Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes.

弧菌病被认为是对虾影响孵化场幼虫的重要疾病。在弧菌物种中，副溶血弧菌，创伤弧菌，弗氏弧菌，坎氏弧菌，哈维氏弧菌，溶藻弧菌和鳗弧菌通常与咸水生态系统的有鳍鱼和贝类疾病有关。需要对生态系统中存在的生物采用准确的物种区分方法，以对物种进行精确分类并采取步骤进行管理。诸如16s rRNA系统发育和多基因座序列分型（MLST）之类的常规方法通常无法正确识别弧菌种类。这就需要对可用于区分与咸淡水养殖系统有关的弧菌物种的方法进行全面研究。为此，属于7个弧菌的35个完整基因组根据16s rRNA基因，MLST基因，单拷贝直系同源基因和单核苷酸多态性对这些物种进行系统发育分析。此外，计算基于基因组的相似性指数，如平均核苷酸同一性（ANI）和计算机DNA-DNA杂交（DDH），作为验证性测试，以验证系统发育关系。基于16s rRNA基因和MLST基因的系统发育关系发生了一些误分类，而单拷贝直系同源基因的系统发育产生了准确的物种水平聚类。研究表明，基于全基因组估计或全基因组变异的物种识别比单个或部分基因的识别更为精确。