title: Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria.
abstract: 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.
authors.affiliation: UMR CNRS 5557/USC INRA 1193 Ecologie Microbienne, Université Claude Bernard (Lyon 1), Villeurbanne, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Sanguin
authors.forename: Aude
authors.initials: A
authors.lastname: Herrera
authors.forename: Christine
authors.initials: C
authors.lastname: Oger-Desfeux
authors.forename: Arnaud
authors.initials: A
authors.lastname: Dechesne
authors.forename: Pascal
authors.initials: P
authors.lastname: Simonet
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Navarro
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Vogel
authors.forename: Yvan
authors.initials: Y
authors.lastname: Moënne-Loccoz
authors.forename: Xavier
authors.initials: X
authors.lastname: Nesme
authors.forename: Geneviève L
authors.initials: GL
authors.lastname: Grundmann
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S