C.N.R.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Barbara Nicolaus
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Luigi Leone
- Consiglio Nazionale delle Ricerche (C.N.R.), Institute of Biomolecular Chemistry (I.C.B.), via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Kar Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Javier Pascual
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Brunswick, Germany.
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Saulnier D, De Decker S, Tourbiez D, Travers MA. Development of a duplex Taqman real-time PCR assay for rapid identification of Vibrio splendidus -related and V. aestuarianus strains from bacterial cultures. J Microbiol Methods 2017; 140:67-69. [DOI: 10.1016/j.mimet.2017.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 10/24/2022]
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10
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Ismail MM, Ibrahim HAA. Phytoplankton and bacterial community structures and their interaction during red-tide phenomena. OCEAN SCIENCE JOURNAL 2017; 52:411-425. [DOI: 10.1007/s12601-017-0042-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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11
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Lasa A, Gibas CJ, Romalde JL. Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish. Front Microbiol 2017; 8:86. [PMID: 28194141 PMCID: PMC5277001 DOI: 10.3389/fmicb.2017.00086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022] Open
Abstract
Vibrio toranzoniae is a Gram-negative bacterium of the Splendidus clade within the Vibrio genus. V. toranzoniae was first isolated from healthy clams in Galicia (Spain) but recently was also identified associated to disease outbreaks of red conger eel in Chile. Experimental challenges showed that the Chilean isolates were able to produce fish mortalities but not the strains isolated from clams. The aim of the present study was to determine the differences at the genomic level between the type strain of the species (CECT 7225T) and the strain R17, isolated from red conger eel in Chile, which could explain their different virulent capacity. The genome-based comparison showed high homology between both strains but differences were observed in certain gene clusters that include some virulence factors. Among these, we found that iron acquisition systems and capsule synthesis genes were the main differential features between both genomes that could explain the differences in the pathogenicity of the strains. Besides, the studied genomes presented genomic islands and toxins, and the R17 strain presented CRISPR sequences that are absent on the type strain. Taken together, this analysis provided important insights into virulence factors of V. toranzoniae that will lead to a better understanding of the pathogenic process.
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Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Cynthia J Gibas
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte Charlotte, NC, USA
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela Santiago de Compostela, Spain
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Pérez-Cataluña A, Lucena T, Tarazona E, Arahal DR, Macián MC, Pujalte MJ. An MLSA approach for the taxonomic update of the Splendidus clade, a lineage containing several fish and shellfish pathogenic Vibrio spp. Syst Appl Microbiol 2016; 39:361-9. [DOI: 10.1016/j.syapm.2016.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/22/2016] [Accepted: 03/30/2016] [Indexed: 11/29/2022]
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13
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Abstract
Vibrio toranzoniae (CECT 7225T) was isolated from healthy reared carpet shell clams in Galicia (Northwest Spain). In addition, this species has been recently identified as a potential pathogen of red conger eel in Chile. The draft genome sequence has 4.5 Mbp, a G+C content of 43.9%, and >3,800 protein-coding genes.
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14
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Travers MA, Boettcher Miller K, Roque A, Friedman CS. Bacterial diseases in marine bivalves. J Invertebr Pathol 2015. [DOI: 10.1016/j.jip.2015.07.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Zhong ZP, Liu Y, Liu HC, Wang F, Zhou YG, Liu ZP. Vibrio salilacus sp. nov., a new member of the Anguillarum clade with six alleles of the 16S rRNA gene from a saline lake. Int J Syst Evol Microbiol 2015; 65:2653-2660. [DOI: 10.1099/ijs.0.000316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive, facultatively aerobic bacterium, strain DSG-S6T, was isolated from Dasugan Lake (salinity 3.1 %, w/w), China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain DSG-S6T were non-spore-forming, slightly bent rods, and motile by means of a single polar flagellum. Growth occurred in the presence of 0–7.0 % (w/v) NaCl (optimum, 2.0 %), at 4–35 °C (optimum, 30 °C) and at pH 6.0–10.5 (optimum, pH 8.0–8.5). C16 : 0, C18 : 1ω7c and C16 : 1ω7c and/or C16 : 1ω6c were the major fatty acids. Six alleles of the 16S rRNA gene sharing 98.9–99.9 % similarity were detected in strain DSG-S6T, which showed highest 16S rRNA gene sequence similarity to Vibrio aestuarianus ATCC 35048T (97.7 %), then to Vibrio pacinii LMG 19999T (97.6 %) and Vibrio metschnikovii CIP 69.14T (96.8 %). Multilocus sequence analysis of four housekeeping genes and 16S rRNA genes clearly clustered it as a member of the Anguillarum clade. Mean DNA–DNA relatedness between strain DSG-S6T and V. aestuarianus NBRC 15629T, V. pacinii CGMCC 1.12557T and V. metschnikovii JCM 21189T was 20.6 ± 2.3, 38.1 ± 3.5 and 24.2 ± 2.8 %, respectively. The DNA G+C content was 46.8 mol% (T
m). Based on the data, it is concluded that strain DSG-S6T represents a novel species of the genus Vibrio, for which the name Vibrio salilacus sp. nov. is proposed. The type strain is DSG-S6T ( = CGMCC 1.12427T = JCM 19265T).
