Table 1.
List of primers used to screen the bacterial collection and food metagenomes
| General function | Gene | Predicted function | Primer |
Melting temp (°C) | Expected amplicon size (bp) | Species used for primer design | Relevant reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Orientation | Sequence (5′to 3′) | Reference | ||||||||
| Survival | ||||||||||
| pH | hdc | Histidine decarboxylase | F | AGATGGTATTGTTTCTTATG | 12 | 52.0 | 367 | Lactobacillus sp. 30A, | 12 | |
| R | AGACCATACACCATAACCTT | Lactobacillus buchneri, Clostridium perfringens | ||||||||
| tdc | Tyrosine decarboxylase | F | CCACTGCTGCATCTGTTTG | 15, 16 | 50.0 | 370 | L. brevis | 12 | ||
| R | CCRTARTCNGGNATAGCRAARTCNGTRTG | |||||||||
| odc | Ornithine decarboxylase | F | TMTWCCAACHGATCGWAATGC | This study | 58.0 | 245 | L. salivarius, L. helveticus, | 2, 12 | ||
| R | CRCCCCAWGCACARTCRAA | L. johnsonii, L. gasseri, L. acidophilus, Lactobacillus delbrueckii, Lactobacillus casei | ||||||||
| aguA | Agmatine deiminase | F | GAACGACTAGCAGCTAGTTAT | 17 | 60.0 | 542 | L. brevis, P. pentosaceus | 39 | ||
| R | CCAATAGCCGATACTACCTTG | |||||||||
| groEL | Heat shock protein 60 | F | TTCCATGGCKTCAGCRATCA | This study | 58.0 | 168 | L. salivarius, Leuconostoc | 37, 38 | ||
| R | GCTAAYCCWGTTGGCATTCG | mesenteroides, L. casei, L. delbrueckii, P. pentosaceus, P. acidilactici | ||||||||
| LBA1272 | Cyclopropane FA synthase | F | GGCTTACCAATGGCCACCTT | This study | 57.5 | 210 | L. fermentum | 32, 49 | ||
| R | GATCAAAAAGCCGGTCACGA | |||||||||
| F | GGCCGGTGTTCCACTAGTCC | This study | 58 | 203 | L. plantarum | |||||
| R | ACGTTGGGTCGATTTGACGA | |||||||||
| F | AAGGACCCGGATTTTGACGA | This study | 58 | 151 | P. pentosaceus | |||||
| R | ACGTGGTTTGACCCAGTGCT | |||||||||
| dltD | d-Alanine transfer protein | F | TTCGCCTGTTCAAGCCACAT | This study | 58 | 283 | L. fermentum | 49 | ||
| R | ACGTGCCCTTCTTTGGTTCC | |||||||||
| La995 | Amino acid permease | F | AACGAAGGTCCCGACAAAGG | This study | 57.5 | 246 | L. fermentum | 2 | ||
| R | ACGACCTTCGGGCTGGTTAC | |||||||||
| La57 | Amino acid antiporter | F | GGTCGGGGGATCTGAAAAGA | This study | 58.0 | 274 | L. plantarum | 2 | ||
| R | GATTTGGGCAAGCACATTGG | |||||||||
| pH and bile salt | gtf | Glucan synthase | F | ACACGCAGGGCGTTATTTTG | This study | 58.0 | 374 | L. diolivorans, P. parvulus, | 58 | |
| R | GCCACCTTCAACGCTTCGTA | P. damnosus, L. suebicus | ||||||||
| clpL | ATPase | F | GCTGCCTTYAAAACATCATCTGG | This study | 56.0 | 158 | L. plantarum, L. salivarius, | 66 | ||
| R | AATACAATTTTGAARAACGCAGCTT | L. fermentum, P. pentosaceus, P. acidilactici | ||||||||
| lr1516 | Putative esterase | F | TRACCACTYTCWCCATTCAACAA | This study | 56.5 | 143 | L. plantarum, P. pentosaceus | 66 | ||
| R | CCACTAGCRATGACYAATACKGGTT | |||||||||
| Bile salt | bsh | Conjugated bile salt acid hydrolase | F | ATTGAAGGCGGAACSGGMTA | This study | 58.0 | 155 | P. pentosaceus, P. acidilactici | 14, 17, 34, 42 | |
| R | ATWACCGGWCGGAAAGCTG | |||||||||
| F | ATTCCWTGGWTWYTGGGACA | This study | 58.0 | 384 | L. plantarum, L. salivarius | |||||
| R | AAAAGCRGCTCTNACAAAWCKAGA | |||||||||
| F | GGTTGGTCGGCCAGTTCTTT | This study | 58.0 | 205 | L. fermentum | |||||
| R | CCAACATGCCCAAGTTCGAC | |||||||||
| lr0085 | Hypothetical protein | F | RCTTTGACCGRTGGGGCTRT | This study | 57.5 | 150 | L. reuteri, Lactobacillus | 67 | ||
| R | NNNATGGCCGCATGGAAA | vaginalis, Lactobacillus antri | ||||||||
| lr1584 | Major facilitator superfamily permease | F | TAYGCCRTTCGGWTGTTTGG | This study | 55.5 | 151 | L. plantarum, L. fermentum | 67 | ||
| R | TCAWRATGGCRGTCCCAATG | |||||||||
| LBA0552 | Major facilitator superfamily permease | F | GTGATTGCCCTAGCCCTGGT | This study | 58.0 | 180 | L. fermentum | 51 | ||
