Table 2.

Targets, assay conditions and primers of quantitative real-time polymerase chain reaction assays

Target bacterial group/phylotype	Positive control strain or clone	MgCl2 (mmol/L)	Detection (°C)	Annealing (°C)	Primer sequences (F: forward, R: reverse)
Bifidobacterium catenulatum/Pseudocatenulatum-like[4]	AM277302	3	87	68	F: 5'-ACTCCTCGCATGGGGTGTC-3'
					R: 5'-CCGAAGGCTTGCTCCCGAT-3'
Bifidobacterium spp.[30]	Bifidobacterium longum	3	85	58	F: 5'-TCGCGTC(C/T)GGTGTGAAAG-3'
	DSM20219				R: 5'-CCACATCCAGC(A/G)TCCAC-3'
Clostridium coccoides/Eubacterium rectale-group[30]	Ruminococcus productus	4	85	55	F: 5'-CGGTACCTGACTAAGAAG-3'
					R: 5'-AGTTT(C/T)ATTCTTGCGAAC-3'
	DSM2950
Clostridium cocleatum 88%[4]	AM275477	4	80	60	F: 5'-AATACATAAGTAACCTGGCRTC-3'
					R: 5'-CGTAGCACTTTTCATATAGAGTT-3'
Collinsella aerofaciens-like[4]	AM276364	4	89	67	F: 5'-CCCGACGGGAGGGGAT-3'
					R: 5'-CTTCTGCAGGTACAGTCTTGAC-3'
Coprococcus eutactus 97%[4]	AM278899	2	83	63	F: 5'-AGCTTGCTCCGGCYGATTTA-3'
					R: 5'-CGGTTTTACCAGTCGTTTCCAA-3'
Desulfovibrio desulfuricans-group[30]	Desulfovibrio desulfuricans	4	85	58	F: 5'-GGTACCTTCAAAGGAAGCAC-3'
	ATCC7757				R: 5'-GGGATTTCACCCCTGACTTA-3'
Eubacterial 16S[31]	Bifidobacterium longum	3	80	50	F: 5'-TCCTACGGGAGGCAGCAGT-3'
	DSM20219				R: 5'-GGACTACCAGGGTATCTAATCCTGTT-3'
Lactobacillus-group[32,33]	Lactobacillus acidophilus	2	85	58	F: 5'-AGCAGTAGGGAATCTTCCA-3'
	ATCC4356				R: 5'-CACCGCTACACATGGAG-3'
Ruminococcus torques 91%[4]	AM276624	5	82	62	F: 5'-TGCTTAACTGATCTTCTTCGGA-3'
					R: 5'-CGGTATTAGCAGTCATTTCTG-3'
Ruminococcus torques 94%[4]	AM277929	2	85	65	F: 5'-AATCTTCGGAGGAAGAGGACA-3'
					R: 5'-ACACTACACCATGCGGTCCT-3'
Streptococcus bovis-like[4]	AM276479	5	80	60	F: 5'-TTAGCTTGCTAAAGTTGGAA-3'
					R: 5'-ATCTACTAGTGAAGCAATTGCT-3'
Veillonella spp.[30]	Veillonella parvula ATCC10790	3	85	62	F: 5'-A(C/T)CAACCTGCCCTTCAGA-3'
					R: 5'-CGTCCCGATTAACAGAGCTT-3'