An unbiased homology search with each of the candidate genes was executed against our initial selection of 11 genomes (table 1). These 11 genomes were selected on the basis that they were phylogenetically related to Lb. helveticus DPC4571 and Lb. acidophilus NCFM, they were fully sequenced genomes and they were isolated from either a dairy or gut environment or were capable of surviving in both. A gene was deemed a gut identifier gene if it has a homologue present in the 4 gut genomes MK-8931 datasheet and absent from the 3 dairy genomes. Conversely, a gene was deemed a dairy identifier if it had a homologue in the 3 dairy organisms

but absent from the gut organisms. Criteria for homologue detection were a threshold of 1e-10 MLN2238 and greater than 30% identity. Therefore, an organism could potentially survive a dairy environment if it contains dairy genes and an organism could potentially survive the gut if

it contains gut genes. Based on these criteria, we identified 9 genes (table 2) that appear to be niche-specific. Simultaneously to this unbiased homology search we identified phenotypic groups of what we deemed to be desirable niche characteristics, namely genes involved in fatty acid metabolism, proteolysis and restriction modification systems, for the dairy environment [3, 4] and for the gut environment genes involved in sugar metabolism, cell- wall and mucus binding and sugar metabolism [4, 18, 19]. Using literature searches and analysis using the ERGO database we identified the genes involved in these selleck inhibitor groupings and a blast search was performed with all genes within the groups against the same 11 genome group using the same selection Thalidomide criteria. Interestingly the unbiased and biased methods of identifying the barcode yielded the same 9-gene set. Furthermore, those organisms which can survive in multiple niches, namely Lb. sakei subsp.sakei 23 K

Lb. brevis ATCC367 and Lb. plantarum WCFS1 contained both dairy-specific and gut-specific genes. Multi-niche organisms will contain some genes from both the dairy and gut gene-set. To validate these niche-specific genes, we performed a broader BLAST search on a non-redundant database, containing all genes submitted to the NCBI database, from both fully and partially sequenced genomes, to ensure that the genes did not occur in any other dairy or gut organisms outside our selection. As with the unbiased and biased tests criteria for homologue detection were a threshold of 1e-10 and greater than 30% identity. Particularly, the niche-specific genes could be categorised into four general functional classes i.e. sugar metabolism, the proteolytic system, restriction modification systems and bile salt hydrolysis. A detailed description of the LAB barcode genes will now be discussed. Table 1 General genome features of eleven completely sequenced LAB. Genome Features Lb. helveticus DPC4571 Lb. acidophilus NCFM Lb. Johnsonii NCC533 Lb.