Microbe Detectives Brings DNA Sequencing to Water

Milwaukee Mayor Tom Barrett wants southeastern Wisconsin to be known as the “Fresh Coast.” Others have thrown around the phrase “Silicon Valley of water.”

Marketing verbiage aside, the conversation around turning this region on the shores of Lake Michigan into a fresh water business hub continues to grow louder.

Southeastern Wisconsin is home to the nation’s first graduate school for studying fresh water (at University of Wisconsin-Milwaukee) and its first water business institute (University of Wisconsin-Whitewater).

The Milwaukee region has a cluster of more than 150 water technology companies, according to The Water Council, a Milwaukee-based organization launched in 2007 with the aim of making southeastern Wisconsin an international hub for fresh water research, education, and economic development. Xconomy plans to explore this sector with a series of stories on interesting water technology startups in the Milwaukee area. First up: Microbe Detectives.

Giving “Wet Lab” New Meaning

The growing speed and affordability of DNA sequencing has opened up all kinds of doors for scientists over the past decade, from pinpointing the genes involved in human diseases to solving the mystery of a dog’s mixed breed.

Now Trevor Ghylin is applying genome sequencing to the water industry.

His Milwaukee startup, Microbe Detectives, uses sequencing to analyze samples of wastewater, well water, and drinking water to identify and quantify all the bacteria present, such as E. coli, Salmonella, and Cryptosporidium. That last one is particularly infamous in Milwaukee, which suffered the worst waterborne disease outbreak in U.S. history 20 years ago. (A smaller set of cases this year was reportedly traced to pool water.)

Could daily monitoring of Milwaukee’s water system using DNA sequencing have prevented the big outbreak? Ghylin said it’s “hard to say for sure,” but there’s evidence that Microbe Detectives’ process is faster and more efficient and provides more complete information than the current test required by federal regulators, he and industry observers said.

“Certainly if a water utility is using this type of DNA monitoring on a daily basis for their water, they would see just about everything in their water,” Ghylin said.

The current standard for water monitoring involves a petri dish test for coliforms, bacteria that indicate potential fecal contamination, Ghylin said. The test is cheap, easy to perform, and largely effective—but not perfect, he said.

“Just because you don’t have coliforms growing in a petri dish does not mean you have safe water,” Ghylin said. “What DNA offers is getting a lot more information than just this one indicator bacteria. It’s a lot more powerful.”

Ghylin, a North Dakota native, has a bachelor’s degree in civil engineering from the University of North Dakota and a master’s in civil and environmental engineering from University of Wisconsin-Madison.

Having worked as an engineering consultant for five years, he’s also in the third and final year of a PhD program in civil and environmental engineering at UW-Madison, where he focuses on fresh water bacterial genetics.

“The science side of me really found [fresh water bacterial genetics] fascinating,” Ghylin said. “The engineering side of me was always wondering, ‘This is interesting, but how can we use this for anything useful? Is this just a science experiment to try and expand our knowledge, or is there something useful to society here?’”

He started talking with environmental engineers who wanted to better understand the bacteria in their wells, wastewater treatment systems, and water distribution systems.

A few engineers sent him water samples and paid him for a DNA-based microbial analysis. Ghylin realized there was a market for this, and he founded Microbe Detectives in 2012 while still pursuing his PhD.

His startup is now housed in the Global Water Center in Milwaukee’s Walker’s Point neighborhood. The facility was opened last year by The Water Council.

Microbe Detectives was accepted in July 2013 into a pilot seed accelerator program for water technology startups at the Global Water Center. The program, which launched in September, earned Ghylin a $50,000 grant from the Wisconsin Economic Development Corp.; office space in the center; access to business model and operations training through UW-Whitewater’s Institute for Water Business; access to faculty and students from UW-Milwaukee’s School of Freshwater Sciences; and guidance from local water technology experts.

Ghylin also kicked in about $2,000 of his own money.

He hired three part-time staff: a biomolecular engineer, a biomolecular engineering undergraduate student at Milwaukee School of Engineering, and a UW-Whitewater graduate with a bachelor’s degree in geography and environmental studies, he said. He also hired three subcontractors to handle graphic design and marketing, patent law, and Web design.

Ghylin said that so far Microbe Detectives is breaking even. He charges clients—so far mainly environmental engineering firms and consultants—between $100 and $600 per order, depending on the scope of the work and if the client plans to be a repeat customer, he said.

With a typical order, the customer mails a sample to Microbe Detectives, which does filtration and other front-end work before sending it to a lab in Texas that performs the DNA sequencing. Microbe Detectives then uses “proprietary knowledge, microbial databases, and bioinformatics algorithms” to analyze the raw data and draw digestible conclusions for the client about what’s lurking in the sample.

The process can help find the source of fecal pollution, detect biofilms in drinking water distribution systems, and investigate taste, odor and color problems in drinking water. The method also has applications for environmental remediation, the food and beverage industry, personal care products, and pharmaceutical manufacturing, according to Microbe Detectives’ website.

Turnaround time for an analysis is currently as low as two days, but with more investment and growth in business, Ghylin wants to shrink that to six hours. Compare that with fecal pollution tracking in urban waterways that in some cases can require more than two months to get data and pinpoint the source of the pollution after sampling from storm sewers, Ghylin said.

“It’s closer to a real-time analysis than what we had before,” said Kevin Shafer, executive director of the Milwaukee Metropolitan Sewerage District, who has met with Ghylin to learn about his business. “It has a lot of potential in making wastewater plants and storm water utilities around the country more efficient in dealing with analysis of water quality in the future.”

The challenges? Although costs are coming down, the equipment for DNA sequencing is still expensive, and applying it to water samples is still relatively unchartered territory for academia, let alone industry, Ghylin said.

“The technology is still not at the point where it could be deployed like that for [municipal water] monitoring, and the [U.S. Environmental Protection Agency] is not requiring it. So that’s a little ways down the road,” Ghylin said. “But in a few years you might see this become a really routine test.”

There’s only been a handful of research papers on the topic. Sandra McLellan, a professor and senior scientist at UW-Milwaukee’s School of Freshwater Sciences, is working on one using genetic sequencing to identify fecal pollution sources.

“The whole idea of using sequence data as a way to look at water…is in its infancy,” McLellan said.

She sees value in Ghylin’s attempt to make such information “useful to the practitioner” in the field. The challenge is in properly interpreting vast, complex data sets containing millions of sequences, she said.

“I think in 10 years what he is proposing is exactly what we ought to be doing,” McLellan said. “He’s really setting the groundwork to create those conduits between research and the end user.”

Jeff Bauter Engel is Deputy Editor, Tech at Xconomy. Email: jengel@xconomy.com Follow @JeffEngelXcon

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