Products from bands were then cloned and PCR amplicons from 10 individual colonies were sequenced. Reliable (> 100 bp) Ruboxistaurin price sequences were obtained for 19 of the 20 TDFs. Each sequence was identified by similarity search using the BLAST program against the GenBank non-redundant check details (nr) public sequence database. As shown in Table 3, 8 transcripts (approximately 42% of selected sequences) showed a significant similarity to sequences with known function, 5 transcripts (26.5% of selected sequences) were closely related to L. casei plasmid sequences, 4 transcripts

(21% of selected sequences) were annotated as hypothetical protein-coding sequences, and 2 transcripts (10.5% of selected sequences) were identified as 5S rRNA. Table 3 Transcript-derived fragments (TDFs) from L. rhamnosus PR1019 over-expressed in CB compared to MRS TDF no Primer combination Length (bp) Biological functiona Organism annotationb Max identity – E-valuec Accession no. Pathway assignmentd COGe KEGG 37 AC/AT 396 Guanylate kinase (EC 2.7.4.8) L. rhamnosus GG 98% – 1e-84 YP_003171760.1 COG0194 [F] ko00230: Purine metabolism 40 AC/AT 302 Putative phosphoketolase (EC 4.1.2.9) L. rhamnosus GG 99% – 3e-57 YP_005864692.1 COG3957 [G] ko00030: Pentose

phosphate pathway 48 AC/AT 199 Monooxygenase L. rhamnosus Lc 705 95% – 6e-17 YP_003174467.1 COG2329: Conserved protein involved in polyketide biosynthesis related to monooxygenase [R] _ 54 AC/AT 137 Hypothetical protein L. rhamnosus 77% – 2e-07 WP_005689523.1 _ _ 72 AC/AT 340 Lipoteichoic acid synthase LtaS Type IIa (EC 3.1.6) L. rhamnosus Lc 705 100% – 5e-43 YP_003173514.1 MM-102 mouse COG1368: Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [M] _ 76 AC/AT 433 Conserved hypothetical protein L. rhamnosus Lc 705 85% – 9e-27 YP_003174890.1 _ _ 86 AC/AT 109 L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.22) L. rhamnosus GG 94% – 9e-13 YP_003172471.1 Epothilone B (EPO906, Patupilone) COG3623 [G] ko00040:

Pentose and glucuronate interconversions 93 AC/AT 305 Pyruvate oxidase (EC 1.2.3.3) L. rhamnosus GG 93% – 5e-40 YP_003171582.1 COG3961: Pyruvate decarboxylase and related thiamine pyrophosphate-requiring enzymes [G] ko00620: Pyruvate metabolism 95 AC/AT 229 Plasmid pNCD0151 L. casei 98% – 4e-68 Z50861.1 _ _ 97 AC/AT 227 Plasmid pNCD0151 L. casei 96% – 3e-64 Z50861.1 _ _ 106 AC/AT 170 Plasmid pNCD0151 L. casei 97% – 9e-48 Z50861.1 _ _ 120 AC/AT 107 Hypothetical protein L. casei 96% – 4e-10 WP_003574536.1 _ _ 121 AC/AT 105 Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) L. rhamnosus Lc 705 92% – 5e-08 YP_003174148.1 COG0131 [E] ko00340: Hystidine metabolism 122 AC/AT 102 Plasmid pNCD0151 L. casei 96% – 5e-23 Z50861.1 _ _ 162 AT/AC 350 Calcineurin-like phosphoesterase family protein L. rhamnosus ATCC 8530 97% – 3e-70 YP_005872999.1 COG0737: 5′-nucleotidase/2′,3′-cyclic phosphodiesterase and related esterases [F] _ 168 AT/AC 238 Plasmid pNCD0151 L. casei 98% – 1e-68 Z50861.