Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria.
Environ Microbiol
; 8(2): 289-307, 2006 Feb.
Article
en En
| MEDLINE
| ID: mdl-16423016
The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Filogenia
/
ARN Bacteriano
/
ARN Ribosómico 16S
/
Análisis de Secuencia por Matrices de Oligonucleótidos
/
Alphaproteobacteria
Tipo de estudio:
Diagnostic_studies
Idioma:
En
Revista:
Environ Microbiol
Asunto de la revista:
MICROBIOLOGIA
/
SAUDE AMBIENTAL
Año:
2006
Tipo del documento:
Article
País de afiliación:
Francia
Pais de publicación:
Reino Unido