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Uniacke-Lowe S, Johnson CN, Stanton C, Hill C, Ross P. Winogradskyella bathintestinalis sp. nov., isolated from the intestine of the deep-sea loosejaw dragonfish, Malacosteus niger. Int J Syst Evol Microbiol 2023; 73:10.1099/ijsem.0.006135. [PMID: 37877999 PMCID: PMC7615552 DOI: 10.1099/ijsem.0.006135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
A novel bacterial strain, APC 3343T, was isolated from the intestine of a deep-sea loosejaw dragon fish, Malacosteus niger, caught at a depth of 1000 m in the Northwest Atlantic Ocean. Cells were aerobic, rod-shaped, yellow/orange-pigmented, non-motile and Gram-negative. Growth of strain APC 3343T was observed at 4-30 °C (optimum, 21-25 °C), pH 5.5-10 (optimum, pH 7-8) and 0.5-8 % (w/v) NaCl (optimum, 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain APC 3343T was most closely related to members of the genus Winogradskyella, with the most closely related type strains being Winogradskyella algae Kr9-9T (98.46 % identity), Winogradskyella damuponensis F081-2T (98.07 %), Winogradskyella eximia CECT 7946T (97.93 %), Winogradskyella litoriviva KMM 6491T (97.79 %) and Winogradskyella endarachnes HL2-2T (97.79 %). Major fatty acids (>10 % of total) were iso-C16 : 0 3-OH, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). Polar lipids were phosphatidylethanolamine, three unknown aminolipids and eight unknown lipids. The draft genome sequence was 3.8 Mb in length with a G+C content of 33.43 mol%. Based on the phenotypic characteristics and phylogenetic analysis, strain APC 3343T is deemed to be a novel species of the genus Winogradskyella, and for which the name Winogradskyella bathintestinalis sp. nov. is proposed. The type strain of this species is APC 3343T (=DSM 115832T=NCIMB 15464T).
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Affiliation(s)
- Shona Uniacke-Lowe
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Crystal N. Johnson
- Department of Biochemistry & Microbiology, Oklahoma State University – Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland
- Teagasc Food Research Centre, Fermoy, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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2
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Yue YY, Ye YQ, Zhou ZY, Zhang MD, Jia YW, Du ZJ. Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750765 DOI: 10.1099/ijsem.0.006039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus Winogradskyella and the phylogenetic similarities to their closest relative, Winogradskyella aquimaris, were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03-OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus Winogradskyella, for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.
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Affiliation(s)
- Yu-Yan Yue
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zi-Yang Zhou
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Meng-Di Zhang
- Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Ya-Wei Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, PR China
- Weihai Research Institute of Industrial Technology of Shandong University, 264209, PR China
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3
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Succession of the intestinal bacterial community in Pacific bluefin tuna (Thunnus orientalis) larvae. PLoS One 2022; 17:e0275211. [PMID: 36201490 PMCID: PMC9536584 DOI: 10.1371/journal.pone.0275211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
We investigated the succession process of intestinal bacteria during seed production in full-cycle aquaculture of Pacific bluefin tuna (Thunnus orientalis). During the seed production, eggs, healthy fish, rearing water, and feeds from three experimental rounds in 2012 and 2013 were collected before transferring to offshore net cages and subjected to a fragment analysis of the bacterial community structure. We identified a clear succession of intestinal bacteria in bluefin tuna during seed production. While community structures of intestinal bacteria in the early stage of larvae were relatively similar to those of rearing water and feed, the bacterial community structures seen 17 days after hatching were different. Moreover, although intestinal bacteria in the late stage of larvae were less diverse than those in the early stage of larvae, the specific bacteria were predominant, suggesting that the developed intestinal environment of the host puts selection pressure on the bacteria in the late stage. The specific bacteria in the late stage of larvae, which likely composed 'core microbiota', were also found on the egg surface. The present study highlights that proper management of the seed production process, including the preparation of rearing water, feeds, and fish eggs, is important for the aquaculture of healthy fish.
