Table 1.
Development of TaqMan real-time PCR for the detection of human oral bacteria.
| Bacterial strain | Sequence of primer or probe (5′–3′) | Target genes | Clinical specimens | Equipment | Reference |
| Organism associated with periodontitis, oral malodor, advanced caries, and pulp inflammation | |||||
| Actinobacillus actinomycetemcomitans | Forward, CAG CAT CTG CGA TCC CTG TA Reverse, TCA GCC CTT TGT CTT TCC TAG GT Probe, TCG AGT ATT CCT CAA GCA TTC TCG CAC G |
lktA | Subgingival plaque Saliva | ABI PRISM 7700 Sequence Detection Systema | 17 |
| Forward, CCC ATC GCT GGT TGG TTA Reverse, GGC ACG TAG GCG GAC C Probe, CCT CTG TAT ACG CCA TTG TAG CAC GTG TGT |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler systemb | 24 | |
| Forward, ACG CAG ACG ATT GAC TGA ATT TAA Reverse, GAT CTT CAC AGC TAT ATG GCA GCT A Probe, TCA CCC TTC TAC CGT TGC CAT GGG |
lktC | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 19 | |
| Porphyromonas gingivalis | Initial forward, GGA TTA GAT ACC CTG GTA GTC Initial reverse, GGA GTA TTT AGC CTT Second forward, CAT CGG TAG TTG CTA ACA GTT TTC G Second reverse, CCG ACC TCT ACA TTA TCA G Probe, ATG ACG TCA AAT CAG CAC GGC CCT TAC AT |
16S rRNA gene and 23S rRNA gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 30 |
| Forward, TCG GTA AGT CAG CGG TGA AAC Reverse, GCA AGC TGC CTT CGC AAT Probe, CTC AAC GTT CAG CCT GCC GTT GAA A |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 | |
| Forward, TAC CCA TCG TCG CCT TGG T Reverse, CGG ACT AAA ACC GCA TAC ACT TG Probe, GCT AAT GGG ACG CAT GCC TAT CTT ACA GCT |
16S rRNA gene | Subgingival plaque Saliva |
ABI PRISM 7700 Sequence Detection System | 17 | |
| Forward, ACC TTA CCC GGG ATT GAA ATG Reverse, CAA CCA TGC AGC ACC TAC ATA GAA Probe, ATG ACT GAT GGT GAA AAC CGT CTT CCC TTC |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler system | 24 | |
| Forward, CCT ACG TGT ACG GAC AGA GCT ATA Reverse, AGG ATC GCT CAG CGT AGC ATT Probe, TCG CCC GGG AAG AAC TTG TCT TCA |
Arg- gingipain gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 19 | |
| Porphyromonas endodontalis | Forward, GCT GCA GTC CAA CTG TAG TCT TG Reverse, TCA GTG TCA GAC GGA GCC TAG TAC Probe, CAT TCC GCA TAC CTT CGG TCT CCT CTA GC |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 |
| Micromonas micros | Forward, AGT GGG ATA GCC GTT GGA AA Reverse, GAC GCG AGC CCT TCT TAC AC Probe, ACC GCA TGA GAC CAC AGA ATC GCA |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 |
| Treponema denticola | Forward, TAA TAC CGA ATG TGC TCA TTT ACA T Reverse, CTG CCA TAT CTC TAT GTC ATT GCT CTT Probe, GAC GGG GGC CCG CAC AAG CGG |
16S rRNA gene | Subgingival plaque | iCycler iQ detection systemc | 39 |
| Forward, AGA GCA AGC TCT CCC TTA CCG T Reverse, TAA GGG CGG CTT GAA ATA ATG A Probe, CAG CGT TCG TTC TGA GCC AGG ATC A |
16S rRNA gene | Subgingival plaque Saliva |
ABI PRISM 7700 Sequence Detection System | 36 | |
| Forward, CCG AAT GTG CTC ATT TAC ATA AAG GT Reverse, GAT ACC CAT CGT TGC CTT GGT Probe, ATG GGC CCG CGT CCC ATT AGC |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler system | 24 | |
| Treponema vincentii | Forward, GTC TCA ATG GTT CAT AAG AA Reverse, CAA GCC TTA TCT CTA AGA CT Probe, GAC GGG GGC CCG CAC AAG CGG |
16S rRNA gene | Subgingival plaque | iCycler iQ detection system | 39 |
| Treponema medium | Forward, CAC TCA GTG CTT CAT AAG Reverse, CCG GCC TTA TCT CTA AGA CC Probe, GAC GGG GGC CCG CAC AAG CGG GG |
16S rRNA gene | Subgingival plaque | iCycler iQ detection system | 39 |
| Tannerella forsythia | Forward, GGG TGA GTA ACG CGT ATG TAA CCT Reverse, ACC CAT CCG CAA CCA ATA AA Probe, CCC GCA ACA GAG GGA TAA CCC GG |
16S rRNA gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 21 |
| Forward, ATC CTG GCT CAG GAT GAA CG Reverse, TAC GCA TAC CCA TCC GCA A Probe, ATG TAA CCT GCC CGC AAC AGA GGG ATA AC |
16S rRNA gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 22 | |
| Forward, AGC GAT GGT AGC AAT ACC TGT C Reverse, TTC GCC GGG TTA TCC CTC Probe, TGA GTA ACG CGT ATG TAA CCT GCC CGC |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler system | 24 | |
