Bacteria |
EUB338f |
ACTCCTACGGGAGGCAGC |
550bp |
Amann et al. 1990AMANN, RI., BINDER, BJ., OLSON, RJ., CHISHOLM, SW., DEVEREUX, R. and STAHL, DA., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, vol. 56, no. 6, p. 1919-1925. PMid:2200342.
|
926Rr |
CCCGTCAATTCMTTTGAGTTT |
|
Watanabe et al. 2001WATANABE, K., KODAMA, Y. and HARAYAMA, S., 2001. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. Journal of Microbiological Methods, vol. 44, no. 3, p. 253-262. http://dx.doi.org/10.1016/S0167-7012(01)00220-2. PMid:11240048 http://dx.doi.org/10.1016/S0167-7012(01)...
|
Nitrosomonadaceae |
EUB338f |
ACTCCTACGGGAGGCAGC |
950bp |
Amann et al. 1990AMANN, RI., BINDER, BJ., OLSON, RJ., CHISHOLM, SW., DEVEREUX, R. and STAHL, DA., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, vol. 56, no. 6, p. 1919-1925. PMid:2200342.
|
Nso1225r |
CGCCATTGTATTACGTGTGA |
|
Mobarry et al. 1996MOBARRY, BK., WAGNER, M., URBAIN, V., RITTMANN, BE. and STAHL, DA., 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Applied and Environmental Microbiology, vol. 62, no. 6, p. 2156-2162. PMid:8787412.
|
Nitrosospira |
Nsv443f |
CGGAACGAAACGGTCACG |
500bp |
Mobarry et al. 1996MOBARRY, BK., WAGNER, M., URBAIN, V., RITTMANN, BE. and STAHL, DA., 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Applied and Environmental Microbiology, vol. 62, no. 6, p. 2156-2162. PMid:8787412.
|
926Rr |
CCCGTCAATTCMTTTGAGTTT |
|
Watanabe et al. 2001WATANABE, K., KODAMA, Y. and HARAYAMA, S., 2001. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. Journal of Microbiological Methods, vol. 44, no. 3, p. 253-262. http://dx.doi.org/10.1016/S0167-7012(01)00220-2. PMid:11240048 http://dx.doi.org/10.1016/S0167-7012(01)...
|
Nitrospira |
EUB338f |
ACTCCTACGGGAGGCAGC |
350bp |
Amann et al. 1990AMANN, RI., BINDER, BJ., OLSON, RJ., CHISHOLM, SW., DEVEREUX, R. and STAHL, DA., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, vol. 56, no. 6, p. 1919-1925. PMid:2200342.
|
Ntspa0685r |
GGGAATTCCGCGCTCCT |
|
Hovanec et al. 1998HOVANEC, TA., TAYLOR, LT., BLAKIS, A. and DELONG, EF., 1998. Nitrospira-like bacteria associated with nitrite oxidation in freshwater aquaria. Applied and Environmental Microbiology, vol. 64, no. 1, p. 258-264. PMid:16349486.
|
Nitrobacter |
EUB338f |
ACTCCTACGGGAGGCAGC |
750bp |
Amann et al. 1990AMANN, RI., BINDER, BJ., OLSON, RJ., CHISHOLM, SW., DEVEREUX, R. and STAHL, DA., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, vol. 56, no. 6, p. 1919-1925. PMid:2200342.
|
NIT3r |
CCTGTGCTCCATGCTCCG |
|
Mobarry et al. 1996MOBARRY, BK., WAGNER, M., URBAIN, V., RITTMANN, BE. and STAHL, DA., 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Applied and Environmental Microbiology, vol. 62, no. 6, p. 2156-2162. PMid:8787412.
|
amoA |
amoAf |
GGGGTTTCTACTGGTGGT |
491bp |
Geets et al. 2007GEETS, J., COOMAN, M., WITTEBOLLE, L., HEYLEN, K., VANPARYS, B., DE VOS, P., VERSTRAETE, W. and BOON, N., 2007. Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Applied Microbiology and Biotechnology, vol. 75, no. 1, p. 211-221. http://dx.doi.org/10.1007/s00253-006-0805-8. PMid:17256118 http://dx.doi.org/10.1007/s00253-006-080...