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Osman E, Kim N, Lee Y, Yoo J, Kim SH, Kim DH. Molecular approaches for detection and quantification of Vibrio scophthalmi based on recA. JOURNAL OF FISH DISEASES 2022; 45:373-378. [PMID: 34779001 DOI: 10.1111/jfd.13551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Ebrahim Osman
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Korea
| | | | | | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Korea
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Turgay E, Steinum TM, Eryalçın KM, Yardımcı RE, Karataş S. The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture. FEMS Microbiol Lett 2021; 367:5719568. [PMID: 32005987 DOI: 10.1093/femsle/fnaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.
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Affiliation(s)
- Emre Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Terje Marken Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Kamil Mert Eryalçın
- Fish Nutrition & Phytoplankton-Zooplankton Culture Laboratory, Aquaculture Department, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Remziye Eda Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Süheyla Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
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Zhang Z, Yu YX, Wang YG, Liu X, Wang LF, Zhang H, Liao MJ, Li B. Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis. BMC Microbiol 2020; 20:341. [PMID: 33176689 PMCID: PMC7661262 DOI: 10.1186/s12866-020-02028-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Vibrio scophthalmi is an opportunistic bacterial pathogen, which is widely distributed in the marine environment. Earlier studies have suggested that it is a normal microorganism in the turbot gut. However, recent studies have confirmed that this bacterial strain can cause diseases in many different marine animals. Therefore, it is necessary to investigate its whole genome for better understanding its physiological and pathogenic mechanisms. Results In the present study, we obtained a pathogenic strain of V. scophthalmi from diseased half-smooth tongue sole (Cynoglossus semilaevis) and sequenced its whole genome. Its genome contained two circular chromosomes and two plasmids with a total size of 3,541,838 bp, which harbored 3185 coding genes. Among these genes, 2648, 2298, and 1915 genes could be found through annotation information in COG, Blast2GO, and KEGG databases, respectively. Moreover, 10 genomic islands were predicted to exist in the chromosome I through IslandViewer online system. Comparison analysis in VFDB and PHI databases showed that this strain had 334 potential virulence-related genes and 518 pathogen-host interaction-related genes. Although it contained genes related to four secretion systems of T1SS, T2SS, T4SS, and T6SS, there was only one complete T2SS secretion system. Based on CARD database blast results, 180 drug resistance genes belonging to 27 antibiotic resistance categories were found in the whole genome of such strain. However, there were many differences between the phenotype and genotype of drug resistance. Conclusions Based on the whole genome analysis, the pathogenic V. scophthalmi strain contained many types of genes related to pathogenicity and drug resistance. Moreover, it showed inconsistency between phenotype and genotype on drug resistance. These results suggested that the physiological mechanism seemed to be complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02028-7.
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Affiliation(s)
- Zheng Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Yong-Xiang Yu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Yin-Geng Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China.
| | - Xiao Liu
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Li-Fang Wang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Hao Zhang
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
| | - Mei-Jie Liao
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, PR China
| | - Bin Li
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academic of Fishery Sciences, Qingdao, Shandong, 266071, PR China
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7
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Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment. Front Microbiol 2020; 11:2015. [PMID: 32983024 PMCID: PMC7476325 DOI: 10.3389/fmicb.2020.02015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 12/19/2022] Open
Abstract
Aquaculture is the fastest growing primary industry worldwide. Marine finfish culture in open ocean net pens, or pontoons, is one of the largest growth areas and is currently the only way to rear high value fish such as bluefin tuna. Ranching involves catching wild juveniles, stocking in floating net pens and fattening for 4 to 8 months. Tuna experience several parasite-induced disease challenges in culture that can be mitigated by application of praziquantel (PZQ) as a therapeutic. In this study, we characterized the microbiome of ranched southern Bluefin Tuna, Thunnus maccoyii, across four anatomic sites (gill, skin, digesta, and anterior kidney) and evaluated environmental and pathological factors that influence microbiome composition, including the impact of PZQ treatment on microbiome stability. Southern bluefin tuna gill, skin, and digesta microbiome communities are unique and potentially influenced by husbandry practices, location of pontoon growout pens, and treatment with the antiparasitic PZQ. There was no significant relationship between the fish mucosal microbiome and incidence or abundance of adult blood fluke in the heart or fluke egg density in the gill. An enhanced understanding of microbiome diversity and function in high-value farmed fish species such as bluefin tuna is needed to optimize fish health and improve aquaculture yield. Comparison of the bluefin tuna microbiome to other fish species, including Seriola lalandi (yellowtail kingfish), a common farmed species from Australia, and Scomber japonicus (Pacific mackerel), a wild caught Scombrid relative of tuna, showed the two Scombrids had more similar microbial communities compared to other families. The finding that mucosal microbial communities are more similar in phylogenetically related fish species exposes an opportunity to develop mackerel as a model for tuna microbiome and parasite research.
