Figure 1.
Classification of Lactobacillus rossiae DSM 15814T.
A) Venn diagram displaying core gene families obtained by MCL clustering, and unique genes of L. rossiae DSM 15814T and selected representatives of the Lactobacillus genus. B) Cluster of Orthologous Groups (COGs) classification of L. rossiae DSM 15814T based on the predicted ORFs. The occurrence of each COG family relative to the total of classified genes is indicated as a frequency percentage.
Figure 2.
Phylogenomics of Lactobacillus rossiae DSM 15814T.
A) 16S neighbor-joining (NJ) tree, resulting from the alignment of the 16S rRNA-encoding gene of L. rossiae DSM 15814T and that of 20 selected representatives of the Lactobacillus genus (L. amylovorus GRL 1112, L. acidophilus 30SC, L. kefiranofaciens ZW3, L. crispatus ST1, L. helveticus DPC 4571, L. gasseri ATCC 33323, L. johnsonii NCC 533, L. delbrueckii subsp. bulgaricus ATCC 11842, L. sakei subsp. sakei 23K, L. rhamnosus ATCC 8530, L. paracasei subsp. paracasei, L. casei ATCC334, L. ruminis ATCC 27782, L. salivarius UCC118, L. fermentum IFO 3956, L. reuteri DSM 20016, L. plantarum WCFS1, L. brevis ATCC 367, L. buchneri NRRL B-30929 and L. sanfranciscensis TMW 1.1304). The corresponding 16S rRNA-specifying sequence of Bifidobacterium breve UCC2003 was used as an outgroup. The positioning of L. rossiae DSM 15814T within the Lactobacillus genus is indicated in red. B) Multilocus supertree resulting from the alignment of the sequence of three housekeeping genes (groEL, dnaK and grpE) of L. rossiae DSM 15814T and 20 selected representatives of the Lactobacillus genus (see above for the species). The positioning of L. rossiae DSM 15814T within the Lactobacillus genus is indicated in red. C) Multilocus supertree resulting from the alignment of 96 selected orthologous genes of L. rossiae DSM 15814T and 20 selected representatives of the Lactobacillus genus (see above for the species). The positioning of L. rossiae DSM 15814T within the Lactobacillus genus is indicated in red.
Figure 3.
Comparative genomics of L. rossiae DSM 15814T.
A) Hierarchical clustering analysis realized in Tmev and restricted to the sole variable genes of L. rossiae DSM 15814T with respect to representatives of the Lactobacillus genus used for the analysis in Figure 2. The positioning of the cobalamin biosynthesis and ethanolamine utilization cluster, and of prophage region and putative plasmid are indicated. B) Pie chart indicating the core, extended core and variable genome with respect to the total of gene families, resulting from the MCL clustering algorithm.
Figure 4.
Vitamin B12 production and related ethanolamine utilization.
A) Schematic representation of the pdu-cbi-cob-hem-eth cluster of L. rossiae DSM 15814T. Locus map displaying the organization of the pdu-cbi-cob-hem-eth of L. rossiae DSM 15814T and BLAST-based comparison with the relative cluster of S. enterica var Typhimurium LT2 and L. reuteri DSM 20016. Synteny map was reconstructed using a combination of reciprocal best BLASTP and CloneManager suite 5 (http://www.scied.com/). B) Growth of L. delbrueckii subsp. lactis ATCC 7830 in vitamin B12-free medium supplemented with increasing concentrations of vitamin B12 or CE of L. rossiae DSM 15814T or L. plantarum DC400 as negative control. Optical density (620 nm) and acidification (ΔpH) are also reported.
Figure 5.
Biosynthesis of riboflavin and folate.
Reconstruction of the biosynthesis of riboflavin (A) and folate (B) in L. rossiae DSM 15814T. Growth and acidification (ΔpH) of DSMZ 15184T at 30°C for 18 h (C). LDMIIIG, modified semi-defined medium LDMIIIG; vitamin-free, LDMIIIG without added vitamins; folate-free, LDMIIIG without folate; riboflavin-free, LDMIIIG without riboflavin. Data are the means of three separate experiments performed in triplicate.