Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 5

sp. nov., isolated from shrimp () pond water No Access

Abstract

A novel strain (CAIM 722=SW9=DSM 24596) was isolated in 2003 from water of a shrimp () culture pond located in Los Mochis, Sinaloa, Mexico, and taxonomically characterized using a polyphasic approach. The 16S rRNA gene sequence clustered within those of the genus , showing high similarity to the type strains of the Porteresiae clade. Multilocus sequence analysis using eight housekeeping genes (, , , , , , , and 16S rRNA) and phylogenetic analysis with 139 single-copy genes showed that the strain forms an independent branch. Whole genome sequencing and genomic analyses (average nucleotide identity, OrthoANI, average amino acid identity and DNA–DNA hybridization) produced values well below the thresholds for species delineation with all methods tested. In addition, a phenotypic characterization was performed to support the description and differentiation of the novel strain from related taxa. The results obtained demonstrate that the strain represent a novel species, for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 139 single-copy genes , AAI , ANI , GGDC , MLSA , porteresiae clade and Vibrio
Funding
This study was supported by the:
  • Centro de Investigacion en Alimentación y Desarrollo AC
    • Principle Award Recipient: BrunoGomez-Gil
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005866
2023-05-11
2025-05-22
Loading full text...

Full text loading...

References

  1. Farmer JJ, Hickman-Brenner FW. The genera Vibrio and Photobacterium. In The Prokaryotes: Volume 6: Proteobacteria: Gamma Subclass New York: Springer; 2006 pp 508–563
     [Google Scholar]
  2. Gomez-Gil B, Roque A, Chimetto L, Moreira APB, Lang E et al. Vibrio alfacsensis sp. nov., isolated from marine organisms. Int J Syst Evol Microbiol 2012; 62:2955–2961 [View Article] [PubMed]
     [Google Scholar]
  3. Ghosh A, Bhadury P. Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal. Curr Microbiol 2019; 76:1118–1127 [View Article] [PubMed]
     [Google Scholar]
  4. Stabb EV. The Vibrio fischeri–Euprymna scolopes light organ symbiosis. In In The Biology of Vibrios American Society of Microbiology; 2006 pp 204–218 [View Article]
     [Google Scholar]
  5. Gómez-León J, Villamil L, Lemos ML, Novoa B, Figueras A. Isolation of Vibrio alginolyticus and Vibrio splendidus from aquacultured carpet shell clam (Ruditapes decussatus) larvae associated with mass mortalities. Appl Environ Microbiol 2005; 71:98–104 [View Article] [PubMed]
     [Google Scholar]
  6. Schiewe MH, Trust TJ, Crosa JH. Vibrio ordalii sp. nov.: A causative agent of vibriosis in fish. Curr Microbiol 1981; 6:343–348 [View Article]
     [Google Scholar]
  7. Soto-Rodriguez SA, Gomez-Gil B, Lozano R. “Bright-red” syndrome in Pacific white shrimp Litopenaeus vannamei is caused by Vibrio harveyi. Dis Aquat Organ 2010; 92:11–19 [View Article] [PubMed]
     [Google Scholar]
  8. Haldar S, Chatterjee S, Sugimoto N, Das S, Chowdhury N et al. Identification of Vibrio campbellii isolated from diseased farm-shrimps from south India and establishment of its pathogenic potential in an Artemia model. Microbiology 2011; 157:179–188 [View Article] [PubMed]
     [Google Scholar]
  9. Soto-Rodriguez SA, Gomez-Gil B, Lozano-Olvera R, Betancourt-Lozano M, Morales-Covarrubias MS. Field and experimental evidence of Vibrio parahaemolyticus as the causative agent of acute hepatopancreatic necrosis disease of cultured shrimp (Litopenaeus vannamei) in Northwestern Mexico. Appl Environ Microbiol 2015; 81:1689–1699 [View Article] [PubMed]
     [Google Scholar]
  10. González-Castillo A, Enciso-Ibarra J, Dubert J, Romalde JL, Gomez-Gil B. Vibrio sonorensis sp. nov. isolated from a cultured oyster Crassostrea gigas. Antonie Van Leeuwenhoek 2016; 109:1447–1455 [View Article] [PubMed]
     [Google Scholar]
  11. Enciso-Ibarra J, González-Castillo A, Soto-Rodriguez SA, Enciso-Ibarra K, Bolán-Mejia C et al. Photobacterium lucens sp. nov., isolated from a cultured shrimp Penaeus vannamei. Curr Microbiol 2020; 77:1111–1116 [View Article] [PubMed]
     [Google Scholar]
  12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  14. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  15. Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Bioinformatics 2022 [View Article]
     [Google Scholar]
  16. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
     [Google Scholar]
  17. Campbell BJ, Yu L, Heidelberg JF, Kirchman DL. Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci U S A 2011; 108:12776–12781 [View Article] [PubMed]
     [Google Scholar]
  18. Sawabe T, Kita-Tsukamoto K, Thompson FL. Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 2007; 189:7932–7936 [View Article] [PubMed]
     [Google Scholar]
  19. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  20. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  21. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
     [Google Scholar]
  22. Weimann A, Mooren K, Frank J, Pope PB, Bremges A et al. From genomes to phenotypes: traitar, the microbial trait analyzer. mSystems 2016; 1:e00101-16 [View Article] [PubMed]
     [Google Scholar]
  23. Sawabe T, Ogura Y, Matsumura Y, Feng G, Amin AR et al. Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 2013; 4:414 [View Article] [PubMed]
     [Google Scholar]
  24. Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL et al. Vibrio clade 3.0: new vibrionaceae evolutionary units using genome-based approach. Curr Microbiol 2021; 79:10 [View Article] [PubMed]
     [Google Scholar]
  25. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
     [Google Scholar]
  26. Tanaka M, Hongyu B, Jiang C, Mino S, Milet Meirelles P et al. Vibrio taketomensis sp. nov. by genome taxonomy. Syst Appl Microbiol 2020; 43:126048 [View Article] [PubMed]
     [Google Scholar]
  27. Thompson CC, Vicente ACP, Souza RC, Vasconcelos ATR, Vesth T et al. Genomic taxonomy of Vibrios. BMC Evol Biol 2009; 9:1–16 [View Article] [PubMed]
     [Google Scholar]
  28. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  29. Lucena T, Arahal DR, Ruvira MA, Navarro-Torre S, Mesa J et al. Vibrio palustris sp. nov. and Vibrio spartinae sp. nov., two novel members of the Gazogenes clade, isolated from salt-marsh plants (Arthrocnemum macrostachyum and Spartina maritima). Int J Syst Evol Microbiol 2017; 67:3506–3512 [View Article] [PubMed]
     [Google Scholar]
  30. Guo Z, Li W, Wang Y, Hou Q, Zhao H et al. Vibrio zhugei sp. nov., a moderately halophilic bacterium isolated from pickling sauce. Int J Syst Evol Microbiol 2019; 69:1313–1319 [View Article] [PubMed]
     [Google Scholar]
  31. Rameshkumar N, Fukui Y, Sawabe T, Nair S. Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 2008; 58:1608–1615 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005866
Loading
Vibrio eleionomae sp. nov., isolated from shrimp (Penaeus vannamei) pond water
Int J Syst Evol Microbiol 73, 005866 (2023); https://doi.org/10.1099/ijsem.0.005866
/content/journal/ijsem/10.1099/ijsem.0.005866
/content/journal/ijsem/10.1099/ijsem.0.005866
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error