Comparison of bacterial quantities in left and right colon biopsies and faeces

Table 2 Real-time polymerase chain reaction primers, probes and assay conditions

qPCR assay	Primers	Chemistry1	Annealing temperature (°C)	Standard species	Primer reference	Reaction condition reference
Akkermansia muciniphila	CAGCACGTGAAGGTGGGGAC	FAST SYBR Green Mastermix;	58	Akkermancia muciniphila ATCC BAA-835	Png et al[20]	This study
	CCTTGCGGTTGGCTTCAGAT	300 nmol/L each primer
Bacteroidetes	GGCGACCGGCGCACGGG	Power SYBR Green Mastermix;	65	Bacteroides fragilis	Nakanishi et al[21]	This study
	GRCCTTCCTCTCAGAACCC	300 nmol/L each primer		ATCC 25285
Bifidobacterium spp.	CCTGGTAGTCCACGCCGTAA	FAST TaqMan Mastermix;	60	Bifidobacterium adolescentis	Mäkivuokko et al[22]	Mäkivuokko et al[22]
	CAGGCGGGATGCTTAACG	300 nmol/L each primer,		JCM 1275
	ATCCAGCATCCACCG
		200 nmol/L probe
Clostridium cluster IV	GCACAAGCAGTGGAGT	SYBR Green Core Reagents; 1.5 nmol/L MgCl2, 250 nmol/L each primer	62	Clostridium leptum	Matsuki et al[23]	This study
	CTTCCTCCGTTTTGTCAA			DSM 753
Clostridium cluster XIVab	GAWGAAGTATYTCGGTATGT	Power SYBR Green Mastermix;	52	Clostridium boltae	Song et al[24]	Lahtinen et al[25]
	CTACGCWCCCTTTACAC	300 nmol/L each primer		DSM 15670
	Clostridium difficile			TTGAGCGATTTACTTCGGTAAAGA			FAST SYBR Green Mastermix;	60	Clostridium difficile	Lahtinen et al[25]	Lahtinen et al[25]
CCATCCTGTACTGGCTCACCT		300 nmol/L each primer	ATCC 9689
Collinsella aerofaciens	CCCGACGGGAGGGGAT	Power SYBR Green Mastermix;	60	Collinsella aerofaciens ATCC25986	Kassinen et al[26]	This study
	CTTCTGCAGGTACAGTCTTGA	300 nmol/L each primer
Domain bacteria	CATRGHYGTCGTCAGCTCGT	FAST SYBR Green Mastermix;	60	Enterococcus faecium	This study	This study
	GCGGTGTGTRCAAGRCCC	200 nmol/L each primer		DGCC 2063
Enterobacteriaceae	TGCCGTAACTTCGGGAGAAGGCA	SYBR Green Core Reagents;	58	Enterococcus faecium DGCC2063	Matsuda et al[27]	This study
	TCAAGGACCAGTGTTCAGTGTC	2 nmol/L MgCl2,
		200 nmol/L each primer
	Escherichia coli						ACTGGAATACTTCGGATTCAGATACGT	FAST TaqMan Mastermix;	60	Escherichia coli ATCC 11775	Kaclíková et al[28]	This study
ATCCCTACAGATTCATTCCACGAAA		100 nmol/L each primer, 30 nmol/L probe
fam-CAGCAGCTGGGTTGGCATCAGTTATTCG-tamra
Faecalibacterium prausnitzii	CCCTTCAGTGCCGCAGT	SYBR Green Core Reagents;	62	Faecalibacterium prausnitzii ATCC 27768	Rinttilä et al[16]	This study
	GTCGCAGGATGTCAAGAC	4 nmol/L MgCl2,
		250 nmol/L each primer
	Human GAPDH						GGTAAGGAGATGCTGCATTCG	Power SYBR Green Mastermix;	60	Human DNA	Png et al[20]	This study
CGCCCAATACGACCAAATCTAA		300 nmol/L each primer
Helicobacterium pylori			GAAGATAATGACGGTATCTAACGAATAA	FAST SYBR Green Mastermix;	58	Helicobacter pylori	Modified from Rinttilä et al[16]	This study
	CATAGGATTTCACACCTGACTGACTAT	400 nmol/L each primer
Staplylococcus aureus	GCGATTGATGGTGATACGGTT	Power SYBR Green Mastermix;	60	Staphylococcus aureus	Brakstad et al[29]	This study
	AGCCAAGCCTTGACGAACTAAAGC	300 nmol/L each primer		ATCC 29213
Veillonella	AYCAACCTGCCCTTCAGA	Power SYBR Green Mastermix;	60	Veillonella parvula	Rinttilä et al[16]	This study
	CGTCCCGATTAACAGAGCTT	200 nmol/L each primer		DSM 2008

¹Manufactured by (Applied Biosystems, Foster City, CA). GAPDH: Glyceraldehyde 3-phosphate dehydrogenase; qPCR: Quantitative polymerase chain reaction.