Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Abstract

The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA, and topA) was established as a rapid and accurate identification tool in 59 Shewanella type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical GϩC contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species was Shewanella algae, followed by Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis, and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Based on the combined genetic, genomic, and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica. IMPORTANCE The MLSA scheme based on six housekeeping genes (HKGs) (gyrA, gyrB, infB, recN, rpoA, and topA) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further stud-2019. Multilocus sequence analysis, a rapid and accurate tool for taxonomic classification, evolutionary relationship determination, and population biology studies of the genus Shewanella. Appl Environ Microbiol 85:e03126-18. https://doi. Downloaded fromies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus Shewanella.

Genomic analysis reveals high intra-species diversity of Shewanella algae

“…Compared with the report by Fang et al . [14], the phylogeny of S. algae in our study was consistent with the topological structure and evolutionary relationship of the phylogenetic tree constructed by MLSA method.…”

“…haliotis has been recently identified as a synonym of S. algae by the previous research [14]. The 12 morphologically well-characterized strains in this study were initially identified by API 20E and 16S rRNA gene analysis.…”

Assessment of Multilocus Sequence Analysis (MLSA) for Identification of Candidatus Liberibacter Solanacearum from Different Host Plants in Spain

“…Moreover, the low frequency of polymorphisms and the absence of positive selection of the studied genes suggest a nearly neutral mechanism for their evolution. Thus, all the selected genes showed similar features and, therefore, could be applied in an MLSA approach, as occurred in other bacterial models [ 35 ].…”

Caracterización fenotípica y molecular, e influencia de medios de cultivo, en el crecimiento y emisión de luz de bacterias del litoral de La Habana, Cuba

“…Los resultados confirman que la combinación de métodos para la identificación de bacterias es lo más adecuado. Por un lado, los métodos tradicionales de identificación de bacterias aun siendo menos sensibles, son ampliamente utilizados ya que brindan información sobre la morfología y la actividad de las cepas en cuestión (Fang et al, 2019). Por otro la práctica recomienda complementar los resultados de la caracterización fisiológica y bioquímica con los análisis filogenéticos de secuencias multilocus para la identificación de bacterias luminiscentes (Ast & Dunlap, 2005;Thompson, et al, 2005;Delgado et al, 2017).…”