Phylogenetic Analysis of the Genus Bifidobacterium and Related Genera Based on 16S rDNA Sequences

Abstract

The 16S rRNA gene sequences were determined for type strains of 21 Bifidobacterium species. A phylogenetic tree was constructed using the determined sequences and sequences from DNA databases, which contain the sequences of 11 type strains of Bifidobacterium species and 11 strains of related genera. All species of the genus Bifidobacterium and Gardnerella vaginalis ATCC 14018 belonged to a cluster phylogenetically distinct from the other genera. The cluster was divided into two subclusters: subcluster 1 composed of most species of Bifidobacterium and G. vaginalis, and subcluster 2 consisting of two species, B. denticolens and B. inopinatum; both of which were isolated from human dental caries. In the genus Bifi dobacterium, four groups of species are known to be moderately to highly related by DNA-DNA hybridiza -tion. The four groups of species exhibited more than 99% similarity among their 16S rDNA sequences within each group. These results indicated that species with around 99% or more similarity in their 16S rDNA sequences should be confirmed for species identities.

Species identification of genus Bifidobacterium based on partial HSP60 gene sequences and proposal of Bifidobacterium thermacidophilum subsp. porcinum subsp. nov.

“…Sequence similarity levels among Bifidobacterium species ranged from 93 to 99 % and were even greater than 99 % within five groups (Miyake et al, 1998); this is too high to distinguish between Bifidobacterium species. DNA-DNA hybridization has been acknowledged to be a superior method to elucidate relationships between closely related taxa, such as species.…”

Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum

“…However, 'B. aerophilum' grouped in subcluster II, which was considered previously to represent an undefined genus that was related closely to Bifidobacterium, but with a lower DNA G+C content (Miyake et al, 1998). Indeed, based on heat-shock protein 60 (HSP60) gene sequencing, the two existing species within subcluster II, Bifidobacterium inopinatum and Bifidobacterium denticolens, were transferred to Scardovia gen. nov. and Parascardovia gen. nov., respectively (Jian & Dong, 2002).…”

Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle

“…The phylogenetic position of the 36 strains was initially investigated using the 16S rRNA gene sequence analysis as described by Miyake et al (1998). Next, the taxonomic positions were analysed using recA gene sequence analysis.…”