Phylogenetic analysis of Shewanella spp. isolated from fish.
Shewanella
fish
whole genome
Journal
Journal of fish diseases
ISSN: 1365-2761
Titre abrégé: J Fish Dis
Pays: England
ID NLM: 9881188
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
revised:
30
06
2023
received:
21
03
2023
accepted:
03
07
2023
pubmed:
15
7
2023
medline:
15
7
2023
entrez:
15
7
2023
Statut:
ppublish
Résumé
Different species of Shewanella spp. widely inhabit freshwater and marine environments. Some of them are opportunistic fish pathogens. The application of high-throughput sequencing enabled the characterization and taxonomic reclassification of many Shewanella spp. species. Still, some strains collected from fish need to be better recognized. The aim of the present study was to classify and determine the phylogenetic relationships of Shewanella spp. collected from fish. The complete genomes of 94 strains of Shewanella spp. from different fish species were sequenced using Illumina platform (MiSeq). The 16S rRNA gene, genomic features and whole-genome relationships of those bacteria were comprehensively analysed in comparison to reference strains. Whole-genome analysis showed that the tested Shewanella spp. strains were clustered into six groups similar to reference strains of S. xiamenensis, S. oneidensis, S. glacialipiscicola, S. hafniensis, S. baltica and S. oncorhynchi. Our study indicates that the whole-genome sequence analysis enabled taxonomic classification and assessment of the diversity of the Shewanella spp. strains, as opposed to recently the gold standard method of 16S rRNA amplicon sequencing. The high genetic diversity and low similarity to the reference genome of S. oneidensis indicate that the group of strains may be a subspecies or even new species. Furthermore, we showed that the most frequent Shewanella spp. species occurring in freshwater fish in our study is the recently described species S. oncorhynchi.
Banques de données
RefSeq
['PRJEB59414']
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1163-1171Subventions
Organisme : National Centre for Research and Development
ID : BIOSTRATEG2/296211/4/NCBR/2016
Organisme : National Veterinary Research Institute
ID : S/403
Informations de copyright
© 2023 John Wiley & Sons Ltd.
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