Development of a LDR-Universal array platform for the phylogenetic fingerprint of the Human Intestinal Microbiota

Human beings are superorganisms in co-evolution with their own intestinal microbiota. Throughout an extensive microbial-mammalian co-metabolism, the intestinal microbiota affects a broad range of physiological features of the human host and contributes to health and well being. The vast majority of the bacteria represented in the human intestinal microbiota belongs only to few bacteria phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobactera. However, at lower taxonomic levels, the intestinal microbiota is highly diverse. 1200 different phylotypes have been described, and each person’s gut microbiome is characterized by a peculiar phylotypes complement. Because of a high degree of functional redundancy between the different phylotypes, such diversity is not related to function, and, at the functional level, individuals share an extensive identifiable core microbiome. Division-wide changes in microbiota composition can cause deviations from such functional core microbiome and seriously impact the host physiological state. In order to monitor the microbiota imbalances towards a potential pathobiota community, a specific Ligase Detection Reaction – Universal Array (LDR-UA) platform was developed. Cluster, family and genus-specific probes were specifically designed to obtain a microbiota phylogenetic fingerprint for the principal bacterial groups which define the core functional microbiome. Species-specific probes were added to detect targets of particular interest, such as probiotic bacteria and enteropathogens. The complex set of LDR probes was developed on the basis of discriminating positions within 16S rRNA gene. A total of 28 ATCC and DSM strains, and 2 isolates, were tested with very good specificity and efficiency. Pilot microarray experiments have been carried out on faecal samples isolated from adults and elderly volunteers. A reproducible microbiota fingerprint has been obtained from 5 subjects for each class