|
amoAr |
CCCCTCKGSAAAGCCTTCTTC |
|
|
napA |
napA V66 |
TAYTTYYTNHSNAARATHATGTAYGG |
415bp |
Smith et al. 2007SMITH, CJ., NEDWELL, DB., DONG, LF. and OSBORN, AM., 2007. Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, vol. 73, no. 11, p. 3612-3622. http://dx.doi.org/10.1128/AEM.02894-06. PMid:17400770 http://dx.doi.org/10.1128/AEM.02894-06...
|
napA V67 |
NGGRTGCATYTCNGCCATRTT |
|
|
nrfA |
nrfAf |
GCNTGYTGGWSNTGYAA |
500bp |
Mohan et al. 2004MOHAN, SB., SCHMID, M., JETTEN, M. and COLE, J., 2004. Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiology Ecology, vol. 49, no. 3, p. 433-443. http://dx.doi.org/10.1016/j.femsec.2004.04.012. PMid:19712292 http://dx.doi.org/10.1016/j.femsec.2004....
|
nrfAr |
TWNGGCATRTGRCARTC |
|
|
Streptococcus |
EUB338f |
ACTCCTACGGGAGGCAGC |
320bp |
Amann et al. 1990AMANN, RI., BINDER, BJ., OLSON, RJ., CHISHOLM, SW., DEVEREUX, R. and STAHL, DA., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology, vol. 56, no. 6, p. 1919-1925. PMid:2200342.
|
STRr |
GTGCAGAAGGGGAGAGTGG |
|
Trebesius et al. 2000TREBESIUS, K., LEITRITZ, L., ADLER, K., SCHUBERT, S., AUTENRIETH, IB. and HEESEMANN, J., 2000. Culture independent and rapid identification of bacterial pathogens in necrotising fasciitis and streptococcal toxic shock syndrome by fluorescence in situ hybridisation. Medical Microbiology and Immunology, vol. 188, no. 4, p. 169-175. http://dx.doi.org/10.1007/s004300000035. PMid:10917153 http://dx.doi.org/10.1007/s004300000035...
|
Enterococcus spp. |
ENRf |
CCCTTATTGTTAGTTGCCATCATT |
144bp |
Rinttilä et al. 2004RINTTILÄ, T., KASSINEN, A., MALINEN, E., KROGIUS, L. and PALVA, A., 2004. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. Journal of Applied Microbiology, vol. 97, no. 6, p. 1166-1177. http://dx.doi.org/10.1111/j.1365-2672.2004.02409.x. PMid:15546407 http://dx.doi.org/10.1111/j.1365-2672.20...
|
ENTr |
ACTCGTTGTACTTCCCATTGT |
|
|
Bacteroides/PrevotellaPorphyromonas |
BPPf |
GGTGTCGGCTTAAGTGCCAT |
140bp |
Rinttilä et al. 2004RINTTILÄ, T., KASSINEN, A., MALINEN, E., KROGIUS, L. and PALVA, A., 2004. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. Journal of Applied Microbiology, vol. 97, no. 6, p. 1166-1177. http://dx.doi.org/10.1111/j.1365-2672.2004.02409.x. PMid:15546407 http://dx.doi.org/10.1111/j.1365-2672.20...
|
BPPr |
CGGA(C/T)GTAAGGGCCGTGC |
|
|
Salmonella sp. |
invA139 |
GTGAAATTATCGCCACGTTCGGGCAA |
284bp |
Fukushima et al. 2003FUKUSHIMA, H., TSUNOMORI, Y. and SEKI, R., 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. Journal of Clinical Microbiology, vol. 41, no. 11, p. 5134-5146. http://dx.doi.org/10.1128/JCM.41.11.5134-5146.2003. PMid:14605150 http://dx.doi.org/10.1128/JCM.41.11.5134...
