A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer

Nucleic acid detection technologies and marker molecules in bacterial diagnostics

“…For example, it has been reported that in case of the genus Streptococcus, the 16S rRNA gene sequence is not variable enough to allow identification of closely related species or subspecies [80]. Similar situations have been described for other bacterial taxa [81][82][83][84][85]. Another difficulty is the presence of multiple copies of nonidentical rRNA genes in certain bacterial genomes.…”

“…Another difficulty is the presence of multiple copies of nonidentical rRNA genes in certain bacterial genomes. Such intragenomic heterogeneity may further hinder the use of this target for precise diagnostic applications [85][86][87]. Low differentiation power of this marker molecule within certain genera combined with copy number heterogeneity has driven analytical scientists to look for alternative marker molecules that can be used for more accurate bacterial diagnostics in these cases.…”

Oligonucleotide microarray for the identification of potential mycotoxigenic fungi

“…Signal intensities of the sixteen replicates were then averaged and intensity values were normalized across slides by global regression on the spot intensity data of the internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4, which were used as a reference for normalization of all spot intensity data (reference design). The net signal intensity of each spot was divided by the median signal intensity of the sixteen replicates and spots with an SNR ((Signal median - Background median) × Standard deviation Background) value below the median were removed from the analysis [32]. Each spot was then either assigned a 1 (present, SNR>/= 3.0) or a 0 (absent, SNR<3.0) according to the median SNR value.…”

Characterization of microbial pathogens by DNA microarrays

“…The underlying concept is to design probes recognizing sequence signatures specific for each node of the phylogenetic tree, extending the scope of oligoarrays to the whole bacterial kingdom. Many phylogenetic markers can be used for the design, such as groEL (Wertz et al, 2003;Wong and Chow, 2002), gyrA/gyrB (Antwerpen et al, 2007), rpoB (Drancourt et al, 2004;Troesch et al, 1999) or rpsA (Martens et al, 2007), but once again the rRNA gene remains the preferred candidate because of the number of available databases dedicated to this marker (see Section 2.2.1). Several teams developed and validated this approach (Palmer et al, 2006;Huyghe et al, 2008;Brodie et al, 2007), proving its efficiency in monitoring the contents of complex bacterial mixtures in a quantitative (fractional abundance <0.1%) and qualitative fashion.…”