ena-STUDY-JUSTUS LIEBIG UNIVERSITY-08-07-2015-12:01:55:227-280
Taxonomic Turmoil: the case of Enterobacter spp.
The genus Enterobacter consists of an important group of bacteria comprising of pathogens as well as environmental strains. However, the taxonomic classification of several Enterobacter species is controversial. Presently, the genus Enterobacter comprises 34 species, of which several have been repeatedly reclassified based on traditional sequencing approaches in taxonomy e.g. based on  16S rDNA or multilocus sequence typing (MLST).  This has led to shifts in the classification and even assignment to new species groups. Here we explore the use of whole genome-based sequences to characterize and derive meaningful taxonomic classification. The whole genome sequences (WGS) of publicly available 110 Enterobacter strains (including four in-house sequenced standard references strains E. kobei DSM-27110, E. ludwigii DSM-16688 and E. agglomerans DSM-3493 along with 43 closely related species of the family Enterobacteriaceae were examined. To refine the taxonomy, comprehensive genetic relationship among the species was determined by Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization estimate (isDDH). The results of our analysis by both methods were congruent. Using standard reference strain as a representative of a particular species, gross misclassification among 39/41 E. cloacae, 14/14 E. aerogenes, 2/2 E. asburiae and 2/2 E. hormaechei isolate was revealed. Surprisingly, all E. aerogenes strains, including the reference strain, are more closely related in their genomic content to the genus Klebsiella. Also E. agglomerans, E. kobei, E. massiliensis and E. lignolyticus were found distantly related to the genus Enterobacter. Using cut-off values for species determination with ANI we now report the presence of at least 10 additional novel species that need to be incorporated into the genus Enterobacter.
The genus Enterobacter consists of an important group of bacteria comprising of pathogens as well as environmental strains. However, the taxonomic classification of several Enterobacter species is controversial. Presently, the genus Enterobacter comprises 34 species, of which several have been repeatedly reclassified based on traditional sequencing approaches in taxonomy e.g. based on  16S rDNA or multilocus sequence typing (MLST).  This has led to shifts in the classification and even assignment to new species groups. Here we explore the use of whole genome-based sequences to characterize and derive meaningful taxonomic classification. The whole genome sequences (WGS) of publicly available 110 Enterobacter strains (including four in-house sequenced standard references strains E. kobei DSM-27110, E. ludwigii DSM-16688 and E. agglomerans DSM-3493 along with 43 closely related species of the family Enterobacteriaceae were examined. To refine the taxonomy, comprehensive genetic relationship among the species was determined by Average Nucleotide Identity (ANI) and in silico DNA-DNA hybridization estimate (isDDH). The results of our analysis by both methods were congruent. Using standard reference strain as a representative of a particular species, gross misclassification among 39/41 E. cloacae, 14/14 E. aerogenes, 2/2 E. asburiae and 2/2 E. hormaechei isolate was revealed. Surprisingly, all E. aerogenes strains, including the reference strain, are more closely related in their genomic content to the genus Klebsiella. Also E. agglomerans, E. kobei, E. massiliensis and E. lignolyticus were found distantly related to the genus Enterobacter. Using cut-off values for species determination with ANI we now report the presence of at least 10 additional novel species that need to be incorporated into the genus Enterobacter.