|
invA141 |
TCATCGCACCGTCAAAGGAACC |
|
|
Aeromonashydrophila |
AHCf |
GAGAAGGTGACCACCAAGAACA |
232bp |
Fukushima et al. 2003FUKUSHIMA, H., TSUNOMORI, Y. and SEKI, R., 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. Journal of Clinical Microbiology, vol. 41, no. 11, p. 5134-5146. http://dx.doi.org/10.1128/JCM.41.11.5134-5146.2003. PMid:14605150 http://dx.doi.org/10.1128/JCM.41.11.5134...
|
AHCr |
AACTGACATCGGCCTTGAACTC |
|
|
Staphylococcus aureus |
SA-1 |
GCGATTGATGGTGATACGGTT |
276bp |
Fukushima et al. 2003FUKUSHIMA, H., TSUNOMORI, Y. and SEKI, R., 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. Journal of Clinical Microbiology, vol. 41, no. 11, p. 5134-5146. http://dx.doi.org/10.1128/JCM.41.11.5134-5146.2003. PMid:14605150 http://dx.doi.org/10.1128/JCM.41.11.5134...
|
SA-2 |
CAAGCCTTGACGAACTAAAGC |
|
|
Pseudomonas aeruginosa |
OPR-1 |
GCTCTGGCTCTGGCTGCT |
230bp |
Qin et al. 2003QIN, X., EMERSON, J., STAPP, J., STAPP, L., ABE, P. and BURNS, JL., 2003. Use of real-time PCR with multiple targets to identify Pseudomonas aeruginosa and other nonfermenting gram-negative bacilli from patients with cystic fibrosis. Journal of Clinical Microbiology, vol. 41, no. 9, p. 4312-4317. http://dx.doi.org/10.1128/JCM.41.9.4312-4317.2003. PMid:12958262 http://dx.doi.org/10.1128/JCM.41.9.4312-...
|
OPR-2 |
AGGGCACGCTCGTTAGCC |
|
|
Escherichia coli |
ECOL1 |
GCTTGACACTGAACATTGAG |
660bp |
Chotár et al. 2006CHOTÁR, M., VIDOVÁ, B. and GODÁNY, A., 2006. Development of specific and rapid detection of bacterial pathogens in dairy products by PCR. Folia Microbiologica, vol. 51, no. 6, p. 639-646. http://dx.doi.org/10.1007/BF02931632. PMid:17455804 http://dx.doi.org/10.1007/BF02931632...
|
ECOL2 |
GCACTTATCTCTTCCGCATT |
|
|
E.coli EPEC (eae)
|
eae1 |
CTGAACGGCGATTACGCGAA |
917bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
eae2 |
CCAGACGATACGATCCAG |
|
|
E.coli EPEC (bfpA) |
BFP1 |
AATGGTGCTTGCGCTTGCTGC |
326bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
BFP2 |
GCCGCTTTATCCAACCTGGTA |
|
|
E.coli ETEC (elt)
|
LTf |
GGCGACAGATTATACCGTGC |
450bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
LTr |
CGGTCTCTATATTCCCTGTT |
|
|
E.coli ETEC (est)
|
STf |
ATTTTTMTTTCTGTATTRTCTT |
190bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
STr |
CACCCGGTACARGCAGGATT |
|
|
E.coli EHEC (stx1)
|
Stx1f |
ATAAATCGCCATTCGTTGACTAC |
180bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
Stx1r |
AGAACGCCCACTGAGATCATC |
|
|
E.coli EHEC (stx2)
|
Stx2f |
GGCACTGTCTGAAACTGCTCC |
255bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
Stx2r |
TCGCCAGTTATCTGACATTCTG |
|
|
E.coli EIEC (ipaH)
|
IpaH1 |
GTTCCTTGACCGCCTTTCCGATACCGTC |
600bp |
Aranda et al. 2004ARANDA, KRS., FAGUNDES-NETO, U. and SCALETSKY, ICA., 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. Journal of Clinical Microbiology, vol. 42, no. 12, p. 5849-5853. http://dx.doi.org/10.1128/JCM.42.12.5849-5853.2004. PMid:15583323 http://dx.doi.org/10.1128/JCM.42.12.5849...
|
IpaH2 |
GCCGGTCAGCCACCCTCTGAGAGTAC |
|
|