Table 1.

Primer mismatch testing in RDP with the CHECK_PROBE algorithm

Sequence source and taxonomic descriptionaNo. of primer/target mismatchesbRDP ribotype descriptionc
Beta (purple) bacteria
Iodobacter fluviatile ATCC 3305130 Neisseriagroup
Burkholderia solanacearum ATCC 1169610 Burkholderia subgroup I
Burkholderia pickettii ATCC 2751210 Burkholderia subgroup I
Spirillum voluntans ATCC 1955403 Spirillum voluntans group
Azoarcus sp. strain S5b210 Rhodocyclus group
Azoarcus indigens VB3210 Rhodocyclus group
Gamma (purple) bacteria
Ectothiorhodospira halochloris ATCC 35916>30 Ectothiorhodospira group
Coxiella burnetiiQ17710 Legionella group
Methylococcus capsulatus bath20 Methylomonas group
Oceanospirillum minutulum ATCC 1919303 Halomonas group
Moraxella osloensis 0 NS Pseudomonasand relatives group
Moraxella osloensisSCB11110 Pseudomonas and relatives group
Pseudomonas aeruginosa ATCC 1014502 Pseudomonas and relatives groupd
Pseudomonas aeruginosaATCC 2533010 Pseudomonas and relatives groupd
Pseudomonas aeruginosaNF130 NS Pseudomonas and relatives groupd
Flavobacterium lutescens ATCC 2795100 Pseudomonas and relatives groupd
Pseudomonas mendocina ATCC 2541100 Pseudomonas and relatives groupd
Pseudomonas flavescens B62 NCPPC 306300 Pseudomonas and relatives groupd
Pseudomonas putida PaW1 isolate mt-200 Pseudomonas and relatives groupd
Pseudomonas syringae A50100 Pseudomonas and relatives groupd
Pseudomonas fluorescensATCC 1352500 Pseudomonas and relatives groupd
Azospirillum sp. strain DSM 172700 Pseudomonas and relatives groupd
Pseudomonas syringae31R-100 Pseudomonas and relatives groupd
Pseudomonas syringaeenv. FIE8 NS0 Pseudomonasand relatives groupd
Pseudomonas fluorescens MS 165000 Pseudomonas and relatives groupd
Shewanella putrefaciens ATCC 807130 Alteromonas group
Delta (purple) Bacteria
Bdellovibrio bacteriovorus ATCC 4382602 Bdellovibrio bacteriovorus group
Desulfobacter sp. strain DSM 20570>3 Desulfobacter subgroup
Nannocystis exedens ATCC 259630>3 Myxobacteria subgroup
Epsilon (purple) bacteria
Bacteroides ureolyticus ATCC 333870>3 Campylobacter and relatives group
Bacteroides gracilis ATCC 3323602 Campylobacter and relatives group
Campylobacter (13 species and 31 sequences)0>3 Campylobacter and relatives group
Fuscobacteria and relatives
Fusobacterium periodonticum ATCC 33693>30 Fuscobacteriaand relatives group
Gram-positive bacteria
Haloanaerobium salsugo VS-7520>3Anaerobic halophiles subgroup
Haloanaerobium praevalens ATCC 3374403Anaerobic halophiles subgroup
Clostridium bifermentans NCIMB 10716>30 Clostridium lituseburense group
Clostridium ghonii ATCC 25757>30 Clostridium lituseburense group
Listeria monocytogenes ATCC 35152>30 Listeria-Brochothrix group
  • a CHECK_PROBE searches of the RDP prokaryotic SSU database. Sequences perfectly matching with at least one primer were extracted and are listed in phylogenetic order.

  • b The CHECK_PROBE searches allowed as many as three mismatches. The numbers of mismatches observed for the Ps-for and Ps-rev primer targets are listed for each sequence. NS, no primer target site sequence was available; >3, primer target sites exceeding the search cutoff of three mismatches.

  • c Ribotype classifications of the listed sequences as defined by RDP.

  • d The 13 sequences of thePseudomonas subgroup in RDP.