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Affiliation(s)
- Jeremiah J. Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Cecilia Power
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
| | - Michaela Melanson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Claire Webber
- Australian Southern Bluefin Tuna Industry Association, Port Lincoln, SA, Australia
| | - Kirsten Rough
- Australian Southern Bluefin Tuna Industry Association, Port Lincoln, SA, Australia
| | - Nathan J. Bott
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
| | - Barbara Nowak
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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Alejandre-Colomo C, Viver T, Urdiain M, Francis B, Harder J, Kämpfer P, Amann R, Rosselló-Móra R. Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and Candidatus "Winogradskyella atlantica" sp. nov. Syst Appl Microbiol 2020; 43:126128. [PMID: 32977081 DOI: 10.1016/j.syapm.2020.126128] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/18/2022]
Abstract
Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus "W. atlantica" sp. nov.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig Universität Giessen, IFZ-Heinrich-Buff-Ring, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain.
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Meron D, Davidovich N, Ofek‐Lalzar M, Berzak R, Scheinin A, Regev Y, Diga R, Tchernov D, Morick D. Specific pathogens and microbial abundance within liver and kidney tissues of wild marine fish from the Eastern Mediterranean Sea. Microb Biotechnol 2020; 13:770-780. [PMID: 32059079 PMCID: PMC7111072 DOI: 10.1111/1751-7915.13537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 11/26/2022] Open
Abstract
This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species-specific microbial characteristics and to screen for candidate pathogens. This issue is especially relevant due to the development of mariculture farms and the possible transmission of pathogens from wild to farmed fish and vice versa. Although fish were apparently healthy, 16S rRNA NGS screening identified three potential fish bacterial pathogens: Photobacterium damselae, Vibrio harveyi and Streptococcus iniae. Based on the distribution patterns and relative abundance, 16 samples were classified as potential pathogenic bacteria-infected samples (PPBIS). Hence, PPBIS prevalence was significantly higher in kidneys than in liver samples and variation was found between the fish species. Significant differences were observed between fish species, organs and sites, indicating the importance of the environmental conditions on the fish microbiome. We applied a consistent sampling and analytical method for monitoring in long-term surveys which may be incorporated within other marine fish pathogens surveys around the world.