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Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, 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
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Lasa A, Avendaño-Herrera R, Estrada JM, Romalde JL. Isolation and identification of Vibrio toranzoniae associated with diseased red conger eel (Genypterus chilensis) farmed in Chile. Vet Microbiol 2015; 179:327-31. [PMID: 26072371 DOI: 10.1016/j.vetmic.2015.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 05/19/2015] [Accepted: 06/05/2015] [Indexed: 11/29/2022]
Abstract
The present study deals with the first isolation of Vibrio toranzoniae from cultured red conger eel (Genypterus chilensis). During the summer season of 2011, mortalities were observed in young red conger eel at one aquaculture experimental rearing system in Quintay, Valparaiso, Chile. The microbiological analysis of the diseased fish resulted in the isolation of three dominant and representative isolates, designated as R.17, R.18 and R.19, which were obtained from gill, fin and external lesions from three different fish, respectively. All isolates were identified as V. toranzoniae by means of a polyphasic taxonomic approach, including phenotypic characterization, sequencing of 16S rRNA and housekeeping genes, and DNA-DNA hybridization. Inoculation of a representative strain (R18) in turbot as model fish species demonstrated the pathogenic potential for fish of the Chilean isolates. Results obtained indicate that the geographical and host distribution of V. toranzoniae is wider than expected, and that this species may have negative incidence in the culture of marine organisms.
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Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología. CIBUS-Facultad de Biología. Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), O'Higgins 1695, Concepción. Chile; Centro de Investigación Marina de Quintay (CIMARQ), Valparaíso, Chile.
| | - Juan M Estrada
- Centro de Investigación Marina de Quintay (CIMARQ), Valparaíso, Chile
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología. CIBUS-Facultad de Biología. Universidad de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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17
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Dubert J, Fernández-Pardo A, Nóvoa S, Barja JL, Prado S. Phytoplankton production systems in a shellfish hatchery: variations of the bacterial load and diversity of vibrios. J Appl Microbiol 2015; 118:1264-75. [PMID: 25728297 DOI: 10.1111/jam.12787] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/27/2022]
Abstract
AIMS Outbreaks of disease caused by some Vibrio species represent the main production bottleneck in shellfish hatcheries. Although the phytoplankton used as food is one of the main sources of bacteria, studies of the associated bacterial populations, specifically vibrios, are scarce. The aim of the study was the microbiological monitoring of the microalgae as the first step in assessing the risk disease for bivalve cultures. METHODS AND RESULTS Two phytoplankton production systems were sampled weekly throughout 1-year period in a bivalve hatchery. Quantitative analysis revealed high levels of marine heterotrophic bacteria in both systems throughout the study. Presumptive vibrios were detected occasionally and at low concentrations. In most of the cases, they belonged to the Splendidus and Harveyi clades. CONCLUSIONS The early detection of vibrios in the microalgae may be the key for a successful bivalve culture. Their abundance and diversity were affected by factors related to the hatchery environment. SIGNIFICANCE AND IMPACT OF THE STUDY This work represents the first long study where the presence of vibrios was evaluated rigorously in phytoplankton production systems and provides a suitable microbiological protocol to control and guarantee the quality of the algal cultures to avoid the risk of transferring potential pathogens to shellfish larvae and/or broodstock.
