TABLE 1.

Real-time PCR assays used to detect Bacteriodes 16S rRNA genes, the primers and probe used for each assay, and the annealing temperature used for each assay

Assay	Primer/probe name and sequence (5′-3′)a	Size (bp) of product	Annealing temp (°C)
AllBac (all Bacteroides)	AllBac296f, 5′-GAGAGGAAGGTCCCCCAC-3′	106	60
	AllBac412r, 5′-CGCTACTTGGCTGGTTCAG-3′
	AllBac375Bhqr, 5′-(FAM)CCATTGACCAATATTCCTCACTGCTGCCT(BHQ-1)-3′
BoBac (bovine cluster of Bacteroides)	BoBac367f, 5′-GAAG(G/A)CTGAACCAGCCAAGTA-3′	100	57
	BoBac467r, 5′-GCTTATTCATACGGTACATACAAG-3′
	BoBac402Bhqf, 5′-(FAM)TGAAGGATGAAGGTTCTATGGATTGTAAACTT(BHQ-1)-3′
HuBac (human cluster of Bacteroides)	HuBac566f, 5′-GGGTTTAAAGGGAGCGTAGG-3′	116	60
	HuBac692r, 5′-CTACACCACGAATTCCGCCT-3′
	HuBac594Bhqf, 5′-(FAM)TAAGTCAGTTGTGAAAGTTTGCGGCTC(BHQ-1)-3′

^aNumbers within the primer/probe name indicate the nucleotide position within the Bacteroides 16S rRNA gene.