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. 2005 Mar;71(3):1373–1386. doi: 10.1128/AEM.71.3.1373-1386.2005

TABLE 4.

16S rRNA-targeted probes used for microarray hybridzation.

Original name Name Full namea Primerb Microarray position(s) Sequence (5′-3′) Tm (°C) ΔG (kcal mol−1) Specificity Reference
CONT-COMP CTT CCT TCC TTC CTT CCT Complementary to control oligonucleotide 35
CONT A1, A48, B1, B48, C1, C48, D1, D48 AGG AAG GAA GGA AGG AAG 51.3 −18.8 Control oligonucleotide 35
NONSENSE A2, A25, A47, C25, D47 AGA GAG AGA GAG AGA GAG 48.5 −17.7 Nonbinding control 35
UNIV1390 UNIV1389a S-D-Univ-1389-a-A-18 R A27, C27, D5 ACG GGC GGT GTG TAC AAG 58.3 −22.2 Bacteria, not Epsilonproteobacteria Modified from 51
UNIV1390 UNIV1389b S-D-Univ-1389-b-A-18 R D6 ACG GGC GGT GTG TAC AAA 58 −21.9 Eucarya Modified from 51
UNIV1390 UNIV1389c S-D-Univ-1389-c-A-18 R D7 ACG GGC GGT GTG TGC AAG 62 −23.9 Archaea Modified from 51
EUB338 EUB338 S-D-Bact-0338-a-A-18 A3, A46, C26, D2, D46 GCT GCC TCC CGT AGG AGT 59.5 −22.4 Most Bacteria 5
EUB338II EUB338II S-*-BactP-0338-a-A-18 D3 GCA GCC ACC CGT AGG TGT 60.7 −23.0 Planctomycetes 14
EUB338III EUB338III S-*-BactV-0338-a-A-18 D4 GCT GCC ACC CGT AGG TGT 60.7 −23.0 Verrucomirobia 14
BTWO23a BTWO663 S-*-Btwo-0663-a-A-18 A34, D9 GGA ATT CCA CCC CCC TCT 57 −21.0 Most Rhodocyclales, but not the Zoogloea and the Azospira lineages Modified from 4
RHC143 S-*-RHC-0143-a-A-18 R A4, A19, A44, D19 TCG CTA CGT TAT CCC CCA 56 −21.2 Most members of the Dechloromonas-Ferribacterium-Quadricoccus-Azonexus, the Azospira, and the Rhodocyclus-Propionivibrio-Accumulibacter lineages, Zoogloea spp., and few members of the Azoarcus-Thauera-Denitromonas lineage This study
S-G-Rhc-0175-a-A-18 RHC175a S-*-RHC-0175-a-A-18 A42, D17 TGC TCA CAG AAT ATG CGG 53 −20.0 Most members of the Dechloromonas-Ferribacterium-Quadricoccus-Azonexus, the Azospira, and the Rhodocyclus-Propionivibrio-Accumulibacter lineages 25
S-G-Rhc-0439-a-A-18 RHC439 S-*-RHC-0439-a-A-18 A43, D18 CNA TTT CTT CCC CGC CGA 54.9-58.3 Rhodocyclus spp., most members of the Candidatus “Accumulibacter” cluster, Azospira lineage 25
RHAC855 S-*-RhAc-0855-a-A-18 A7 TCA CGC GTT AGC TAC GGC 58.2 −22.8 Rhodocyclus spp., most members of the Candidatus “Accumulibacter” cluster This study
PAO846 ACCBA846 S-G-Accba-0846-a-A-18 A10 AGC TAC GGC ACT AAA AGG 52.6 −19.7 Most members of the Candidatus “Accumulibacter” cluster Modified from 13
PAO651 ACCBA651 S-G-Accba-0651-a-A-18 A6 CCC TCT GCC AAA CTC CAG 55.8 −20.9 Most members of the Candidatus “Accumulibacter” cluster 13
