Table 2 Oligonucleotide primers, probes and genomic standards used in biomolecular analyses.
Microbial Target | Sequences | Standard Genomic DNA | Ref | |
|---|---|---|---|---|
Total Bacteria 16 s rDNA | F R | 5′ACTCCTACGGGAGGCAGCAG3' 5′ATTACCGCGGCTGCTGG3' | Desulfovibrio vulgaris ATCC 29579D-5 | |
Total Bacteria 16 s rDNA | F R Probe | 5′AGAGTTTGATCMTGGCTCAG3’ 5′TTACCGCGGCKGCTGGCAC3’ 5′CCAKACTCCTACGGGAGGCAGCAG3’ | Desulfovibrio vulgaris ATCC 29579D-5 | |
Bacteroidetes 16 s rDNA | F R | 5′CATGTGGTTTAATTCGATGAT3' 5′AGCTGACGACAACCATGCAG3' | Bacteroides fragilis ATCC 25285D-5 | |
Bacteroides 16 s rDNA | F R | 5′GAGAGGAAGGTCCCCCAC3' 5′CGCTACTTGGCTGGTTCAG3' | Bacteroides fragilis ATCC 25285D-5 | |
Firmicutes 16 s rDNA | F R | 5′ATGTGGTTTAATTCGAAGCA3' 5′AGCTGACGACAACCATGCAC3' | Clostridium acetobutylicum ATCC 824D-5 | |
Bifidobacteria 16 s rDNA | F R | 5′CTCCTGGAAACGGGTGG3' 5′GGTGTTCTTCCCGATATCTACA3' | Bifidobacterium longum infantis ATCC 15697D-5 | |
Akkermansia muciniphila 16 s rDNA | F R | 5′CAGCACGTGAAGGTGGGGAC3' 5′CCTTGCGGTTGGCTTCAGAT3' | Akkermansia municiphila ATCC-BAA835D-5 | |
M. smithii 16 s rDNA | Smit.16S-740 F Smit.16S-862 R Smit.16S FAM | 5′CCGGGTATCTAATCCGGTTC-3’ 5′CTCCCAGGGTAGAGGTGAAA3’ 5′CCGTCAGAATCGTTCCAGTCAG3’ | M. smithii DSM 861 | |
M. smithii nifH | Mnif 202 F Mnif 353 R Mnif Probe | 5′GAAAGCGGAGGTCCTGAA3' 5′ACTGAAAAACCTCCGCAAAC3' 5′CCGGACGTGGTGTAACAGTAGCTA3' | M. smithii DSM 861 | |
Bacterial 16 s rRNA | 357 F-GC 518 R | 5′GCclampCTCCTACGGGAGGCAGCAG3' 5′GTATTACCGCGGCTGCTGG3' | ||
16 s rDNA V3-V4 | Pro 341 F Pro 805 R | 5′TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNBGCASCAG3' 5′GTCTCGTGGGCTCGGAGATGTGTATAAGAGCAGGACTACNVGGGTATCTAATCC3' | ||