| R | GATCCCGATCACGATGCAAG | |||||||||
| LBA1429 | Major facilitator superfamily permease | F | AATTTCAGGATGCCCCGGTA | This study | 58.0 | 196 | P. pentosaceus | 50 | ||
| R | CCAAGCTCCCAACAATGCAC | |||||||||
| F | CTACAGCCCGCTGCTAACCA | This study | 58.0 | 174 | L. plantarum | |||||
| R | AGTTTGCATGGCAACCTGGA | |||||||||
| LBA1446 | Multidrug resistance protein | F | GCTGGAGCCACACCGATAAC | This study | 58.0 | 275 | L. plantarum, L. salivarius, P. acidilactici | 51 | ||
| R | CAACGGGATTATGATTCCCATTAGT | |||||||||
| LBA1679 | ABC transporter | F | ATGACAACGTCGTCGGGAGA | This study | 58.0 | 267 | L. fermentum | 51 | ||
| R | GCTCCTCGTTGTTGGGACCT | |||||||||
| F | GGBATVTACGGTGGVCTDGAA | This study | 58.0 | 101 | L. plantarum, L. salivarius, P. pentosaceus, P. acidilactici | |||||
| R | NGYTCCAGAAAGAATCTTGAACATYA | |||||||||
| LBA1432 | Hypothetical protein | F | TCCCATTCATCAYATGGAACAA | This study | 56.5 | 352 | P. pentosaceus, P. acidilactici | 50 | ||
| R | CTGGCCCACATATCCATWCC | |||||||||
| apf | Aggregation-promoting factors | F | YAGCAACACGTTCTTGGTTAGCA | This study | 53.0 | 112 | L. plantarum, L. salivarius, | 22 | ||
| R | GAATCTGGTGGTTCATAYWCAGC | L. fermentum, P. pentosaceus, P. acidilactici | ||||||||
| Synthesis of B vitamins | ||||||||||
| Folate synthesis | folP | Dihydropteroate synthase/dihydropteroate pyrophosphorylase | F | CCASGRCSGCTTGCATGAC | This study | 59.5 | 261 | L. plantarum, L. fermentum | 13 | |
| R | TKACGCCGGACTCCTTTTWY | |||||||||
| folK | 2-Amino-4-hydroxy-6- | F | CCATTTCCAGGTGGGGAATC | This study | 59.5 | 214 | L. plantarum, L. | 13, 59 | ||
| hydroxymethyldihydropteridine diphosphokinase | R | GGGGTGGTCCAAGCAAACTT | fermentum | |||||||
| Riboflavin synthesis | ribH | 6,7-Dimethy-8-ribityllumazine synthase | F | AGGGCGAAACCGACCACTAC | This study | 60.0 | 179 | L. fermentum | 7 | |
| R | CGATTGGGCAGTCATCGAAC | |||||||||
| ribB | Riboflavin synthase subunit alpha | F | AGTAAACGGAACGGGCAAGC | This study | 60.0 | 235 | L. fermentum | 7 | ||
| R | GTTGACCAGGGCACCAACTG | |||||||||
| ribA | 3,4-Dihydroxy-2-butanone 4-phosphate synthase/ | F | TTTACGGGCGATGTTTTAGG | This study | 60.0 | 121 | L. fermentum, P. | 7 | ||
| GTP cyclohydrolase II | R | CGACCCTCTTGCCGTAAATA | pentosaceus, L. plantarum | |||||||
| ribG | Diaminohydroxyphosphoribosylaminopyrimidine deaminase | F | TGGKAAGACGCCKCCKTGT | This study | 56.0 | 351 | P. pentosaceus, L. plantarum | 7 | ||
| R | TTCACCAAYCARAATYGCTTGA | |||||||||
| Starch metabolism | glgP | Glycogen phosphorylase | F | GCGGGTGTTCAAAGTATCGT | This study | 60.0 | 229 | L. plantarum | 30 | |
| R | TCTCGAGGGCCTCTTGTAAA | |||||||||
| malL | Oligo-1,6-glucosidase | F | TTGCCTAACAACTGGGGTTC | This study | 60.0 | 177 | L. plantarum | 30 | ||
| R | ATCAACGCCTTTGTTCAACC | |||||||||
| agl | α-Glucosidase | F | GCSAAAATGCTAGCGACYMT | This study | 59.5 | 236 | L. plantarum | 30 | ||
| R | CCACTGCATYGGYGTACGY | |||||||||
| F | AACCTGGTGAAATGGCAGAC | This study | 60.0 | 206 | L. fermentum | |||||
| R | TTGGTCATTCCCAGTTCCTC | |||||||||
| α-amy | α-Amylase | F | AGATCAGGCGCAAGTTCAGT | This study | 60.0 | 220 | L. plantarum | 16, 30 | ||
| R | TTTTATGGGCACACCACTCA | |||||||||
| dexC | Neopullulanase | F | CCAGACGAGCAAGAACAACA | This study | 60.0 | 212 | L. plantarum | 30 | ||
| R | ATTGGCGATACGCCACTTAC | |||||||||
| F | ACTTTTCTGCAGCCTGGTGT | This study | 60.0 | 249 | L. fermentum | |||||
| R | ACGGCCATTAAACTGTCGTC | |||||||||
| malP | Maltose phosphorylase | F | TGCCAYAAYGARTGGGARAT | This study | 60.0 | 161 | L. plantarum, L. | 30 | ||
| R | ACSCKATCWGCCCARAAAC | fermentum, P. pentosaceus | ||||||||