ACCBA443 S-*-Accba-0443-a-A-18 A8 CAA GCA ATT TCT TCC CCG 52.2 −19.6 Some members of the Candidatus “Accumulibacter” cluster This study
S-G-Rhx-0456-a-A-17 ACCBA455 S-*-Accba-0455-a-A-18 A9 AGG GTA TTA ACC CAA GCA 51.4 −18.8 Some members of the Candidatus “Accumulibacter” cluster 25
RHO828 S-G-Rho-0828-a-A-18 A12 TTA ACC CCA CCA ACA CCT 54.4 −20.0 Rhodocyclus spp. This study
RHO842 S-G-Rho-0842-a-A-18 A13 CGG CAC TAA TGG GTT TAA 50.5 −18.8 Rhodocyclus spp. This study
RHOTE1280 S-S-Rho.te-1280-a-A-18 A15 CGA TCG GCT TTG CGG GAT 58.9 −22.6 Rhodocyclus tenuis This study
AZP471 S-G-Azp-0471-a-A-18 A29 GTA CCG TCA TCA ACA ACG 51.4 −19.5 Most Azospira spp. This study
AZP456 S-G-Azp-0456-a-A-18 A30 ACG GAT ATT AGC CGT TGC 53.1 −20.1 Most Azospira spp. This study
AZP737 S-G-Azp-0737-a-A-18 A28 GTC AGT ACT AAC CCA GGG 51.6 −19.1 Most Azospira spp. This study
DAF1030 S-*-D.A.F-1030-a-A-18 A22, A45, D20 TGT GTT CCA GCT CCC TTT 54.7 −20.2 Some bacteria of the Dechloromonas-Ferribacterium-Quadricoccus-Azonexus lineage This study
DEMFE455 S-*-DemFe-0455-a-A-18 A21 AGG GTA TTA ACC CAT GCG 52.5 −19.5 Ferribacterium limneticum, few Dechloromonas spp. This study
QUACO135 S-*-Quaco-0135-a-A-18 D40 TTA TCC CCC ACT CAA TGG 51.8 −19.0 Quadricoccus australiensis, reactor clone PHOS-HE23 This study
DCMAG455 S-S-Dcm.ag-0455-a-A-18 A20 CAG GTA TTA GCT GAT GCG 50.7 −19.1 Dechloromonas agitata This study
A08KA458 S-*-A08KA-0459-a-A-18 D44 ACA CCC CGT ATT AGA GAG 50.7 −18.7 Oral strain A08KA lineage This study
TH14 RHC175b S-*-RHC-0175-b-A-18 A39, C4, C28, C40, D14 CCC TCA GGA CGT ATG CGG 57.9 −22.1 Some Thauera, Azoarcus, Zoogloea, Sterolibacterium, and Azovibrio spp. Modified from 26
TH3 RHC222 S-*-RHC-0222-a-A-18 A36, B2, C2, C41, D11 ACA TCG GCC GCT CCA ATC 58.6 −22.4 Some members of the Azoarcus-Thauera-Denitromonas, Zoogloea, and Azovibrio lineages 26
AZV211 S-G-Azv-0211-a-A-18 C42 TCC AAT CGC ACA AGG TCC 55.7 −21.2 Azovibrio spp. This study
AZVRE847 S-*-Azv.re-0847-a-A-18 C43 TAG CTC CGT TAC TAA TAG 45.1 −17.1 Azovibrio restrictus This study
AT1458 ATD1459 S-*-ATD-1459-a-A-18 A,R,Z A35, D10 TCT CAC CGT GGT AAG CGC 58 −22.4 Most members of the Azoarcus-Thauera-Denitromonas lineage Modified from 43
RHC630 S-*-RHC-0630-a-A-18 A40, D15, D25 TGC AGT CAC AAA CGC AGT 56.1 −21.2 Most Thauera, Zoogloea, and Rhodocyclus spp. This study
AZA1006 S-*-Aza-1006-a-A-18 A38, B4, D13 TCC CTG ATC TCT CAA GGA 52.1 −19.5 Most members of the Azoarcus cluster This study
AZA483 S-*-Aza-0483-a-A-18 B6 CTT CTT CTG ACA GTA CCG 49.7 −18.6 Azoarcus cluster This study
