salivarius UCC118 Lb. delbrueckii subsp.bulgaricus ATCC11842 Lb. plantarum WCFS1 S. thermophilus LMG18311 Lb. brevis ATCC3567 Lb. reuteri F25 Lb. gasseri ATCC 33323 Length (bp) 2080931 1993564

1922676 1884664 1827111 1864998 3308274 1796846 2291220 2039414 1894360 G+C content (%) 37.8 34.7 34.6 41.3 32.9 49.0 44.4 39.0 46.0 38.0 35.0 Gene number 1618 1864 1821 1884 1765 1562 3051 1890 2314 1820 1898 Pseudogenes 217 0 0 30 49 533 39 180 49 0 48 Table 2 Niche Specific Genes Dairy Specific Genes Gut Specific Genes 1) Proteolytic System 1) Bile Salt Hydrolysis Carboxypeptidase (lhv_1161, lhv_1171) Bile Salt Hydrolase (lba_0892, lba_1078) 2) R/M system CX-6258 in vitro 2) Sugar metabolism Restriction Modification enzyme Type I (lhv_1031, lhv_1152, lhv_1978) Restriction Modification Enzyme Type III (lhv_0028) Maltose-6-phosphate glucosidase (lba_1689) Sugar Metabolism Maltose-6-phosphate glycosidase (lba_1689 in Lb. acidophilus NCFM) is found solely in gut organisms and is absent even in multi-niche organism. Further analysis of this gene by BLAST comparison to all of the LAB genomes sequenced indicated that similar proteins are only present SYN-117 in vitro in Lb. acidophilus, Lb. johnsonii, Lb. casei, Enterococcus faecalis, E. faecium and Streptococcus suis. The three lactobacilli listed are classified as commensal gut strains, while the enterococci and S. suis are also considered commensal gut bacteria, associated more with

humans and animals than with the dairy environment. Maltose uptake and metabolism in LAB can occur by 4 different mechanisms, as discussed by Le Breton et al. 2005 [20]. In two of these, maltose is taken into the cytoplasm by a permease; it is not phosphorylated and therefore, maltose-6-phosphate

glycosidase is not required. PtdIns(3,4)P2 In the other systems described, a phosphotransferase (PTS) is used to transport maltose and therefore, there is no necessity to assimilate the resulting maltose-6-phosphate. Metabolism of maltose-6-phosphate either occurs by a maltose-6-phosphate phosphorylase, converting maltose to glucose-1-phosphate and glucose-6-phosphate, or a maltose-6-phosphate glycosidase, converting maltose to glucose and glucose-6-phosphate. It is the latter check details mechanism that appears to be present in the ‘gut’ strains. An analysis of 40 strains of LAB demonstrated that 32 of the strains could metabolise maltose and of these, 20 used a permease to transport maltose into the cell followed by conversion to glucose and β-glucose-1-phosphate by maltose phosphorylase [21]. The PTS/maltose-6-phosphate glycosidase pathway is therefore less common than the alternative mechanisms. Maltose is one of the least abundant disaccharides in the environment. It is present in germinating grain due to the action of amylases on starch and also presumably in other locations where starch breakdown products are present, such as in the gut.