Table 1.

Primers used for the detection of different bacterial groups in inoculum or fermentation samples by real-time qPCR analysis.

Target organisms	Gene	Sequence 5′–3′	Reference
All bacteria	16S	f: TCCTACGGGAGGCAGCAGT	Hopkins et al., 2005
		r: GGACTACCAGGGTATCTAATCCTGTT
Ruminococcaceae (Clostridium leptum)	16S	f: GCACAAGCAGTGGAGT	Kanno et al., 2009
		r: CTTCCTCCGTTTTGTCAA
Lachnospiraceae (Blautia coccoides)	16S	f: AAATCACGGTACCTGACTAA	Matsuki et al., 2002
		r: CTTTGAGTTCATTCTTGCGAA
Bifidobacteria sp.	16S	f: TCGCGTC(C/T)GGTGTGAAAG	Rinttilä et al., 2004
		r: CCACATCCAGC(A/G)TCCAC
Enterobacteriaceace sp.	16S	f: CATGCCGCGTGTATGAAGAA	Huijsdens et al., 2002
		r: CGGGTAACGTCAATGAGCAAA
Bacteroidetes	16S	f: GGTGTCGGCTTAAGTGCCAT	Rinttilä et al., 2004
		r: CGGA(C/T)GTAAGGGCCGTGC
Lactobacillaceae/Leuconostocaceae group	16S	f: AGCAGTAGGGAATCTTCCA	Rinttilä et al., 2004
		r: CGCCACTGGTGTTCYTCCATATA
C. difficile	tcdA	f: CTCCTGGACCACTTAAACTTATTGTG	This study
		r: GCTACCGCAGAAAACTCTATGTTTT
Lactococcus lactis UL719	nisI	f: CTGAAGTACGTGTGTTTGATTCAGTTAG	Trmčiać et al., 2011
		r: TCGCCATAATCCCATTCCGTC