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Affiliation(s)
- Dalit Meron
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | | | | | - Ran Berzak
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Aviad Scheinin
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Yael Regev
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Rei Diga
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Dan Tchernov
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
| | - Danny Morick
- Morris Kahn Marine Research StationDepartment of Marine BiologyLeon H. Charney School of Marine SciencesUniversity of HaifaHaifaIsrael
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10
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Patel NP, Haldar S. Evaluation of traditional fish preservation method of Masmin from skipjack tuna (Katsuwonus pelamis) in Lakshadweep, India, with respect to nutritional and environmental perspectives. J FOOD PROCESS PRES 2019. [DOI: 10.1111/jfpp.14124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Neha P. Patel
- Analytical Environmental Science Division and Central Instrumental Facility CSIR‐Central Salt and Marine Chemicals Research Institute Bhavnagar India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Soumya Haldar
- Analytical Environmental Science Division and Central Instrumental Facility CSIR‐Central Salt and Marine Chemicals Research Institute Bhavnagar India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
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11
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Xaxiri NA, Nikouli E, Berillis P, Kormas KA. Bacterial biofilm development during experimental degradation of Melicertus kerathurus exoskeleton in seawater. AIMS Microbiol 2019; 4:397-412. [PMID: 31294223 PMCID: PMC6604942 DOI: 10.3934/microbiol.2018.3.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/29/2018] [Indexed: 11/28/2022] Open
Abstract
Chitinolytic bacteria are widespread in marine and terrestrial environment, and this is rather a reflection of their principle growth substrate's ubiquity, chitin, in our planet. In this paper, we investigated the development of naturally occurring bacterial biofilms on the exoskeleton of the shrimp Melicertus kerathurus during its degradation in sea water. During a 12-day experiment with exoskeleton fragments in batch cultures containing only sea water as the growth medium at 18 °C in darkness, we analysed the formation and succession of biofilms by scanning electron microscopy and 16S rRNA gene diversity by next generation sequencing. Bacteria belonging to the γ- and α-Proteobacteria and Bacteroidetes showed marked (less or more than 10%) changes in their relative abundance from the beginning of the experiment. These bacterial taxa related to known chitinolytic bacteria were the Pseudolateromonas porphyrae, Halomonasaquamarina, Reinekea aestuarii, Colwellia asteriadis and Vibrio crassostreae. These bacteria could be considered as appropriate candidates for the degradation of chitinous crustacean waste from the seafood industry as they dominated in the biofilms developed on the shrimp's exoskeleton in natural sea water with no added substrates and the degradation of the shrimp exoskeleton was also evidenced.
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Affiliation(s)
- Nikolina-Alexandra Xaxiri
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Eleni Nikouli
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Panagiotis Berillis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
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12
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Riiser ES, Haverkamp THA, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S, Star B. Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod. Environ Microbiol 2019; 21:2576-2594. [PMID: 31091345 DOI: 10.1111/1462-2920.14652] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 12/29/2022]
Abstract
Atlantic cod (Gadus morhua) is an ecologically important species with a wide-spread distribution in the North Atlantic Ocean, yet little is known about the diversity of its intestinal microbiome in its natural habitat. No geographical differentiation in this microbiome was observed based on 16S rRNA amplicon analyses, yet such finding may result from an inherent lack of power of this method to resolve fine-scaled biological complexity. Here, we use metagenomic shotgun sequencing to investigate the intestinal microbiome of 19 adult Atlantic cod individuals from two coastal populations in Norway-located 470 km apart. Resolving the species community to unprecedented resolution, we identify two abundant species, Photobacterium iliopiscarium and Photobacterium kishitanii, which comprise over 50% of the classified reads. Interestingly, the intestinal P. kishitanii strains have functionally intact lux genes, and its high abundance suggests that fish intestines form an important part of its ecological niche. These observations support a hypothesis that bioluminescence plays an ecological role in the marine food web. Despite our improved taxonomical resolution, we identify no geographical differences in bacterial community structure, indicating that the intestinal microbiome of these coastal cod is colonized by a limited number of closely related bacterial species with a broad geographical distribution.
