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Background  Comparative genomic hybridization (CGH) constitutes a powerful tool for identification and characterization of bacterial strains. In this study we have applied this technique for the characterization of a number of  Lactobacillus  strains isolated from the intestinal content of rats fed with a diet supplemented with sorbitol.    Results  Phylogenetic analysis based on 16S rRNA gene,  recA ,  pheS ,  pyrG  and  tuf  sequences identified five bacterial strains isolated from the intestinal content of rats as belonging to the recently described  Lactobacillus taiwanensis  species. DNA-DNA hybridization experiments confirmed that these five strains are distinct but closely related to  Lactobacillus johnsonii  and  Lactobacillus gasseri . A whole genome DNA microarray designed for the probiotic  L. johnsonii  strain NCC533 was used for CGH analysis of  L. johnsonii  ATCC 33200 T ,  L. johnsonii  BL261,  L. gasseri  ATCC 33323 T  and  L. taiwanensis  BL263. In these experiments, the fluorescence ratio distributions obtained with  L. taiwanensis  and  L. gasseri  showed characteristic inter-species profiles. The percentage of conserved  L. johnsonii  NCC533 genes was about 83% in the  L. johnsonii  strains comparisons and decreased to 51% and 47% for  L. taiwanensis  and  L. gasseri , respectively. These results confirmed the separate status of  L. taiwanensis  from  L. johnsonii  at the level of species, and also that  L. taiwanensis  is closer to  L. johnsonii  than  L. gasseri  is to  L. johnsonii .    Conclusion  Conventional taxonomic analyses and microarray-based CGH analysis have been used for the identification and characterization of the newly species  L. taiwanensis . The microarray-based CGH technology has been shown as a remarkable tool for the identification and fine discrimination between phylogenetically close species, and additionally provided insight into the adaptation of the strain  L. taiwanensis  BL263 to its ecological niche.

bmc genomics

Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods