for the 4-13%, B. subtilis et rel. for the 0.6-2.5%, Fusobacterium for the 1.2-4.4%, and Cyanobacterium for 0.6-4.5%. As expected, opportunistic pathogens showed together the lowest relative IF contribution in all the subjects under study (from 5 to 10%). Figure 3 Phylogenetic fingerprints. Cluster analysis of the phylogenetic fingerprint of 16 faecal samples from 8 young adults. Response of each of the HTF-Microbi.Array probes for what concerns
presence/absence of the target group is showed: positive response in red (P < 0.01), negative responses in blue (P > 0.01). Gary lines below the samples indicate adjacent replicated LDR of the same sample. Figure 4 IF relative contribution. For each sample the entire HTF-Microbi.Array probe set was click here considered and their relative IF contribution was calculated as
percentage of the total IF. Wnt inhibitor Sub-probes were excluded and for each subject data from two separate LDR-universal array experiments were taken Syk inhibitor onto consideration. The averaged IF from both the LDR-Universal Array experiments was considered. The principal intestinal groups of major mutualistic symbionts are indicated: Bacteroides/Prevotella (B/P) blue, Clostridium cluster IV (Cl.IV) green, Clostridium cluster IX (Cl.IX) brown, Clostridium cluster XIVa (Cl.XIVa) dark brown. Lactobacillus, B. clausii, B. subtilis, Fusobacterium and Cyanobacteria are grouped as minor mutualistic symbionts (minor) indicated in yellow. second Proteus, Yersinia and E. faecalis are grouped as opportunistic pathogens (opp) in red. Discussion In these last years, 16S rRNA microarrays emerged as a sensitive and efficient way to screen complex bacterial communities. Here we describe and validate
the HTF-Microbi.Array, a new phylogenetic DNA microarray designed for the high taxonomic level fingerprint of the human intestinal microbial community. The HTF-Microbi.Array is based on the LDR-UA approach, which is a fast and sensitive tool for the characterization of complex microbial communities with high sensitivity and specificity [25, 26]. The use of this molecular technique allows overcoming the major limitations of DNA microarrays whose discriminative power is based on hybridization. In fact, a) optimization of the hybridization conditions for each probe set is not required; b) problems due to the secondary structures of the target DNA are minimized, c) steric hindrances of differentially sized nucleic acid hybrids formed on the array after the hybridization are decreased . The final probe set of the HTF-Microbi.Array allows a high taxonomic level fingerprint of the human intestinal microbiota, with a good coverage of the major and minor components, as well as some of the most important pathogens and opportunistic bacteria . The LDR probes were designed by choosing DS oligonucleotides whose 3′end allowed the perfect discrimination of the target species from the non-target ones on the basis of our 16S rRNA sequence database.