Published March 2024 | Version 1.1
Data paper Open

Vibrio 16S rRNA gene sequences

Authors/Creators

  • 1. SciLifeLab
  • 2. Leibniz Institute for Baltic Sea Research
  • 3. KTH Royal Institute of Technology

Contributors

  • 1. ROR icon Leibniz Institute for Baltic Sea Research
  • 2. ROR icon University of Copenhagen
  • 3. Estonian University of Life Sciences
  • 4. Åbo Akademi University
  • 5. ROR icon Klaipėda University
  • 6. ROR icon National Marine Fisheries Research Institute
  • 7. ROR icon GEOMAR Helmholtz Centre for Ocean Research Kiel
  • 8. ROR icon Vilnius University

Description

This database includes 16S rRNA gene sequences of complete Vibrio genomes from RefSeq (51 species, 317 strains - including 22 V. vulnificus strains), 41 draft V. vulnificus genomes from clinical isolates from the Baltic Sea region, and 84 draft V. vulnificus genomes from environmental Baltic Sea isolates.

Fasta headers contain accession number and strain name for RefSeq complete genomes (e.g, >16S_rRNA::NZ_CP046839.1_Vibrio_cholerae_strain_2011EL-1271_chromosome_1:1902691-1904230(+)).

Source and isolate name are given for the clinical (e.g, >16S_rRNA::Baltic_Sea.1_Vibrio_vulnificus_strain_FI_VV_18_01_contig00074:40-1579(-)) and for the (BaltVib) environmental Baltic Sea isolates (e.g,>16S_rRNA::Baltic_Sea.1_Vibrio_vulnificus_strain_BaltVib6-S-1_contig00004:5-455(-))

A number of non-16S sequences were included in the previous version by mistake. This has now been solved.

Files

Files (156.2 kB)

Additional details

Funding

BiodivERsA
Pathogenic Vibrio bacteria in the current and future Baltic Sea waters: mitigating the problem” (BaltVib) BiodivClim ERA-Net COFUND

Dates

Submitted
2024-03
Upload to Zenodo

References

  • Amato, E. et al. Epidemiological and microbiological investigation of a large increase in vibriosis, northern Europe, 2018. Eurosurveillance 27, 2101088 (2022).
  • Brehm, T. T. et al. Heatwave-associated Vibrio infections in Germany, 2018 and 2019. Eurosurveillance 26, 2002041 (2021).
  • O'Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016).