Selection of species-specific DNA probes which detect strain restriction polymorphism in four Bifidobacterium species

Randomly cloned fragments (in a size range 1 to 2.5 kb) of DNA from Bifidobacterium longum ATCC 15707, B. adolescentis CIP 64.59T, B. bifidum CIP 64.65 and B. animalis ATCC 25527 were used as hybridization probes to characterize strains of these species and distinguish them from closely related Bifidobacterium species. The fragments were screened for hybridization with native DNA from 41 different Bifidobacterium strains. For each species, a fragment hybridizing specifically with DNA from strains of the same species was isolated. Each fragment was then hybridized with restriction digests in order to study the genome polymorphism. In some of the tested B. longum strains including strain ATCC 15707, the species-specific fragment L6/45 hybridized with 2 fragments instead of one as expected. Sequence of the fragment revealed the presence of an ORF which had an amino acid sequence similar to the site-specific recombinases of lambda integrase family. Moreover, Southern analysis demonstrated that at least 3 copies of this fragment are present in the chromosome of B. longum ATCC 15707 and in some other B. longum strains. The species-specific fragment A6/17 of B. adolescentis hybridized with the same restriction fragment on the eight strains of this species tested. The B. bifidum-specific fragment hybridized with different DNA restriction fragments according to the strain. The restriction fragment an1 from B. animalis ATCC 25527 hybridized with the same restriction fragment from strain B. animalis ATCC 27536. However, these two strains could be differentiated by another restriction pattern. Thus, hybridization results highlight the genetic polymorphism which exists among Bifidobacterium strains of the same species.