TABLE 3.

16S rRNA-targetted primers and probes (when applicable) sequences used in this study with the RT-PCR conditions.

	Primers and probes			RT-PCR conditions for the 40 cycles
Target	Primers	Sequence 5′-3′	References	Denaturing (°C; s)	Annealing and extension (°C; s)
F. prausnitzii	Fpra_F	TGTAAACTCCTGTTGTTGAGGAAGATAA	Lopez-Siles et al., 2014	95; 15	60; 60
	Fpra_R	GCGCTCCCTTTACACCCA
	Fpra_PR	FAM-CAAGGAAGTGACGGCTAACTACGTGCCAG-TAMRA
F. prausnitzii	PHG_F	CTCAAAGAGGGGGACAACAGTT	Lopez-Siles et al., 2016	95; 15	64; 60
phylogroup I and	PHG_R	GCCATCTCAAAGCGGATTG
phylogroup II	PHGI_PR	FAM-TAAGCCCACGACCCGGCATCG-BHQ1
	PHGII_PR	HEX-TAAGCCCACRGCTCGGCATC-BHQ1
A. muciniphila	AKK_F	CAGCACGTGAAGGTGGGGAC	Collado et al., 2007	95; 15	60; 60
	AKK_R	CCTTGCGGTTGGCTTCAGAT
Roseburia spp.	ROS_F	TACTGCATTGGAAACTGTCG	Larsen, 2019	95;15	60; 60
	ROS_R	CGGCACCGAAGAGCAAT
B46	B46_F	GTACGGGGAGCAGCAGTG	Malagón et al., 2019	95; 15	62; 45
	B46_R	GACACTCTAGA GCACAGTTTCC