| Forward, TCC CAA AGA CGC GGA TAT CA Reverse, ACG GTC GCG ATG TCA TTG T Probe, CCG CGA CGT GAA ATG GTA TTC CTC |
BspA antigen gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 19 | |
| Fusobacterium spp. | Forward, CGC AGA AGG TGA AAG TCC TGT AT Reverse, TGG TCC TCA CTG ATT CAC ACA GA Probe, ACT TTG CTC CCA AGT AAC ATG GAA CAC GAG |
16S rRNA gene | Subgingival plaque | ABI PRISM 7700 Sequence Detection System | 22 |
| Forward, AAG CGC GTC TAG GTG GTT ATG T Reverse, TGT AGT TCC GCT TAC CTC TCC AG Probe, CAA CGC AAT ACA GAG TTG AGC CCT GCA TT |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 | |
| Prevotella spp. | Forward, CCA GCC AAG TAG CGT GCA Reverse, TGG ACC TTC CGT ATT ACC GC Probe, AAT AAG GAC CGG CTA ATT CCG TGC CAG |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 |
| Prevotella melaninogenica | Forward, GTG GGA TAA CCT GCC GAA AG Reverse, CCC ATC CAT TAC CGA TAA ATC TTT A Probe, CAA ATC TGA TGC CGT CAT CGA AGA CTA TGC |
16S rRNA gene | Carious dentine | ABI PRISM 7700 Sequence Detection System | 23 |
| Prevotella intermedia | Forward, TCC ACC GAT GAA TCT TTG GTC Reverse, ATC CAA CCT TCC CTC CAC TC Probe, CGT CAG ATG CCA TAT GTG GAC AAC ATC G |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler system | 24 |
| Prevotella nigrescens | Forward, CCG TTG AAA GAC GGC CTA A Reverse, CCC ATC CCT TAC CGG RA Probe, CCC GAT GTG TTT CAT TGA CGG CAT C |
16S rRNA gene | Subgingival plaque Tongue surface debris |
LightCycler system | 24 |
| Cariogenic pathogen | |||||
| Streptococcus mutans | Forward, GCC TAC AGC TCA GAG ATG CTA TTC T Reverse, GCC ATA CAC CAC TCA TGA ATT GA Probe, TGG AAA TGA CGG TCG CCG TTA TGA A |
gtfB | Dental plaque Saliva |
ABI PRISM 7700 Sequence Detection System | 18 |
| Streptococcus sobrinus | Forward, TTC AAA GCC AAG ACC AAG CTA GT Reverse, CCA GCC TGA GAT TCA GCT TGT Probe, CCT GCT CCA GCG ACA AAG GCA GC |
gtfT | Dental plaque Saliva |
ABI PRISM 7700 Sequence Detection System | 18 |
| Early microbial colonizer in human dental biofilm | |||||
| Streptococcus gordonii | Forward, GGT GTT GTT TGA CCC GTT CAG Reverse, AGT CCA TCC CAC GAG CAC AG Probe, AAC CTT GAC CCG CTC ATT ACC AGC TAG TAT G |
The gene encoding putative type I site- specific DNase | Dental plaque | ABI PRISM 7700 Sequence Detection System | 58 |
| Streptococcus mitis | Forward, GAG TCC TGC ATC AGC CAA GAG Reverse, GGA TCC ACC TTT TCT GCT TGA C Probe, TGT TCC CAA GTG GAG CCA ACC AAA CT |
The gene encoding putative Glycine-rich protein | Dental plaque | ABI PRISM 7700 Sequence Detection System | 58 |
| Actinomyces naeslundii | Forward, TCG AAA CTC AGC AAG TAG CCG Reverse, AGA GGA GGG CCA CAA AAG AAA Probe, GGG TAC TCT AGT CCA AAC TGG CGG ATA GCG |
The gene encoding unknown protein | Dental plaque | ABI PRISM 7700 Sequence Detection System | 58 |
| Actinomyces viscosus | Forward, ATG TGG GTC TGA CCT GCT GC Reverse, CAA AGT CGA TCA CGC TCC G Probe, ACG GAG GTC GGG AAC GGT GGA AG |
The gene encoding unknown protein | Dental plaque | ABI PRISM 7700 Sequence Detection System | 58 |
| Universal | |||||
| Forward, GGA TTA GAT ACC CTG GTA GTC Initial reverse, GGA GTA TTT AGC CTT Second reverse, TAC CTT GTT ACG ACT T Probe, TGA CGG GCG GTG TGT ACA AGG C |
16S rRNA gene and 23S rRNA gene | ABI PRISM 7700 Sequence Detection System | 30 | ||
| Forward, CCA TGA AGT CGG AAT CGC TAG Reverse, GCT TGA CGG GCG GTG T Probe, TAC AAG GCC CGG GAA CGT ATT CAC CG |
16S rRNA gene | ABI PRISM 7700 Sequence Detection System | 21 | ||
| Forward, TCC TAC GGG AGG CAG CAG T Reverse, GGA CTA CCA GGG TAT CTA ATC CTG TT Probe, CGT ATT ACC GCG GCT GCT GGC AC |
16S rRNA gene | ABI PRISM 7700 Sequence Detection System | 49 | ||
| Forward, CGC TAG TAA TCG TGG ATC AGA ATG Reverse, TGT GAC GGG CGG TGT GTA Probe, CAC GGT GAA TAC GTT CCC GGG C |
16S rRNA gene | ABI PRISM 7700 Sequence Detection System | 17 | ||
a Applied Biosystems, Foster City, CA
b Roche Diagnostics GmbH, Penzberg, Germany
c Bio-Rad Laboratories Inc., Hercules, CA