TABLE 1.

Oligonucleotides used in this study

Oligonucleotidea	Sequence (5′ to 3′)	Target site (positions)b	Td/Ta (°C)c	Assay(s)d
GM5Fe	CCT ACG GGA GGC AGC AG	341–357	—/55	1
907R	CCG TCA ATT CCT TTR AGT TTf	907–926	—/55	1
TMS128F	GAA TCT RCC CTT TAG TTGf	128–145	—/44	1,2
TMS849R	CTT TTT AAT AAG RCC AAC AGf	830–849	52/44	1,2,3
TMS849A	CTT TTT AAT AAG ACC AAC A	831–849	41/—	4
TMS849G	CTT TTT AAT AAG GCC AAC A	831–849	41/—	4
S-*-Univ-1392-a-A-15g	ACG GGC GGT GTG TRCf	1392–1406	44/—	4
S-D-Bact-0338-a-A-18g	GCT GCC TCC CGT AGG AGT	338–355	54/—	4

^aThe suffixes F and R (forward and reverse, respectively) indicate the primer orientation in relation to the rRNA gene. 

^bE. coli numbering of 16S rRNA nucleotides (10). 

^cT_d, dissociation temperature in the hybridization assays; T_a, annealing temperature in the PCR; —, not applicable. 

^d1, PCR; 2, sequencing; 3, DNA hybridization; 4, rRNA slot blot hybridization. 

^eThis primer has a GC-clamp attached to its 5′ end (23). 

^fR, adenine-guanine degeneracy. 

^gDesignation according to the Oligonucleotide Probe Database (http://www.cme.msu.edu./OPD/) (1).