Table 1.
Column A: universal and genera-specific primer and probe sets employed for qPCR. See Supplementary data for details on DNA library preparation and real time PCR conditions. Column B: extracted DNA of bacteria used for PCR test of specificity of designed primer and probe sets
| Primer and probe sets for selected bacteria | List of species/strains primer sets were PCR tested against | ||
|---|---|---|---|
| Sequence | |||
| 5′→3′ | (A) | Tma | (B) |
| Universalb (Amplicon size = 466 bp) | Lactobacillus rhamnosus ATCC 7469 | ||
| Forward: | |||
| TCCTACGGGAGGCAGCAGT | 60.8 | Lactobacillus salivarius ATCC 11741 | |
| Reverse: | Lactobacillus casei ATCC 393 | ||
| GGACTACCAGGGTATCTAATCCTGTT | 57.2 | Lactobacillus plantarum ATCC 14917 | |
| Probec: | Lactobacillus gasseri ATCC 33323 | ||
| CGTATTACCGCGGCTGCTGGCAC | 64.8 | Streptococcus mutans NCTC 10449 | |
| Streptococcus oralis NCTC 11427 | |||
| Lactobacillusd (SYBR® Green)(Amplicon size = 223 bp) | Streptococcus mitis NCTC 12261 | ||
| Forward: | |||
| TGGAAACAGRTGCTAATACCG | 52.4 – 54.8 | Streptococcus parasanguinis ATCC 15912 | |
| Reverse: | Streptococcus gordonii ATCC 10558 | ||
| GTCCATTGTGGAAGATTCCC | 53.4 | Streptococcus thermophilus ATCC 19258 | |
| Streptococcus vestibularis ATCC 49124 | |||
| Streptococcus (Amplicon size = 86 bp) | Fusobacterium nucleatum ATCC 25586 | ||
| Forward: | |||
| CGGATCGTAAAGCTCTGTTGTAAG | 55.5 | Fusobacterium necrophorum ATCC 25286 | |
| Reverse: | Bifidobacterium breve ATCC 15700 | ||
| GCCGTCCCTTTCTGGTAAG | 55.6 | Actinomyces israelii ATCC 12102 | |
| Probe: | Neisseria meningitidis ATCC 13077 | ||
| GTGTGAGAGTGGAAAGTTCACACWGTGACGGT | 64.1 | Neisseria gonorrhoeae ATCC 19424 | |
| Neisseria elongata ATCC 25295 | |||
| Prevotella (Amplicon size = 116 bp) | Pseudomounas aeruginosa ATCC 10145 | ||
| Forward: | |||
| GAAGGTGCGGGTATCGAAC | 55.8 | Porphyromonas gingivalis W83 | |
| Reverse: | Haemophilus influenzae ATCC 33391 | ||
| GGG ATGCTTAATGCTTTCGCTT | 56.2 | Haemophilus parainfluenzae ATCC 33392 | |
| Probe: | Prevotella intermedia ATCC 25611 | ||
| CCGCACAGTAAACGATGGATGCCCGC | 65.7 | Prevotella denticola ATCC 35308 | |
| Prevotella bivia ATCC 29303 | |||
| Fusobacterium (Amplicon size = 87 bp) | Prevotella melaninogenica ATCC 25845 | ||
| Forward: | |||
| GCG GAACTACAAGTGTAGAGGT | 56.4 | Alloprevotella tannerae ATCC 51259 | |
| Reverse: | Bacteroides uniformis ATCC 8492 | ||
| AGCGTCAGTATCTGTCCAGT | 55.4 | Bacteroides eggerthii ATCC 27754 | |
| Probe: | Tannerella forsythia ATCC 43037 | ||
| AGCTGGCTTCCCCATCGGCATTCCTACAA | 66.5 | Parvimonas micra ATCC 33270 | |
| Escherichia coli JM109 | |||
a
Melting temperature (Tm) of oligonucleotide determined by Integrated DNA Technologies (Coralville, Iowa) www.idtdna.com/scitools
b
From Nadkarni et al. [18]
c
Oligonucleotide probes were labeled with 6-carboxyfluorescein (FAM) fluorescent reporter at the 5′ end and Iowa Black® FQ dark quencher at the 3′ end
d
From Byun et al. [14]