Azo644 AZA645 S-*-Aza-0645-a-A-18 B5, B43 GCC GTA CTC TAG CCG TGC 58.3 −22.5 Most members of the Azoarcus cluster 24
Azo1251 AZA1252 S-*-Aza-1252-a-A-18 B7 TCG CGC TTT GGC AGC CCT 64.1 −24.8 Azoarcus evansii, Azoarcus toluvorans, Azoarcus tolulyticus, Azoarcus toluclasticus, and related Azoarcus spp. Modified from 24
AZA444 S-*-Aza-0444-a-A-18 B9 GGA AGC GTT TTC TTT CCG 52.4 −19.9 Azoarcus evansii, Azoarcus tolulyticus str. Td-3, Azoarcus tolulyticus str.Td-19, Azoarcus sp. ToN1 This study
AZTOLY452 S-S-Az.toly-0452-a-A-18 B10 GTA TTG ACC CAC CCG ATT 52.4 −19.5 Azoarcus tolulyticus This study
AZANBU228 S-*-Az.an.bu-0228-a-A-18 B12 AAT CCG ACA TCA GCC GCT 57.7 −21.8 Azoarcus anaerobius, A. buckelli, and related Azoarcus spp. This study
AZA844 S-*-Aza-0844-a-A-18 B20 TGC GTC ACT CAG CGC GTT 61.1 −23.7 Azoarcus spp. PH002 and CR23 This study
AZA452 S-*-Aza-0452-a-A-18 B19 CTA TTC ACG CAC CCG ATT 53 −20.0 Azoarcus spp. PH002 and CR23 This study
AZA463 S-*-Aza-0463-a-A-18 B15 ATC CAG GCA CGC TAT TCA 54.6 −20.3 Azoarcus spp. PbN1 and HxN1 This study
AZA835 S-*-Aza-0835-a-A-18 B16 CAG AAA GTT ACC TTC CCG 50.5 −18.8 Azoarcus sp. PbN1 This study
AZAN465 S-S-Az.an-0465-a-A-18 B14 TCA TCC AGG CTC GCT ATT 54 −20.3 Azoarcus anaerobius This study
AZAN130 S-S-Az.an-0130-a-A-18 R B13 CCC CTC GAC TGG GTA CGT 59 −22.2 Azoarcus anaerobius This study
S-*-OTU2-0132-a-A-18 ATDe132 S-*-ATDe-0132-a-A-18 R B24 CCC CCA CAA CAT GGG TAC 55.9 −20.9 Activated sludge clones A33, H25, H30, H35, S3, S10, and S23 of the Azoarcus-Thauera-Denitromonas lineage 27
Original name Name Full namea Primerb Microarray position(s) Sequence (5′-3′) Tm (°C) ΔG (kcal mol−1) Specificity Reference
ATDe442 S-*-ATDe-0442-a-A-18 B25 ACC CCG TTT CTT CCC AAC 55.7 −20.8 Activated sludge clones A33, H25, H30, H35, S3, S10, and S23 of the Azoarcus-Thauera-Denitromonas lineage This study
ATDe830 S-*-ATDe-0830-a-A-18 B26 CGT TAC CGC TCC GAA CAA 55.8 −21.4 Activated sludge clones A33, H25, H30, H35, S3, S10, and S23 of the Azoarcus-Thauera-Denitromonas lineage This study
S-*-OTU2-0467-a-A-20 ATDe467 S-*-ATDe-0467-a-A-18 B27 CGT CAT TAG GAT CCT ATG 46.6 −17.2 Activated sludge clones A33, H25, H30, H35, S3, S10, and S23 of the Azoarcus-Thauera-Denitromonas lineage Modified from 27
S3-486 S-*-S3-0486-a-A-18 B31 GTG CTT CTT CCG TCG GTA 54.9 −21.4 Activated sludge clone S3 This study
A33-587 S-*-A33-0587-a-A-18 B34 CAC CTG TCT TAC CAA ACC 50.7 −18.9 Activated sludge clone A33 This study
