Sarmiento-Rubiano et al. BMC Genomics 2010, 11:504 http://www.biomedcentral.com/1471-2164/11/504 Page 8 of 16 Figure 3 Phylogenetic tree showing relationships among pyrG (A) and tuf (B) gene sequences of species in the Lactobacillus acidophilus group, including Lactobacillus taiwanensis, and species representing different lineages within the genus Lactobacillus. The trees were created using a maximum-likelihood approach and numbers at branch points are bootstrap values (based on 500 samplings expressed in percentages). Only bootstrap values over 75% are shown. Bar indicates sequence divergence. The trees have been arbitrarily rooted. In parenthesis are shown the GenBank accession numbers. operon and glycosyltransferases (Fig. 5B, marked with an asterisk). Notably, the most similar genes, thus showing the highest log2 ratios (≥ -0.34) for a complete cluster, between L. johnsonii and L. taiwanensis form a clear-cut cluster containing an ABC transporter and hypothetical proteins, which is flanked by transposases (LJ1292- LJ1298). This cluster is absent in all other strains of L. johnsonii and L. gasseri analyzed to date. Taken together, these observations strongly argue for an hori- zontal gene transfer. Considering the marked conserva- tion of this cluster compared to the rest of the L. taiwanensis genome, the hypothesis of its loss in the rest of the analysed strains is very unlikely. In order to compare the genome conservation of L. taiwanensis BL263, L. gasseri ATCC 33323T and L. johnsonii ATCC 33200T versus L. johnsonii NCC533, their CGH results were combined in Fig. 6. Interestingly, variable or absent genes in L. taiwanensis and L. gasseri were not always shared by the two species. These “spe- cies-related” variable genes counted for almost one quarter of the L. johnsonii NCC533 genome. Since they were in minority related to mobile elements, this obser- vation strongly supports three evolutionary branches. The number of genes conserved in L. taiwanensis and absent/divergent in L. gasseri was 257, whereas those conserved in L. gasseri and absent/divergent in L. taiwa- nensis were only 186. These results clearly showed that L. taiwanensis is closer to L. johnsonii than L. gasseri is to L. johnsonii. The colour code of the Fig. 6 shows that most of the L. johnsonii ATCC 33200T absent/variable genes are also absent in the two other tested species. However, 63 genes absent in the L. johnsonii type strain are present in L. taiwanensis (Additional file 1). In con- trast, a similar analysis performed with the CGH results of L. johnsonii BL261 instead of L. johnsonii ATCC 33200T retrieves only 34 genes absent in L. johnsonii BL261 and present in L. taiwanensis (Additional file 1). This difference may reflect the adaptation to different ecological niches, since L. johnsonii type strain have been isolated from human blood, whereas L. johnsonii strains NCC533 and BL261 and L. taiwanensis strain BL263 were isolated from intestinal content. Several genes conserved in L. taiwanensis BL263 and L. johnso- nii BL261, but not in L. johnsonii ATCC 33200T, would help to survival in such highly populated and competi- tive microbial environment. Among those genes are the bacteriocin lactacin F gene cluster, which is flanked by components of the L. johnsonii NCC533 mobilome, and