Table 2.

Primers used in quantitative PCR.

Target	Primers	Sequence from 5′ to 3′a	Annealing temperature	Reference
Akkermansia muciniphila	AM1	CAGCACGTGAAGGTGGGGAC	50°C	[18]
	AM2	CCTTGCGGTTGGCTTCAGAT
Bifidobacterium genus	Bifido5′	GAT TCT GGC TCA GGA TGA ACG C	60°C	[19, 20]
	Bifido3′	CTG ATA GGA CGC GAC CCC AT
Bifidobacterium adolescentis	Ado-Ang5′	GGA TCG GCT GGA GCT TGC TCC G	63°C	[21]
	Ado3′	CCC CGA AGG CTT GCT CCC AGT
Bifidobacterium bifidum	Bifidum5′	TGA CCG ACC TGC CCC ATG CT	61°C	[21]
	Bifidum3′	CCC ATC CCA CGC CGA TAG AAT
Bifidobacterium breve	Breve5′	AAT GCC GGA TGC TCC ATC ACA C	62°C	[21]
	Breve3′	GCC TTG CTC CCT AAC AAA AGA GG
Bifidobacterium catenulatum group	Caten5′	GCC GGA TGC TCC GAC TCC T	64°C	[21]
	Caten3′	ACC CGA AGG CTT GCT CCC GAT
Bifidobacterium longum group	Longum5′	TTC CAG TTG ATC GCA TGG TCT TCT	65°C	[21]
	Longum3′	GGC TAC CCG TCG AAG CCA CG
Clostridium coccoides group	g-Ccoc-F	AAA TGA CGG TAC CTG ACT AA	53°C	[22]
	g-Ccoc-R	CTT TGA GTT TCA TTC TTG CGA A
Clostridium difficile	Cdif-F	TTG AGC GAT TTA CTT CGG TAA AGA	62°C	[23]
	Cdif-R	TGT ACT GGC TCA CCT TTG ATA TTY A
Clostridium leptum subgroup	sg-Clept-F	GCA CAA GCA GTG GAG T	60°C	[24]
	sg-Clept-R3	CTT CCT CCG TTT TGT ACC
Clostridium perfringens	CPerf165F	CGC ATA AYbG TTG AAA GAT GG	64°C	[25]
	CPerf269R	CCT TGG TAG GCC GTT ACC C
Staphylococcus aureus nuc gene	NUC1	GCG ATT GAT GGT GAT ACG GTT	55°C	[26]
	NUC2	AGC CAA GCC TTG ACG AAC TAA AGC

^aR represents a (A/G) wobble nucleotide; Y represents a (C/T) wobble nucleotide.

^bC in the reference was replaced by Y to detect better different C. perfringens strains.