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	36
Total Bacteria 16 s rDNA	F R Probe	5′AGAGTTTGATCMTGGCTCAG3’ 5′TTACCGCGGCKGCTGGCAC3’ 5′CCAKACTCCTACGGGAGGCAGCAG3’	Desulfovibrio vulgaris ATCC 29579D-5	36
Bacteroidetes 16 s rDNA	F R	5′CATGTGGTTTAATTCGATGAT3' 5′AGCTGACGACAACCATGCAG3'	Bacteroides fragilis ATCC 25285D-5	19,38
Bacteroides 16 s rDNA	F R	5′GAGAGGAAGGTCCCCCAC3' 5′CGCTACTTGGCTGGTTCAG3'	Bacteroides fragilis ATCC 25285D-5	19,38
Firmicutes 16 s rDNA	F R	5′ATGTGGTTTAATTCGAAGCA3' 5′AGCTGACGACAACCATGCAC3'	Clostridium acetobutylicum ATCC 824D-5	40
Bifidobacteria 16 s rDNA	F R	5′CTCCTGGAAACGGGTGG3' 5′GGTGTTCTTCCCGATATCTACA3'	Bifidobacterium longum infantis ATCC 15697D-5	39
Akkermansia muciniphila 16 s rDNA	F R	5′CAGCACGTGAAGGTGGGGAC3' 5′CCTTGCGGTTGGCTTCAGAT3'	Akkermansia municiphila ATCC-BAA835D-5	37
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	36
M. smithii nifH	Mnif 202 F Mnif 353 R Mnif Probe	5′GAAAGCGGAGGTCCTGAA3' 5′ACTGAAAAACCTCCGCAAAC3' 5′CCGGACGTGGTGTAACAGTAGCTA3'	M. smithii DSM 861	21
Bacterial 16 s rRNA	357 F-GC 518 R	5′GCclampCTCCTACGGGAGGCAGCAG3' 5′GTATTACCGCGGCTGCTGG3'		34
16 s rDNA V3-V4	Pro 341 F Pro 805 R	5′TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNBGCASCAG3' 5′GTCTCGTGGGCTCGGAGATGTGTATAAGAGCAGGACTACNVGGGTATCTAATCC3'		41