Whole-genome sequence-based taxonomic reassessment of the genus Enterobacter. WGS based taxonomy of Enterobacter spp.

The taxonomic assignments of a number of bacterial genera and species are in conflict since they so far rely on phenotypic or limited molecular data that are not sufficient to discriminate between closely related isolates. Whole genome sequences (WGS) typically contain more information and allow to differentiate between closely related bacteria. With the increased possibilities of generating WGS and availability of the ensuing data, it is now possible to rapidly address taxonomic inconsistencies. Here we review the taxonomic history of the genus Enterobacter, by analyzing genome sequences from both publicly available sources and in-house genome sequences, if data on type strains was missing. Pre-standardized and validated WGS-based in silico DNA-DNA hybridization (isDDH) >70% were used to delineate species. Our data indicate that 5 of 17 Enterobacter type species are misclassified as members of the genus Enterobacter, while E. muelleri is a synonym of E. asburiae. 89% of the analyzed Enterobacter species genomes, including 65 of 67 E. cloacae, 9 of 14 E. asburiae and three of three E. hormaechei were found to be misidentified. Moreover, isDDH indicates that the genus Enterobacter contains 15 novel species. The comprehensive genome-based taxonomic analysis subsequently enabled us to correctly identify or classify all hitherto unidentified strains within the genus Enterobacter. This study identified a large number of misclassifications among the known members of the genus Enterobacter and represents a WGS-based digital approach to accurately identify and classify strains within the genus Enterobacter.