Comparative evaluation of Vibrio delineation methodologies in post‐genomic era

Summary Vibrios are widespread in both marine and coastal water environments and are recognized as one of the most important prokaryotic pathogens because they may potentially threaten the health of both aquacultures and human beings. However, owing to highly similar physiological and biochemical properties, accurate classification and identification of Vibrio strains remains challenging. This hampers further research on the physiology, pathogeny, genomics, epidemics, and ecology of vibrios. Here, we comparatively evaluated multiple approaches including 16S rRNA gene identity, average nucleotide identity (ANI), gene content similarity and mutilocus sequence analysis (MLSA) to investigate their ability in delineating Vibrio strains. In addition, we also evaluated the possibility of applying bacterial prophages in classifying and identifying Vibrio strains. Our results showed that MLSA outperformed other methods in discriminating Vibrio species, suggesting that the other four approaches should be used with cautions in Vibrio delineation. Interestingly, we also found that prophages identified in Vibrio strains were highly specific at strain‐ and species‐level, suggesting that prophages held the potential to be used for microbial species, sub‐species, and strain‐level identifications. This study is expected to provide valuable insights into the taxonomic identification and classification of complex microbial groups in the post‐genomic era.