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Affiliation(s)
- J Dubert
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Fernández-Pardo
- Centro de Cultivos Mariños, Consellería do Mar, Xunta de Galicia, Ribadeo, Lugo, Spain
| | - S Nóvoa
- Centro de Cultivos Mariños, Consellería do Mar, Xunta de Galicia, Ribadeo, Lugo, Spain
| | - J L Barja
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - S Prado
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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A European epidemiological survey of Vibrio splendidus clade shows unexplored diversity and massive exchange of virulence factors. World J Microbiol Biotechnol 2015; 31:461-75. [DOI: 10.1007/s11274-015-1800-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/05/2015] [Indexed: 02/01/2023]
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19
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Rojas R, Miranda CD, Opazo R, Romero J. Characterization and pathogenicity of Vibrio splendidus strains associated with massive mortalities of commercial hatchery-reared larvae of scallop Argopecten purpuratus (Lamarck, 1819). J Invertebr Pathol 2015; 124:61-9. [DOI: 10.1016/j.jip.2014.10.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/27/2014] [Accepted: 10/28/2014] [Indexed: 11/15/2022]
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20
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Farto Seguín RM, Bermúdez MB, Rivera L, Nieto TP. Increased survival of juvenile turbot Scophthalmus maximus by using bacteria associated with cultured oysters. JOURNAL OF AQUATIC ANIMAL HEALTH 2014; 26:251-262. [PMID: 25361445 DOI: 10.1080/08997659.2014.920734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Preventing vibriosis in juvenile cultured Turbot Scophthalmus maximus caused by Vibrio anguillarum frequently requires the use of feed supplemented with antibiotics in addition to vaccines. Whether the use of probiotics instead of antibiotics in juvenile Turbot is a safer strategy requires more study. The antibacterial potential of 148 Vibrio spp. strains (mostly isolated from cultures of healthy oysters, clams, and Turbot) was analyzed in vitro against V. anguillarum and other pathogens by means of an agar diffusion assay. A wide spectrum of inhibitory activity was shown by 9 strains. Based on their easy phenotypic differentiation from V. anguillarum, we selected two strains (S1 and S2, both isolated from the European flat oyster Ostrea edulis) for testing in juvenile Turbot (3 g). None of the strains were virulent by intraperitoneal or bath challenges, and all were susceptible to the antibiotics most frequently used in aquaculture. Three different stocks of Turbot, which were assayed separately, were significantly protected from infection with V. anguillarum. The final survival rates of fish treated in mixed challenges with S1 or S2 and V. anguillarum were 44% and 66%, respectively, whereas only 17% of the fish treated with only the pathogenic strain survived. The application of probiotic strains also increased the survival time of juvenile Turbot after infection with V. anguillarum. Both strains persisted in the epidermal mucus layer of the fish for 30 d, and they were not displaced by the pathogen. These data prove the efficacy of using bacteria well adapted to the dynamics of culture production as a way to provide juvenile Turbot immediate protection against infection by V. anguillarum. Moreover, the epidermal mucus sampling was useful for investigating the persistence of both probiotic strains when exposed to the pathogen.
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Multilocus sequence analysis of putative Vibrio mediterranei strains and description of Vibrio thalassae sp. nov. Syst Appl Microbiol 2014; 37:320-8. [DOI: 10.1016/j.syapm.2014.05.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/02/2014] [Accepted: 05/02/2014] [Indexed: 11/21/2022]
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22
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Romalde JL, Dieguez AL, Lasa A, Balboa S. New Vibrio species associated to molluscan microbiota: a review. Front Microbiol 2014; 4:413. [PMID: 24427157 PMCID: PMC3877837 DOI: 10.3389/fmicb.2013.00413] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/16/2013] [Indexed: 01/22/2023] Open
Abstract
The genus Vibrio consists of more than 100 species grouped in 14 clades that are widely distributed in aquatic environments such as estuarine, coastal waters, and sediments. A large number of species of this genus are associated with marine organisms like fish, molluscs and crustaceans, in commensal or pathogenic relations. In the last decade, more than 50 new species have been described in the genus Vibrio, due to the introduction of new molecular techniques in bacterial taxonomy, such as multilocus sequence analysis or fluorescent amplified fragment length polymorphism. On the other hand, the increasing number of environmental studies has contributed to improve the knowledge about the family Vibrionaceae and its phylogeny. Vibrio crassostreae, V. breoganii, V. celticus are some of the new Vibrio species described as forming part of the molluscan microbiota. Some of them have been associated with mortalities of different molluscan species, seriously affecting their culture and causing high losses in hatcheries as well as in natural beds. For other species, ecological importance has been demonstrated being highly abundant in different marine habitats and geographical regions. The present work provides an updated overview of the recently characterized Vibrio species isolated from molluscs. In addition, their pathogenic potential and/or environmental importance is discussed.
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Affiliation(s)
- Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de CompostelaSpain
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2013. [DOI: 10.1099/ijs.0.054650-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological
Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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