Phylogenetic analysis of Shewanella spp. isolated from fish

被引：4

作者：

Ewa, Pazdzior ^{[1
,6
]}

Arkadiusz, Bomba ^{[2
]}

Katarzyna, Tluscik ^{[2
]}

Katarzyna, Nadolna-Altyn ^{[3
]}

Magdalena, Podolska ^{[3
]}

Michal, Reichert ^{[1
]}

Dariusz, Wasyl ^{[2
,4
]}

Agnieszka, Pekala-Safinska ^{[5
]}

机构：

[1] Natl Vet Res Inst, Dept Fish Dis, Pulawy, Poland

[2] Natl Vet Res Inst, Dept Om Anal, Pulawy, Poland

[3] Natl Marine Fisheries Res Inst, Dept Fisheries Resources, Gdynia, Poland

[4] Natl Vet Res Inst, Dept Microbiol, Pulawy, Poland

[5] Poznan Univ Life Sci, Fac Vet Med & Anim Sci, Dept Preclin Sci & Infect Dis, Poznan, Poland

[6] Natl Vet Res Inst, Dept Fish Dis, Al Partyzantow 57, PL-24100 Pulawy, Poland

来源：

JOURNAL OF FISH DISEASES | 2023年 / 46卷 / 11期

关键词：

fish; Shewanella; whole genome; DNA-DNA HYBRIDIZATION; PUTREFACIENS GROUP; IDENTIFICATION; INFECTION; NOV; RNA;

D O I：

10.1111/jfd.13834

中图分类号：

S9 [水产、渔业];

学科分类号：

0908 ;

摘要：

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.

引用

页码：1163 / 1171

页数：9