Sarmiento-Rubiano et al. BMC Genomics 2010, 11:504 http://www.biomedcentral.com/1471-2164/11/504 the CGH analysis showing that a putative operon encod- ing a BSH and two bile salt transporters (LJ0056 to LJ0058) on L. johnsonii NCC533 genome is conserved in L. taiwanensis BL263, although this strain has only one of the two transporter encoding genes. Homologues of these genes in L. johnsonii 100-100 were shown to be gene duplicates and to have a function in taurocholic acid uptake [51,52]. The ability of L. johnsonii NCC533 to interact with mucins and epithelial cells has been shown to likely rely on cell-surface associated elongation factor Tu and heat shock protein GroEL [53,54]. As expected for these classes of proteins, their encoding genes (LJ1009 and LJ0461) are also conserved on L. tai- wanensis BL263, offering a putative role of the encoded proteins in the interaction of this strain with the host. This interaction may also be influenced by the presence of another conserved gene encoding a putative adhesin (LJ0391) that showed similarities with Fap1 fimbrial pro- tein from Streptococcus parasanguinis [55]. Previous studies using DNA microarray-based CGH and in silico comparative genomic analysis showed a wide sequence similarity and an accurate genome syn- teny between L. johnsonii and L. gasseri species [13,26]. In spite of this tight relationship, the novel Lactobacillus species described here is placed in a third branching of similar closeness, which raised once more the question about the limits of species delineation. Additionally, the CGH analysis showed that the new species is genetically slightly closer to L. johnsonii than L. gasseri is. This result is also supported by our DNA-DNA hybridization data and our phylogenetic analysis of recA, pheS, pyrG and tuf sequences in these three species. Conclusion Since the genome is the final target of all the molecular taxonomic indicators of species determination, the DNA microarray-based CGH analysis is the most powerful technology for strain typing and species assignment, just behind the costly genome sequencing. In this work we have characterized with conventional taxonomic ana- lyses a novel Lactobacillus species within the L. acido- philus group, and with microarray-based CGH analysis we confirmed the status of L. taiwanensis BL263 as spe- cies showing gene by gene differences and similarities with its closest relative L. johnsonii strain NCC533. Additional material Additional file 1: Genes on L. johnsonii NCC533 that are conserved on L. taiwanensis BL263 but not in L. johnsonii ATCC 33200T or L. johnsonii BL261. This table contains 63 and 34 genes on L. johnsonii NCC533 that are conserved on L. taiwanensis BL263 and absence on L. johnsonii type strain or L. johnsonii BL261, respectively. Page 14 of 16 Acknowledgements This work was financed by funds of the Project AGL2004-03886 and Consolider Fun-c-Food CSD2007-00063 from the Spanish Ministry of Science and Innovation. We thank Fabienne Praplan for sharing and discussing unpublished results of proteomics. Author details 1Laboratorio de Bacterias Lácticas y Probióticos. IATA-CSIC, P.O. Box 73, 46100 Burjassot, Valencia, Spain. 2Nestlé Research Center, CH-1000 Lausanne 26, Vers-chez-les-Blanc, Switzerland. Authors’ contributions LASR has isolated the five strains of the L. taiwanensis species and performed all the experiments related to conventional taxonomic analyses. BB designed and analyzed the microarray-based CGH experiments. DM performed the microarray-based CGH experiments. MZ designed and performed the phylogenetic analyses. GPM and MJY designed the study and supervised it. MJY drafted the manuscript. LSAR, BB, MZ and GPM helped improving the draft. All authors read and approved the final manuscript. Competing interests The authors declare that they have no competing interests. Received: 4 February 2010 Accepted: 17 September 2010 Published: 17 September 2010 References 1. Sazawal S, Hiremath G, Dhingra U, Malik P, Deb S, Black RE: Efficacy of probiotics in prevention of acute diarrhoea: a meta-analysis of masked, randomised, placebo-controlled trials. Lancet Infect Dis 2006, 6(6):374-382. 2. Sheil B, Shanahan F, O’Mahony L: Probiotic effects on inflammatory bowel disease. J Nutr 2007, 137(3 Suppl 2):819S-824S. 3. de Vrese M, Marteau PR: Probiotics and prebiotics: effects on diarrhea. J Nutr 2007, 137(3 Suppl 2):803S-811S. 4. Johnson JL, Phelps CF, Cummins CS, London J, Gasser F: Taxonomy of the Lactobacillus acidophilus group. Int J Syst Bacteriol 1980, 30:53-68. 5. Fujisawa T, Benno Y, Yaeshima T, Mitsuoka T: Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981). Int J Syst Bacteriol 1992, 42(3):487-491. 6. Zhang W, Azevedo MS, Wen K, Gonzalez A, Saif LJ, Li G, Yousef AE, Yuan L: Probiotic Lactobacillus acidophilus enhances the immunogenicity of an oral rotavirus vaccine in gnotobiotic pigs. Vaccine 2008, 26(29- 30):3655-3661. 7. Candela M, Perna F, Carnevali P, Vitali B, Ciati R, Gionchetti P, Rizzello F, Campieri M, Brigidi P: Interaction of probiotic Lactobacillus and Bifidobacterium strains with human intestinal epithelial cells: adhesion properties, competition against enteropathogens and modulation of IL-8 production. Int J Food Microbiol 2008, 125(3):286-292. 8. Inoue R, Otsuka M, Nishio A, Ushida K: Primary administration of Lactobacillus johnsonii NCC533 in weaning period suppresses the elevation of proinflammatory cytokines and CD86 gene expressions in skin lesions in NC/Nga mice. FEMS Immunol Med Microbiol 2007, 50(1):67-76. 9. Tanaka A, Fukushima Y, Benyacoub J, Blum S, Matsuda H: Prophylactic effect of oral administration of Lactobacillus johnsonii NCC533 (La1) during the weaning period on atopic dermatitis in NC/NgaTnd mice. Eur J Dermatol 2008, 18(2):136-140. 10. Fukushima Y, Miyaguchi S, Yamano T, Kaburagi T, Iino H, Ushida K, Sato K: Improvement of nutritional status and incidence of infection in hospitalised, enterally fed elderly by feeding of fermented milk containing probiotic Lactobacillus johnsonii La1 (NCC533). Br J Nutr 2007, 98(5):969-977. 11. Haller D, Blum S, Bode C, Hammes WP, Schiffrin EJ: Activation of human peripheral blood mononuclear cells by nonpathogenic bacteria in vitro: evidence of NK cells as primary targets. Infect Immun 2000, 68(2):752-759. 12. Ibnou-Zekri N, Blum S, Schiffrin EJ, von der Weid T: Divergent patterns of colonization and immune response elicited from two intestinal