DENAR176 S-S-Denar-0176-a-A-18 C16 TCC CTC AGG AAA TAT GCG 52.1 −19.6 Denitromonas aromaticus This study
DENAR453 S-S-Denar-0453-a-A-18 C17 CGT ATT CGG GGC GAT GAT 55.3 −21.0 Denitromonas aromaticus This study
DENAR845 S-S-Denar-0845-a-A-18 C18 GCT GCG TTA CCC AGA AAG 54.2 −20.6 Denitromonas aromaticus This study
AZCOM447 S-S-Az.com-0447-a-A-18 B42 AGC CCA CAC GTT TTC TTC 53.8 −20.2 Azoarcus communis This study
TH5 AZIND1023 S-S-Az.ind-1023-a-A-18 A37, B3, B38, C3, D12 CTG GTT CCC GAA GGC ACC 58.9 −22.3 Azoarcus indigens, Azoarcus sp. BH72 Modified from 26
AZIND433 S-S-Az.ind-0433-a-A-18 B39 CTT TCC GTC CGA AAG AGC 53.8 −20.5 Azoarcus indigens, Azoarcus sp. BH72 This study
AZIND449 S-St-Az.ind-0449-a-A-18 B40 TTA GCC CGC GCG ATT TCT 58.2 −22.2 Azoarcus sp. BH72 This study
AZIND455 S-St-Az.ind-0455-a-A-18 B41 CGG GTA TTG GCC GAA GCG 59.4 −23.0 Azoarcus indigens (T) This study
THAU832 S-G-Thau-0832-a-A-18 C5 TGC ATT GCT GCT CCG AAC 57 −21.7 Thauera spp. This study
THAU455a S-*-Thau-0455-a-A-18 C6 ACT ATG TTA GAG TGC GCG 52.6 −19.9 Thauera chlorobenzoica, Thauera mechernichensis This study
THAU443 S-*-Thau-0443-a-A-18 C7 AAC ACG ATT TCT TCC CGG 53.2 −20.0 Thauera selenatis, Thauera phenylacetica, and related Thauera spp. This study
THAU580 S-*-Thau-0580-a-A-18 C8 CTT ACA AAA CCG GCC TCG 54.2 −20.6 Thauera selenatis, soil clone AX39 This study
THAU455b S-*-Thau-0455-b-A-18 C9 ACT ATG TTA GAG TCG CCG 51.6 −19.4 Thauera sp. PIV-1, TCB-transforming microbial consortium clone SJA-186 This study
THAU468 S-*-Thau-0468-a-A-18 C10 CCG TCA TCC AGC GAC TAT 54.5 −20.6 Thauera sp. PIV-1, TCB-transforming microbial consortium clone SJA-186 This study
THATE461 S-S-Tha.te-0461-a-A-18 C11 CCA CAC CCT ATG TTA GAG 49.2 −18.2 Thauera terpenica This study
ZOGLO828 S-G-Zoglo-0828-a-A-18 C30 TCT CCT CAC CGA ACA ACT 53.6 −20.1 Zoogloea spp. This study
S-*-OTU1-1415-a-A-20 ZOGLO1416 S-G-Zoglo-1416-a-A-18 C29 TCT GGT AAA CCC CAC TCC 54.1 −20.2 Zoogloea spp. Modified from 27
ZRA (ZRA23a) ZOGLO647 S-*-Zoglo-0647-a-A-18 C31 CTG CCG TAC TCT AGT TAT 48.2 −17.8 Most members of the Zoogloea lineage, not Z. resiniphila 45
ZOGLO455 S-*-Zoglo-0455-a-A-18 C32 AGA GTA TTA TCC TGC GCG 52.1 −19.6 Some members of the Zoogloea lineage (activated sludge clones H13, H11, H22, H10, H40, H27, and S21), not Z. ramigera and Z. resiniphila This study
S-*-H7-1014-a-A-18 H7-1014 S-*-H7-1014-a-A-18 C33 TCG GGC ACC CCT CAA TCT 59.4 −22.3 Activated sludge clone H7 27
ZORAM211 S-S-Zo.ram-0211-a-A-18 C34 TCG TAT AAC GTG AGG CCT 53.4 −20.2 Zoogloea ramigera This study
