title: A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer.
abstract: To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.
authors.affiliation: Laboratorium voor Microbiologie (WE10), Universiteit Gent, B-9000 Ghent, Belgium.
authors.forename: Miet
authors.initials: M
authors.lastname: Martens
authors.forename: Stefan
authors.initials: S
authors.lastname: Weidner
authors.forename: Burkhard
authors.initials: B
authors.lastname: Linke
authors.forename: Paul
authors.initials: P
authors.lastname: de Vos
authors.forename: Monique
authors.initials: M
authors.lastname: Gillis
authors.forename: Anne
authors.initials: A
authors.lastname: Willems
mesh_terms: D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000235:genetics; D012230:Rhizobiaceae / Q000145:classification* / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D012336:RNA, Ribosomal, 16S; D012269:Ribosomal Proteins; C015494:ribosomal protein S1