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The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set

Daims, Holger ; Brühl, Andreas ; Amann, Rudolf ; Schleifer, Karl-Heinz ; Wagner, Michael

Systematic and applied microbiology, 1999-09, Vol.22 (3), p.434-444 [Periódico revisado por pares]

Jena: Elsevier GmbH

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Título:
The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set
Autor: Daims, Holger ; Brühl, Andreas ; Amann, Rudolf ; Schleifer, Karl-Heinz ; Wagner, Michael
Assuntos: Bacteria - genetics ; Bacteria - isolation & purification ; Bacteria-specific probes ; Bacteriological methods and techniques used in bacteriology ; Bacteriology ; Biological and medical sciences ; digital image analysis ; DNA, Bacterial - analysis ; EUB338 ; fluorescent in situ hybridization ; Fundamental and applied biological sciences. Psychology ; Genetic Variation - genetics ; Image Processing, Computer-Assisted ; In Situ Hybridization, Fluorescence ; Indoles ; Microbiology ; Microscopy, Confocal ; Oligonucleotide Probes - analysis ; Oligonucleotide Probes - genetics ; probe EUB338 ; RNA, Bacterial - analysis ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - analysis ; RNA, Ribosomal, 16S - genetics ; Staining and Labeling
É parte de: Systematic and applied microbiology, 1999-09, Vol.22 (3), p.434-444
Notas: ObjectType-Article-2
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Descrição: In situ hybridization with rRNA-targeted oligonucleotide probes has become a widely applied tool for direct analysis of microbial population structures of complex natural and engineered systems. In such studies probe EUB338 (Amann et al., 1990) is routinely used to quantify members of the domain Bacteria with a sufficiently high cellular ribosome content. Recent reevaluations of probe EUB338 coverage based on all publicly available 16S rRNA sequences, however, indicated that important bacterial phyla, most notably the Planctomycetales and Verrucomicrobia, are missed by this probe. We therefore designed and evaluated two supplementary versions (EUB338-II and EUB338-III) of probe EUB338 for in situ detection of most of those phyla not detected with probe EUB338. In situ dissociation curves with target and non-target organisms were recorded under increasing stringency to optimize hybridization conditions. For that purpose a digital image software routine was developed. In situ hybridization of a complex biofilm community with the three EUB338 probes demonstrated the presence of significant numbers of probe EUB338-II and EUB338-III target organisms. The application of EUB338, EUB338-II and EUB338-III should allow a more accurate quantification of members of the domain Bacteria in future molecular ecological studies.
Editor: Jena: Elsevier GmbH
Idioma: Inglês

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The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set

Daims, Holger ; Brühl, Andreas ; Amann, Rudolf ; Schleifer, Karl-Heinz ; Wagner, Michael

Jena: Elsevier GmbH

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