Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis

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.

Meta-genomic analysis of Halobacillus trueperi S61 isolated from the Qarhan Salt Lake

“…Previous studies found that bacteriophages were able to dissolve certain pathogenic microbes which may bene cial for diseases curing, while at the same time may also dissolve bene cial or other harmful microbes. Thus, it is widely used as carrier for horizontal transfer of bene cial microbes [29]. Present study identi ed two prophages with total length 82682 in Halobacillus trueperi S61, contained 43.86 CDs of 44 and 61 genes with 44.85 and 38.43% GC respectively.…”

“…The pathogenic host interaction gene database pathogen host interactions (PHI) included diverse pathogenic genes related to different types of hosts, its crucial to nd target genes for drug intervention [29]. Through gene annotation, strain Halobacillus trueperi S61 has a total of 4416 PHI-related genes, which most dominant pathogen species distributed in Burkholderia glumae that caused bacterial grain rot disease with function of DNA gyrase (bacterial topoisomerase II), followed by Flavobacterium psychrophilum (DNA gyrase), Cryptococcus neoformans (GTP Biosynthesis), Bacillus anthracis (Tellurite Resistance), Pectobacterium wasabiae (Posttranscriptional regulator) which caused bacterial cold-water disease, meningoencephalitis, anthrax and soft rot.…”

“…Currently, whole-genome sequencing as novel and culture-independent technology for explore the genetic diversity and evolutionary history of microorganisms [14]. Various genomic project has been carried out [15][16][17][18][19][20]. Although the second-generation Illumina sequencing has large sequencing throughput, high sequencing accuracy and low cost, while its read length is relatively short (150-400bp).…”

Active colonisers of the gastrointestinal tract of Atlantic salmon farmed in a warm water region

“…We have hypothesised previously Aliivibrio colonisers are a possible cause of the production of faecal casts in sh sampled during summer [16]. Faecal cast production in n sh has been attributed to disease or stress [86][87][88][89][90]. The expected higher growth rates and biomass of Aliivibrio and Vibrio spp.…”

Correction to: Complete genome analysis of a virulent Vibrio scophthalmi strain VSc190401 isolated from diseased marine fish half-smooth tongue sole, Cynoglossus semilaevis

“…Following publication of the original article [ 1 ], we were notified that Prof. Yin-geng Wang needs to be marked as the second corresponding author.…”