Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

Abstract

Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA-DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05(T) = LMG 24057(T) = DSM 19144(T)) and Franconibacter helveticus comb. nov. (type strain 513/05(T) = LMG 23732(T) = DSM 18396(T)), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05(T) = LMG 23730(T) = DSM 18397(T)).

Fig. 1.

Phylogenetic tree of partial 16S rRNA gene sequences of type species from the genus Cronobacter, Enterobacter cloacae, Enterobacter turicensis, Enterobacter helveticus and Enterobacter pulveris. The rRNA gene sequences were downloaded from the NCBI GenBank repository and were aligned with clustal w using the mega5 phylogeny suite (Tamura et al. 2011). The tree was generated using maximum-likelihood algorithm. The bootstrap values obtained from 1000 bootstrap replicates are reported as percentages at the nodes. Bar, 0.05 changes per nucleotide value.

Fig. 2.

Evolutionary relationships of 23 members of the genus Cronobacter, 10 members of the genus Enterobacter and eight genomes of members of related genera. Clades are represented by roman numerals I–V. Clade I represents genomes from 23 strains of members of the genus Cronobacter, Clade II represents genomes from strains of Enterobacter helveticus and Enterobacter pulveris. Clade III represents genomes from three strains of Enterobacter cloacae, genomes from members of the genera Citrobacter, Salmonella, Escherichia and Klebsiella. Clade IV represents genomes from strains of Enterobacter turicensis. Lastly, genomes from two strains of a member of the genus Pantoea are represented in clade V. Neighbour-joining phylogeny is based on the alignment of SNPs from 300 orthologous genes. The bootstrap values obtained from 1000 bootstrap replicates are reported as percentages at the nodes. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Bar, 0.01 base substitutions per site.