PMID- 12724385
OWN - NLM
STAT- MEDLINE
DCOM- 20030731
LR  - 20200826
IS  - 1350-0872 (Print)
IS  - 1350-0872 (Linking)
VI  - 149
IP  - Pt 5
DP  - 2003 May
TI  - Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the 
      Gammaproteobacteria radiation.
PG  - 1239-1247
LID - 10.1099/mic.0.26112-0 [doi]
AB  - The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with 
      the uncultured gammaproteobacterium 'Candidatus Competibacter phosphatis' where 
      some cells bound GAM42a and other cells bound BET42a in fluorescence in situ 
      hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 
      1027-1043 in the 23S rRNA and differ from each other by one nucleotide at 
      position 1033. Clone libraries were prepared from PCR products spanning the 16S 
      rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures 
      enriched in 'Candidatus C. phosphatis'. With individual clone inserts, the 16S 
      rDNA portion was used to confirm the source organism as 'Candidatus C. 
      phosphatis' and the 23S rDNA portion was used to determine the sequence of the 
      GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a 
      probe target (T at position 1033) and 11 had G at position 1033, the only 
      mismatch with GAM42a. However, none of the clones had the BET42a probe target (A 
      at 1033). Non-canonical base-pairing between the 23S rRNA of 'Candidatus C. 
      phosphatis' with G at position 1033 and GAM42a (G-A) or BET42a (G-T) is likely to 
      explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in 
      FISH, targeting cells with G at position 1033, and was found to highlight not 
      only some 'Candidatus C. phosphatis' cells, but also other bacteria. This 
      demonstrates that there are bacteria in addition to 'Candidatus C. phosphatis' 
      with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.
FAU - Yeates, Christine
AU  - Yeates C
AD  - Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 
      4072, Australia.
FAU - Saunders, Aaron M
AU  - Saunders AM
AD  - Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 
      4072, Australia.
FAU - Crocetti, Gregory R
AU  - Crocetti GR
AD  - Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 
      4072, Australia.
FAU - Blackall, Linda L
AU  - Blackall LL
AD  - Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 
      4072, Australia.
LA  - eng
SI  - GENBANK/AY172146
SI  - GENBANK/AY172147
SI  - GENBANK/AY172148
SI  - GENBANK/AY172149
SI  - GENBANK/AY172150
SI  - GENBANK/AY172151
SI  - GENBANK/AY172152
SI  - GENBANK/AY172153
SI  - GENBANK/AY172154
SI  - GENBANK/AY172155
SI  - GENBANK/AY172156
SI  - GENBANK/AY172157
SI  - GENBANK/AY172158
SI  - GENBANK/AY172159
SI  - GENBANK/AY172160
SI  - GENBANK/AY172161
SI  - GENBANK/AY172162
SI  - GENBANK/AY172163
SI  - GENBANK/AY172164
SI  - GENBANK/AY172165
SI  - GENBANK/AY172166
SI  - GENBANK/AY172167
SI  - GENBANK/AY172168
SI  - GENBANK/AY172169
SI  - GENBANK/AY172170
SI  - GENBANK/AY172171
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Microbiology (Reading)
JT  - Microbiology (Reading, England)
JID - 9430468
RN  - 0 (DNA, Bacterial)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (RNA, Ribosomal, 23S)
SB  - IM
MH  - Betaproteobacteria/genetics
MH  - Cloning, Molecular
MH  - DNA, Bacterial/analysis
MH  - Gammaproteobacteria/*genetics
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Microscopy, Confocal
MH  - Molecular Sequence Data
MH  - *Oligonucleotide Probes
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
MH  - RNA, Ribosomal, 23S/genetics
MH  - Sequence Analysis, DNA
MH  - Species Specificity
EDAT- 2003/05/02 05:00
MHDA- 2003/08/02 05:00
CRDT- 2003/05/02 05:00
PHST- 2003/05/02 05:00 [pubmed]
PHST- 2003/08/02 05:00 [medline]
PHST- 2003/05/02 05:00 [entrez]
AID - 10.1099/mic.0.26112-0 [doi]
PST - ppublish
SO  - Microbiology (Reading). 2003 May;149(Pt 5):1239-1247. doi: 10.1099/mic.0.26112-0.