ZORAM441 S-S-Zo.ram-0441-a-A-18 C35 TGC GAT TTC TTT CCA CCT 52.6 −19.5 Zoogloea ramigera This study
S-*-OTU3-1426-a-A-18 STEBA1426 S-*-Steba-1426-a-A-18 A, R, Z D26 ACT ACC TAC TTC TGG TGG 50.6 −18.5 Some members of the Sterolibacterium lineage 27
STEBA468 S-*-Steba-0468-a-A-18 D28 CCG TCA TTA GTA GCC CGT 54.5 −20.5 Some members of the Sterolibacterium lineage (activated sludge clones S28, A13, S40, H12, H23, and H20) This study
S-*-OTU3-0445-a-A-20 STEBA448 S-*-Steba-0448-a-A-18 D27 TAG GGG CCA CCG TTT CGT 59.8 −23.1 Some members of the Sterolibacterium lineage (activated sludge clones S28, A13, S40, H12, H23, and H20) Modified from 27
STEBA635 S-*-Steba-0635-a-A-18 D29 AGT CCT ACA GTC ACA AAC 49.3 −18.2 Few members of the Sterolibacterium lineage (activated sludge clones S28 and A13) This study
STEBA643 S-*-Steba-0643-a-A-18 D30 CAC ACT CGA GTT ATG CAG 50.8 −19.2 Few members of the Sterolibacterium lineage (activated sludge clones S40, H12, H23, and H20) This study
STEBA214 S-*-Steba-0214-a-A-18 D32 CGC TCC TCT CGC GCG AGG 63.5 −25.1 Few members of the Sterolibacterium lineage (clones SBR1001, SBR2080, and GC24) This study
BONE23a BONE663c S-*-Bone-0663-a-A-18 A33, D8 GGA ATT CCA TCC CCC TCT 54.1 −19.9 Beta1 group of Betaproteobacteria Modified from 4
RHOTE206c S-S-Rho.te-0206-a-A-18 A14 AAG CGC AAG GTC CTA AGA 54.4 −20.5 Rhodocyclus tenuis This study
PPV1239c S-*-Ppv-1239-a-A-18 A11 ACC CTC TGA ACC GAC CAT 56.4 −20.9 Propionivibrio spp., few members of the Candidatus “Accumulibacter” cluster This study
AZA1269c S-*-Aza-1269-a-A-18 B8 AAG GGA TTG GCT CCA GCT 57.2 −21.1 Azoarcus evansii, Azoarcus toluvorans, Azoarcus tolulyticus, Azoarcus toluclasticus, and related Azoarcus spp. This study
AZA829c S-*-Aza-0829-a-A-18 B18 GTT ACC GCA CCG AAC AAC 54.7 −21.0 Azoarcus spp. EbN1 and pCyN1 This study
AZA234c S-*-Aza-0234-a-A-18 B17 CCA GCT AAT CCG ACA TCA 52.1 −19.4 Azoarcus spp. EbN1 and pCyN1 This study
AZA221c S-S-Aza-0221-a-A18 B45 CAT CGG CCA CTC CAA TCA 55.5 −20.9 Azoarcus sp. LU1 This study
a

Name of 16S rRNA gene-targeted oligonucleotide probe based on the nomenclature of Alm et al. (2).

b

When “Rhodocyclales” subgroup-selective primer pair A, R, or Z was used for microarray analysis, this probe has its target site outside the amplified 16S rRNA gene fragments and must be ignored during interpretation of the hybridization pattern.

c

Probe was removed from the RHC-PhyloChip because it hybridized nonspecifically to many reference organisms that have mismatches in the 16S rRNA gene target site.

HHS Vulnerability Disclosure