Probe specificity was confirmed on the entire known 16S rRNA gene sequences environment by the RDP Probe Match tool. This requirement is fundamental, since the primer set used for the PCR amplification was the “”universal”" 16S rRNA primer set designed by Edwards and co-workers [32]. The HTF-Microbi.Array recognized without ambiguity the 16S rRNA amplicons obtained from 28 members of the intestinal microbiota belonging to Bacteroides/Prevotella,

Selleckchem PF01367338 Clostridium clusters IV, IX, XIVa, XI, I and II, Bifidobacteriaceae, Lactobacillaceae, Bacillus, Enterococcus, Enterobacteriaceae and Campylobacter, demonstrating the specificity of all the probe pairs. The sensitivity of the HTF-Microbi.Array was evaluated by using different concentrations Alvocidib supplier of Selleckchem PCI-32765 an artificial mix of 16S rRNA amplicons obtained from 6 microorganisms members of the human intestinal microbiota. To compensate the eventual drop in the signal due to a very low target concentrations, lower than 0.7 fmol (i.e. a percentage lower than 1.5%

of the commonly used quantity of 50 fmol), a slightly relaxed criteria for significance of the t-test to α = 0.05 was chosen. All PCR products were specifically recognized in a concentration range from 75 to 0.7 fmol, showing high array sensitivity. The efficiency of the HTF-Microbi.Array in the detection of a particular target in a complex DNA environment was also determined. According to our data, the array is able to detect a specific DNA target down to 0.02% of the total 16S rRNA, which is comparable to the values obtained by Rajilic-Stojanovic et al. [23] and Palmer et al. [21]. Thus the HTF-Microbi.Array shows the potentiality to sense low abundant species of the gastrointestinal microbiota, enabling the detection of the 16S rRNA of a peculiar target group

present at a fractional abundance <0.1% in an artificial mixture. The HTF-Microbi.Array was used in a pilot study to characterize the faecal microbiota of eight young adults. Faecal microbiota was chosen as DNA source since sample collection is not invasive, samples contain large amount Erlotinib cost of microbes, and, most important, it is representative of interpersonal differences in distal gut microbial ecology [33]. In order to have a good representation of the less abundant species of the intestinal microbial community, LDR reactions were performed starting from 50 fmol of PCR product. Cluster analysis of the presence-absence probes profiles enabled the identification of a reproducible high taxonomic level microbiota fingerprint for each subject. As expected, the intestinal microbial community of the voluntaries in the study resembled the typical fingerprint of healthy adults [28]. According to our data, the faecal microbiota of the enrolled subjects was dominated by major mutualistic symbionts.