The current state-of-the-art in DNA testing of water samples is using qPCR (quantitative polymerase chain reaction) to detect a single or few indicator bacteria to predict a potential source of fecal pollution. The PhyloChip is unique by tracking thousands of identifying microbial signatures, which provides a higher-resolution source detection with statistical confidence. There are a couple of reasons why this fundamental difference matters in watershed management and assessing water quality.
Reason #1 - Sensitivity
When the sources of pollution are greatly diluted as the contamination moves through the environment, they become a very minor, but still detectable portion of the downstream microbial community. The PhyloChip approach that we have developed has a very wide dynamic range so that species representing less than 1:10,000 of the dominant species in the community is still reliably identified. Detection of these source-specific microbes at very low quantities combined with the power of detecting multiple, confirmatory organisms increases our confidence we have identified the correct source of the contamination. We successfully used the PhyloChip to identify sources of fecal pollution at several watersheds, beaches, rivers, and other surface waters throughout California and Hawaii. The EPA is currently using the Veracet PhyloChip method in 16 different locations throughout the US to assess reproducibility on a national scale. We have also started projects in Singapore and other international locations as well.
Reason #2 - Discovery
The power of the PhyloChip is that it has been extensively validated as a molecular biology tool for analyzing environmental samples. The comprehensive and reproducible identification of the total microbial community composition can be used to reliably identify if something new (i.e. a contaminant) has been introduced into a location. An example of this would be when a fecal source from a leaking septic system enters an uncontaminated watershed. As we demonstrated in numerous peer-reviewed scientific publications, the PhyloChip can identify DNA sequences for microbes that are present in only one type of fecal, or other types of contaminant sources. With thousands of unique DNA sequences representing hundreds of unique species we can, for example, distinguish sewage or septic waste from cow, pig, bird, or dog sources. In a blinded study by the State of California Water Resources Control Board for the detection of twelve distinctive fecal sources in varying mixtures, the PhyloChip was the only method that was able to correctly identify every source.