DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov

Abstract

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.

Fig. 1

Neighbour-joining phylogenetic tree showing the relationships of 16S rRNA gene sequences from the type strains of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov. and Chryseobacterium nakagawai sp. nov. with sequences of the type strains of all other species of the genus Chryseobacterium. The tree is rooted, with Weeksella virosa ATCC 43766^T as the outgroup (not shown; GenBank accession no. M93152). GenBank accession numbers are given in parentheses. Bootstrap support from 1000 resamplings at nodes is displayed as percentages. Bar, 0.005 substitutions per nucleotide position. Strains described in this study are highlighted in bold. Full-length sequences were not available for all strains, so the alignment was trimmed to the 1336 bp for which data were available for all strains. The full tree is available as Fig. S1. Shown here is the node of the tree that supports the assertion that the species named Planobacterium taklimakanense is actually a species of Chryseobacterium.

Fig. 2

Three of the newly identified Chryseobacterium species, which were derived from clinical specimens, belong to a cluster of species that includes the known human pathogen C. indologenes. The rooted tree was generated using the same parameters as described for Fig. 1, but an additional 111 bp was available for all of the selected strains, and was included in the alignment. The tree included all 16S rRNA gene sequence data that were available for all of the selected strains.

Fig. 3

This analysis supports the suggestion that species of the genus Sejongia be transferred to the genus Chryseobacterium. As with Fig. 2, this analysis was done using the parameters described in Fig. 1.