salivaruis subsp. salivarius UCC118 (CP000233) This study 36 F-14-3a (EF442310) Enterococcus gallinarum F02025 (DQ465366) This study 38 G-14-1a (EF44211) Staphylococcus lugdunensis ATCC 43809 (AB009941) This study 40 G0-2a (EF44212) Enterococcus sanguinicola BAA-781 This study 39 P-14-2a (EF44213) Enterococcus gallinarum F02025 (DQ465366) This study 43 P0-1a (EF44214) L. rhamnosus LR2 (AY675254) This study 41 P0-1b (EF44215) L. rhamnosus LR2 (AY675254)

This study 41 P0-2a (EF44216) Staphylococcus sp. CNJ924 PL04 (DQ448767) This study 42 P+28-2a (EF44217) Staphylococcus warneri click here PB1 (AY186059) This study 44 Q-14-2a (EF44218) L. paracasei subsp. paracasei DJ1 (DQ462440) This study 47 Q-14-4a (EF44219) Streptococcus salivarius clone (AM157451) This study 48 Q0-1a (EF44220) Enterococcus faecalis ABPL 007 (DQ983196) This study 45 Q0-4a (EF44221) Staphylococcus sp. CNJ924 PL04 (DQ448767) This study 46 Q+28-2a (EF44222) Streptococcus sp. clone (EF151147) This study 49 R-14-4a

(EF44223) Enterococcus faecalis ABPL 007 (DQ983196) This study 51 R-14-5a (EF44224) Enterococcus Adriamycin order faecalis ABPL 007 (DQ983196) This study 52 R0-1b (EF44225) Weissella cibaria ACA-DC 3411t2 (AJ422031) This study 50 S-14-2a (EF44226) L. fermentum strain L18 (DQ523484) This study 53 T+28-1a (EF44227) L. rhamnosus LR2 (AY675254) This study 41 T+28-4b (EF44228) Streptococcus agalactiae A909 (CP000114) This study 54 a Strain

widely used in commercial applications however specific original source was not known b Strain cultivated from a commercially marketed probiotic formulation Figure 2 Phylogenetic Glycogen branching enzyme distribution of LAB probiotics and bacteria cultivated during the feeding study. A phylogenetic tree of aligned 16S rRNA genes from representative Lactobacillus reference strains, commercial probiotic strains and dominant find more isolates recovered during the feeding trial is shown. Probiotic strains are shown in bold font and isolates from the feeding study are highlighted by the grey boxes. The tree was rooted with the 16S rRNA gene from Staphylococcus warneri ATCC 27836 and the genetic distance scale and bootstrap values indicated. Testing the discriminatory power of the RAPD method on other LAB species The broad collection of systematically identified LAB isolates (Table 2) were used to test the efficacy of the RAPD typing scheme. The reproducibility of the RAPD method was excellent, with all 14 reference strains demonstrating identical fingerprint profiles after duplicate analysis. In addition L. acidophilus LMG 9433T was analysed by RAPD at multiple points throughout the study as an internal control; the same fingerprint profile was obtained on each occasion demonstrating that the LAB PCR genotyping scheme demonstrated the same high reproducibility as had been observed with previous RAPD studies on other bacterial species [13, 14].