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Affiliation(s)
- Even Sannes Riiser
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Srinidhi Varadharajan
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Ørnulf Borgan
- Department of Mathematics, University of Oslo, PO Box 1053, Blindern, N-0316 Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
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13
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Tarnecki AM, Wafapoor M, Phillips RN, Rhody NR. Benefits of a Bacillus probiotic to larval fish survival and transport stress resistance. Sci Rep 2019; 9:4892. [PMID: 30894554 PMCID: PMC6426941 DOI: 10.1038/s41598-019-39316-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/18/2019] [Indexed: 01/06/2023] Open
Abstract
The need for sustainable bacterial management approaches in aquaculture is crucial for advancement of the industry. Probiotics are a promising strategy as evidenced by benefits demonstrated in intensive larviculture of various marine fish species. In this study we investigate the effects of a mixed Bacillus species (B. licheniformis and B. amyloliquefaciens) probiotic on rearing of larval common snook (Centropomus undecimalis). Experimental treatments included (1) probiotics supplemented to the water and live feed, (2) probiotics supplemented to the water only, and (3) no probiotic controls. Data from two separate trials indicated up to 2.5 times higher survival with probiotic addition, as well as 20% higher survival 7 days following a transport event. These benefits were not explained by faster growth, measured water quality parameters, or innate immune enzyme activities. Microbiota analysis indicated the importance of system stabilization prior to larval stocking to improve rearing success and probiotic performance. ied Potential probiotic benefits include accelerated gastrointestinal tract development, enhanced immunity, inhibition of opportunistic bacteria, and improvements to water quality parameters. Results suggest this probiotic should be tested in other marine fish species in order to reduce larval rearing bottlenecks.
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Affiliation(s)
- Andrea M Tarnecki
- Mote Marine Laboratory, Marine Immunology Program, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA.
| | - Marzie Wafapoor
- Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, Massachusetts, 01908, USA
| | - Remy N Phillips
- Mote Marine Laboratory, Marine and Freshwater Aquaculture Program, 874 WR Mote Way, Sarasota, FL, 34240, USA
| | - Nicole R Rhody
- Mote Marine Laboratory, Marine and Freshwater Aquaculture Program, 874 WR Mote Way, Sarasota, FL, 34240, USA
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14
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King WL, Siboni N, Williams NLR, Kahlke T, Nguyen KV, Jenkins C, Dove M, O'Connor W, Seymour JR, Labbate M. Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease. Front Microbiol 2019; 10:473. [PMID: 30915058 PMCID: PMC6421512 DOI: 10.3389/fmicb.2019.00473] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/22/2019] [Indexed: 11/13/2022] Open
Abstract
Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.
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Affiliation(s)
- William L King
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nachshon Siboni
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Nathan L R Williams
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Khue Viet Nguyen
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Michael Dove
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, NSW, Australia
| | - Wayne O'Connor
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Port Stephens, NSW, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Maurizio Labbate
- The School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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15
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Tarnecki AM, Rhody NR, Walsh CJ. Health Characteristics and Blood Bacterial Assemblages of Healthy Captive Red Drum: Implications for Aquaculture and Fish Health Management. JOURNAL OF AQUATIC ANIMAL HEALTH 2018; 30:339-353. [PMID: 30269412 DOI: 10.1002/aah.10047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
The newly emerging tissue microbiota hypothesis suggests that bacteria found in blood and tissues play a role in host health, as these bacterial communities have been associated with various noncommunicable diseases such as obesity, liver disease, and cardiovascular disease. Numerous reports have identified bacteria in the blood of healthy finfish, indicating bacteremia may not always indicate disease. Current research priorities in aquaculture include the development of technologies and practices that will allow for an effective reduction in antibiotic use for the prevention and treatment of disease. Overall, a better understanding of fish health is needed, particularly among species selected for commercial-scale production. This study investigated blood characteristics of cultured Red Drum Sciaenops ocellatus with the tissue microbiota hypothesis in mind. Bacterial assemblages within the blood were characterized using next-generation sequencing and compared with other various blood characteristics, including innate immune function enzymes, between two fish cohorts reared in aquaculture. A total of 137 prokaryotic operational taxonomic units (OTUs) were identified from the blood of Red Drum. Microbiota diversity and structure varied greatly among individuals, for which the number of OTUs ranged from 4 to 58; however, predicted metagenomic function was highly similar between individuals and was dominated by the metabolism of carbohydrates and amino acids and membrane transport. Communities were dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, and Actinobacteria. The most commonly identified genera included Acinetobacter, Bacillus, Corynebacterium, and Pseudomonas. Three genera previously identified as containing marine fish pathogens were detected: Corynebacterium, Pantoea, and Chryseobacterium. A subset of bacterial OTUs were positively correlated with superoxide dismutase activity and negatively correlated with lysozyme activity, indicating a relationship between blood microbiota and the innate immune system. The results of this study provide further evidence for the tissue microbiota hypothesis and demonstrate the potential for these bacterial communities to be linked to immunological characteristics often used as biomarkers for fish health.
