Sarmiento-Rubiano et al. BMC Genomics 2010, 11:504 http://www.biomedcentral.com/1471-2164/11/504 R E S E A R C H A R T I C L E Open Access Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods Luz-Adriana Sarmiento-Rubiano1, Bernard Berger2, Déborah Moine2, Manuel Zúñiga1, Gaspar Pérez-Martínez1, María J Yebra1* Abstract 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 33200T, L. johnsonii BL261, L. gasseri ATCC 33323T 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. Background A number of species belonging to the genus Lactobacil- lus are indigenous to the gastrointestinal tract of humans and animals [1-3]. Due to their ecological and commercial interest, substantial efforts have been con- centrated in the past years to isolate and identify new strains of lactobacilli. Many of those strains belong to the Lactobacillus acidophilus complex. The first major * Correspondence: yebra@iata.csic.es 1Laboratorio de Bacterias Lácticas y Probióticos. IATA-CSIC, P.O. Box 73, 46100 Burjassot, Valencia, Spain Full list of author information is available at the end of the article study on this group using DNA-DNA hybridization defined two main homology groups, A and B, with six subgroups [4], that later became distinct species [5]. Strains of the group A were classified as the species L. acidophilus, Lactobacillus amylovorus, Lactobacillus crispatus and Lactobacillus gallinarum, and strains of the group B became Lactobacillus gasseri and Lactoba- cillus johnsonii [5]. Some strains of L. acidophilus and L. johnsonii are commercialized as probiotics and they have been subjected to extensive studies aimed to infer the mechanisms governing their beneficial health effects. L. acidophilus strain NCFM increased the © 2010 Sarmiento-Rubiano et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.