DNA microarrays represent one of the most popular platforms in molecular technologies, allowing a highthroughput format for the parallel detection of 16S rRNA genes from environmental samples (2) . DNA chips have been developed as a preferred device for the identification of different microorganisms based on 16S gene sequences. The multiplicity of species which can be arrayed on a single-DNA chip allows a high multiplexing capability, with the possibility of identifying many different targets at one time (3) . Single-base variations by microarray analysis can be detected by differential hybridization techniques using allele-specific oligonucleotide probes (4), or by enzyme-mediated detection methods (5) . One of the most critical points of the molecular recognition procedures is the design of the specific probes needed to perform the entire analysis. In genotyping experiments, this is accomplished on the basis of the already-known information about each single-base variation. In detection experiments, on the other hand, in order to explore whether a certain target sequence is present in a DNA sample or not, the main problem is searching for a priori not yet identified specific positions that can discriminate exactly between one target and another.