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Affiliation(s)
- Andrea M Tarnecki
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, Florida, 34236, USA
| | - Nicole R Rhody
- Mote Aquaculture Research Park, 874 WR Mote Way, Sarasota, Florida, 34240, USA
| | - Catherine J Walsh
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, Florida, 34236, USA
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16
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Rasheeda MK, Rangamaran VR, Srinivasan S, Ramaiah SK, Gunasekaran R, Jaypal S, Gopal D, Ramalingam K. Comparative profiling of microbial community of three economically important fishes reared in sea cages under tropical offshore environment. Mar Genomics 2017; 34:57-65. [PMID: 28476580 DOI: 10.1016/j.margen.2017.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/12/2017] [Accepted: 04/28/2017] [Indexed: 01/14/2023]
Abstract
The present study was undertaken to evaluate the microbial composition of farmed cobia pompano and milkfish, reared in sea-cages by culture-independent methods. This study would serve as a basis for assessing the general health of fish, identifying the dominant bacterial species present in the gut for future probiotic work and in early detection of potential pathogens. High-throughput sequencing of V3-V4 hyper variable regions of 16S rDNA on Illumina MiSeq platform facilitated unravelling of composite bacterial population. Analysis of 1.3 million quality-filtered sequences revealed high microbial diversity. Characteristic marine fish gut microbes: Vibrio and Photobacterium spp. showed prevalence in cobia and pompano whereas Pelomonas and Fusobacterium spp. dominated the gut of milkfish. Pompano hindgut with 10,537 operational taxonomy units (OTUs) exhibited the highest alpha-diversity index followed by cobia (10,435) and milkfish (2799). Additionally unique and shared OTUs in each gut type were identified. Gammaproteobacteria dominated in cobia and pompano while Betaproteobacteria showed prevalence in milkfish. We obtained 96 shared OTUs among the three species though the numbers of reads were highly variable. These differences in microbiota of farmed fish reared in same environment were presumably due to differences in the gut morphology, physiological behavior and host specificity.
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Affiliation(s)
- M K Rasheeda
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Vijaya Raghavan Rangamaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Senthilkumar Srinivasan
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Sendhil Kumar Ramaiah
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Rajaprabhu Gunasekaran
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Santhanakumar Jaypal
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Dharani Gopal
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India
| | - Kirubagaran Ramalingam
- Marine Biotechnology Division, Ocean Science and Technology for Islands Group, National Institute of Ocean Technology, Ministry of Earth Sciences (MoES), Government of India, Pallikaranai, Chennai, India.
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17
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Tarnecki AM, Patterson WF, Arias CR. Microbiota of wild-caught Red Snapper Lutjanus campechanus. BMC Microbiol 2016; 16:245. [PMID: 27769187 PMCID: PMC5073461 DOI: 10.1186/s12866-016-0864-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 10/14/2016] [Indexed: 01/10/2023] Open
Abstract
Background The microbiota plays an essential role in host health, particularly through competition with opportunistic pathogens. Changes in total bacterial load and microbiota structure can indicate early stages of disease, and information on the composition of bacterial communities is essential to understanding fish health. Although Red Snapper (Lutjanus campechanus) is an economically important species in recreational fisheries and a primary aquaculture candidate, no information is available on the microbial communities of this species. The aim of this study was to survey the microbiota of apparently healthy, wild-caught Red Snapper from the Gulf of Mexico. Sampled Red Snapper showed no physical signs of disease. Tissues that are either primary entry routes for pathogens (feces, gill) or essential to disease diagnosis (blood) were sampled. Bacteria were enumerated using culture-based techniques and characterized by pyrosequencing. Results Aerobic counts of feces and gill samples were 107 and 104 CFU g-1, respectively. All individuals had positive blood cultures with counts up to 23 CFU g-1. Gammaproteobacteria dominated the microbiota of all sample types, including the genera Pseudoalteromonas and Photobacterium in feces and Pseudomonas in blood and gill. Gill samples were also dominated by Vibrio while blood samples had high abundances of Nevskia. High variability in microbiota composition was observed between individuals, with percent differences in community composition ranging from 6 to 76 % in feces, 10 to 58 % in gill, and 52 to 64 % in blood. Conclusions This study provides the first characterization of the microbiota of the economically significant Red Snapper via pyrosequencing. Its role in fish health highlights the importance of understanding microbiota composition for future work on disease prevention using microbial manipulation.
