Bacteria Detective: PhyloTech's Chip Identifies Friend and Foe Microbes

With quicker testing methods, authorities could prevent illness by shutting beaches more quickly when bacteria makes the water dangerous.
With quicker testing methods, authorities could prevent illness by shutting beaches more quickly when bacteria makes the water dangerous.

Bacteria, which can thrive in places where humans wouldn't dare linger, can be friends or foes. Take E. coli. Some strains are harmless and settle comfortably in animals' lower intestines. Others take free rides in lettuce and end up causing kidney failure and other serious ailments for salad lovers.

A new San Francisco company called PhyloTech is setting out to offer what it claims is a speedier and more precise method of identifying the types of bacteria and other single-cell organisms in our environment. The technology could solve some of the mysteries of food- and water-related illnesses and also help with environmental-cleanup efforts.

PhyloTech, founded in May of last year, says Tuesday it has raised $1.2 million from individual investors and Seraph Group and Wavepoint Ventures. With the seed money, the company says it will start offering its services and develop other products.

The startup's technology comes from research by co-founder Gary Anderson, a scientist at the Lawrence Berkeley National Laboratory in Berkeley, Calif. It won a spot on R&D Magazine's annual Top 100 technology awards in 2008, the same year the technology also grabbed the bronze at The Wall Street Journal's Technology Innovation Awards.

How It Works

The technology, called PhyloChip, is a chip that uses DNA samples to detect patterns and determine the presence of more than 50,000 different types of bacteria and other single-celled organisms in water, soil, air and tissue samples, the company says. PhyloTech has obtained an exclusive license from Berkeley Lab to commercialize the third generation of the technology.

Even a few years ago, when it could only identify nearly 9,000 types of organisms in a single sample in less than nine hours -- a far cry from the 50,000 organisms today -- PhyloChip was recognized as far quicker than conventional methods, which require researchers to grow bacteria in petri dishes to isolate and identify the microbes. Speed and accuracy are key challenges for public agencies and private businesses tackling health and environmental disasters.

Of course, just knowing the presence and types of microbes isn't enough to solve most health or environmental problems. The samples must go to a lab for in-depth analysis to determine the composition and abundance of various microbes from a test area, for example. It takes a few weeks of lab work to generate a comprehensive report, says Thane Kreiner, PhyloTech's CEO and co-founder.

The company is hiring Affymetrix (AFFX), a biotech company in Silicon Valley, to make the PhyloChips, Kreiner says.

From Beaches to Oil Spills

Before forming PhyloTech, Anderson and members of his research group at Berkeley had been using the PhyloChip in research projects that tested the technology's effectiveness in real-world problems. One project involved figuring out which combinations of bacteria species could clean up toxic spills in Tennessee. Another project took researchers to the beaches of Northern California to look for disease-causing pathogens.

Federal and state agencies have been looking for ways to quickly detect high levels of pathogens in public beaches, some of which are caused by sewage or other runoffs. Contaminated beaches have led to reports of skin rashes, stomach upsets and other infections.

But PhyloTech isn't the only one working to accelerate bacteria testing. The University of North Carolina also has developed a method that promises to deliver results in two hours, and a research institute plans to test the method in field trials at nine Southern California beaches this summer. The test is intended to detect bacteria from human waste in water samples. If it works as expected, the fast turnaround could help health agencies post warning signs or close beaches far sooner when dangerous organisms are in the water, thereby minimizing the spread of illnesses.

Bacteria-detecting technology could have applications beyond public-health crises to oil-spill cleanup efforts as well. Some naturally occurring organisms in the ocean can feed on crude oil, and a number of companies have tried to sell BP (BP) their cultivations of oil-eating microbes to reduce the spread of oil flowing from the Deepwater Horizon rig in the Gulf of Mexico. Knowing what types and how many of these microbes exist in the sea water could help the oil giant and the government evaluate the cleanup.