Table 1.

Primers targeting 16S rRNA gene used for the determination of ileal and cecal mucosa-associated and luminal digesta microbiota composition, by quantitative real-time PCR.

Target	Primer sequence (5′–3′)	Annealing temperature, oC	Reference
Total bacteria	F: ACTCCTACGGGAGGCAGCAG R: ATTACCGCGGCTGCTGG	60	Clifford et al. (2012)
Escherichia coli	F: CATGCCGCGTGTATGAAGAA R: GGGTAACGTCAATGAGCAAAGG	60	Silkie and Nelson, 2009
Lactobacillus spp.	F: GAGGCAGCAGTAGGGAATCTTC R: GGCCAGTTACTACCTCTATCCTTCTTC	60	Delroisse et al. (2008)
Bifidobacterium spp.	F: CGCGTCYGGTGTGAAAG R: CCCCACATCCAGCATCCA	58	Peinado et al. (2013)
Bacteroides spp.	F: GAGAGGAAGGTCCCCCAC R: CGCTACTTGGCTGGTTCAG	58	Peinado et al., 2013
Clostridium cluster I	F: TACCHRAGGAGGAAGCCAC R: GTTCTTCCTAATCTCTACGCAT	56	Boroojeni  et al., 2014
C. cluster IV	F: GCACAAGCAGTGGAGT R: CTTCCTCCGTTTTGTCAA	52	Matsuki et al. (2004)
C. cluster XIVa	F: ACTCCTACGGGAGGCAGC R: CTTCTTAGTCAGGTACCGTCAT	60	Schwiertz et al. (2010)