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Affiliation(s)
- Andrea M Tarnecki
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA.
| | - William F Patterson
- Department of Marine Sciences, University of South Alabama, Life Sciences Building Room 25, Mobile, AL, 36688, USA
| | - Covadonga R Arias
- Auburn University, School of Fisheries, Aquaculture, and Aquatic Sciences, 203 Swingle Hall, Auburn, AL, 36849, USA
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18
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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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19
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Tarazona E, Pérez-Cataluña A, Lucena T, Arahal DR, Macián MC, Pujalte MJ. Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio. Syst Appl Microbiol 2015; 38:169-75. [PMID: 25861826 DOI: 10.1016/j.syapm.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 01/25/2023]
Abstract
A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoenteri, both the other individual gene trees and the trees obtained from the five-genes concatenated sequences were able to consistently differentiate four subclades within the main clade, corresponding to the bona fide V. scophthalmi, V. ichthyoenteri, and two small ones that may represent a new species each. The best genes to differentiate V. scophthalmi from V. ichthyoenteri were rpoD, recA, and mreB. Vibrio ponticus failed to associate to the clade in the MLSA and in most single gene trees for which it should not be considered part of it. In this study we also confirm using genomic indexes that V. ichthyoenteri and V. scophthalmi are two separate species.
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Affiliation(s)
- Eva Tarazona
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - Alba Pérez-Cataluña
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - Teresa Lucena
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - David R Arahal
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - M Carmen Macián
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain
| | - María J Pujalte
- Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Universitat de València, Spain.
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20
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Llewellyn MS, Boutin S, Hoseinifar SH, Derome N. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 2014; 5:207. [PMID: 24917852 PMCID: PMC4040438 DOI: 10.3389/fmicb.2014.00207] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/18/2014] [Indexed: 01/10/2023] Open
Abstract
Indigenous microbiota play a critical role in the lives of their vertebrate hosts. In human and mouse models it is increasingly clear that innate and adaptive immunity develop in close concert with the commensal microbiome. Furthermore, several aspects of digestion and nutrient metabolism are governed by intestinal microbiota. Research on teleosts has responded relatively slowly to the introduction of massively parallel sequencing procedures in microbiomics. Nonetheless, progress has been made in biotic and gnotobiotic zebrafish models, defining a core microbiome and describing its role in development. However, microbiome research in other teleost species, especially those important from an aquaculture perspective, has been relatively slow. In this review, we examine progress in teleost microbiome research to date. We discuss teleost microbiomes in health and disease, microbiome ontogeny, prospects for successful microbiome manipulation (especially in an aquaculture setting) and attempt to identify important future research themes. We predict an explosion in research in this sector in line with the increasing global demand for fish protein, and the need to find sustainable approaches to improve aquaculture yield. The reduced cost and increasing ease of next generation sequencing technologies provides the technological backing, and the next 10 years will be an exciting time for teleost microbiome research.
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Affiliation(s)
- Martin S Llewellyn
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada ; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Wales Bangor, UK
| | - Sébastien Boutin
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
| | - Seyed Hossein Hoseinifar
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources Gorgan, Iran
| | - Nicolas Derome
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, QC, Canada
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