By Matt Jones
NEW YORK (GenomeWeb News) – Researchers at the University of British Columbia and the BC Centre for Disease Control have launched a CA$3.2 million (US$3.2 million) project to use metagenomics to develop new ways to monitor watersheds for fecal pollution and E. coli, as well as new tools for tracking the sources of water contamination.
Genome BC — which is funding the project along with Genome Canada — Simon Fraser University, and the Public Health Agency of Canada, said today that the three-year, multi-partner project will develop a prototype for more effective water testing, and will "fundamentally change the current paradigm of slow and often imprecise culture-based bacterial testing."
The researchers will use metagenomics approaches – including shotgun sequencing and deep amplicon sequencing on the Illumina HiSeq 2000 – to generate microbial genomics data that will eventually be used to create real-time PCR tests for monitoring water health.
Current testing for drinking water supplies involves sampling from the tap, instead of at the watershed, when E. coli and other contaminants have already reached people's homes. In addition such methods do not always include contaminants such as non-bacterial pathogens such as parasites or viruses.
Source water testing will enable more effective interventions when contamination is found, and, through a new microbial source-tracking tool the partners are developing, it will enable monitors to avoid the need to use E. coli as a baseline bacteria for indicating fecal contamination.
Using a metagenomics approach for source water testing will make it possible to test for many pollutants at once, will reduce the time required for the testing from days to hours, and will provide profiles of all the microbes that are present in a water sample, according to Genome BC.
“The tools we currently have at our disposal are simply inadequate. Through the work of the multidisciplinary team, substantial improvements to current water protection approaches will be realized. These new tools will go a long way towards water quality improvements," UBC Professor Judith Isaac-Renton, a co-leader on the project, said in a statement.
Patrick Tang, a co-leader on the project and a clinical assistant professor at UBC, told GenomeWeb Daily News today that the team will take water samples and perform a large number of filtrations to separate all the different sizes of organisms to make it easier to conduct the studies.
"We separate the viruses, the bacteria, and then larger protists… and once we have all of these different types and sizes separated, then we attack each one with either deep amplicon sequencing, or shotgun sequencing," Tang said.
To target the large organisms, such as the protists, the team will use deep amplicon sequencing of conserved eukaryotic genes, and for the bacterial group they will sequence conserved genes and use a shotgun metagenomics approach to conduct a functional analysis of that population. The aim is to be able to taxonomically and functionally classify all of the organisms that are in the water samples.
"What we're trying to do with all of this is to come up with metagenomics patterns that correlate with pollution. … We're not necessarily trying to detect the pathogens that are in the water or any of the already known indicators for fecal pollution in water," he said, adding that they also are looking for changes in the natural microbiome of the watershed that results from pollution.
"Once we understand the changes in the metagenomics, then we will take the most statistically significant markers that we find that best correlate with pollution and develop these into real-time PCR assays," he said.
One of the new assays the team plans to develop, a panel of microbial markers that can quantify the health of the ecosystem in the water, will first require comparative metagenomics studies that measure the microbial fingerprints from healthy and contaminated water. This Watershed Health Profile will generate a number that will be incorporated into the Canadian Water Quality Index, which monitors for potential threats in the water.
Another tool, the Microbial Health Pollution Profile, will use microbial fingerprints related to human or animal feces to identify the specific source of fecal pollution in watersheds. Watershed managers will be able to use this as part of their pollution abatement and monitoring efforts.