The Second Genome Drug Discovery Platform utilize the award-winning PhyloChip® assay developed by Dr. Gary Andersen at the Lawrence Berkeley National Laboratory. The PhyloChip assay represents years of research and development resulting in what is now a mature technology capable of providing the most detailed measurements of microbial community dynamics in a high-throughput and reproducible manner. Second Genome has an exclusive right to this technology, making it the only platform with this high resolution analysis tool.

The PhyloChip assay is a microarray-based method that identifies and measures the relative abundance of more than 50,000 individual microbial taxa. This approach relies on the analysis of the 16S ribosomal RNA gene sequence. This gene is present in every bacterial genome but varies in a way that provides a fingerprint for specific microbial types. Unlike sequencing methods, PhyloChip relies on the analysis of all nine variable regions of the 16S gene, providing more in-depth taxonomic classification than other common approaches. With 1.2 million probes per chip, the microarray-based hybridization approach ensures that measurements on important low abundance bacteria are not overwhelmed by commonplace, dominant microbial community members. Importantly, this platform also demonstrates the capabilities required to be considered for regulated applications, including high within-lab repeatability and between-lab reproducibility.

Microbial communities found in human and environmental samples contain thousands of different microbial species. Typically, these communities include a few dominant organisms and a large number of microbes at very small overall abundance levels. These rare bugs can be important in driving vital processes and ecosystem function. The PhyloChip provides the ability to identify these minority abundance community members and determine relative differences that sequencing technologies can miss.