Additionally, we also identified an association selleckchem between sucrose fermentation and nisin production in L. lactis. Both sucrose utilization and nisin biosynthesis genes were earlier reported to be encoded on a transposon in strain NIZO R5 [23]. Additionally, linkage between these phenotypes has been observed in 13 L. lactis strains [24]. Visualization of identified Alvocidib gene-phenotype relations

revealed that sucrose-negative strains lack part or all of the genes related to nisin production. For example, KF147 – a nisin non-producer strain – contains only part of the nisin gene cluster, conferring immunity but not production (see LLKF_1296, LLKF_1298 and LLKF_1300 in Figure 2) [9]. However, we found no strong relation between growth on sucrose and presence of nisin biosynthesis genes, confirming a previous observation that the presence of nisin biosynthesis genes in a strain does not always

confer its growth on sucrose [25]. Figure 1 Integration of gene significance with its presence/absence. A gene that is present in at least 75% of strains of a phenotype is assumed to be predominantly present and a gene that is absent in at least 75% of strains of a phenotype is assumed to be predominantly absent; otherwise a gene is assumed to be present in a subset of strains. Gene-phenotype relations were selleck kinase inhibitor visualized by integrating each gene’s phenotype importance with its predominant presence/absence in strains of this particular phenotype, whereas in visualizing gene-strain relations gene’s contribution score and presence/absence in a corresponding strain were used. Figure 2 L. lactis KF147 gene clusters correlated to growth on the sugars

arabinose, melibiose and sucrose. Colours represent strength of relationship between a Palmatine gene and a phenotype (Figure 1). Phenotypes are either shown as last digits in column names or with suffixes “high” or “low”, where 0 indicates there is no growth and other numbers indicate different growth levels in different experiments as described in the Additional file 1. Here “high” and “low” phenotypes indicate high and low growth levels, respectively. For gene annotations see Additional file 3. A large cluster of 11 genes (Figure 2) was found to be related to growth on melibiose, a plant disaccharide, but not to any of the other carbohydrates tested. This confirms an earlier observation that strain KF147 can utilize this disaccharide while 3 other strains IL1403 (dairy), SK11 (dairy) and KF282 (plant) strains cannot grow on melibiose [9, 26]. We also investigated whether a genomic region that encompasses these genes was deleted in melibiose-negative strains, because chromosomal deletion of a 12 kb region in Streptococcus mutans strains leads to melibiose-negative phenotype [27, 28]; this 12 kb region contains orthologs of LLKF_2260-2262 of strain KF147.