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PhyloTech Highlights Environmental-Testing Play with Gulf of Mexico Oil Plume Study


By Justin Petrone

PhyloTech is hoping a series of recent publications will raise its profile in the environmental-testing and human health-research markets.

Founded last year, the San Francisco startup recently launched services based around the PhyloChip platform, an Affymetrix-manufactured research tool developed by scientists at Lawrence Berkeley National Laboratory.

PhyloChip is a custom-designed microarray that relies on 1.1 million probes to determine the presence and relative abundance of nearly 60,000 bacterial and archaeal taxa from microbial DNA samples.

PhyloTech has positioned its microarray-based offering as an alternative to older, lower-throughput technologies, like RT-PCR, as well as newer technologies, like next-generation sequencing, that are still constrained by cost and data-analysis issues.

"Assembling the data and output of next-gen sequencing takes a long time," said Janet Warrington, co-founder and senior vice president of operations and development at PhyloTech. "We are there today and we have semi-automated output and rapid turnaround time."

Warrington told BioArray News last week that the company is seeking to win new customers through studies that feature its technology. The latest paper to highlight the PhyloChip appeared last week in Science.

In the study, a team led by researchers at LBNL used the PhyloChip assay to screen water samples collected almost a mile deep in the Gulf of Mexico between May 25 and June 2 near the center of the Deepwater Horizon oil leak.

Using the chip, LBNL scientists found "distinct differences" between plume samples with parts per billion levels of dispersed oil and non-plume samples.

In plume samples, the researchers detected 952 distinct bacterial taxa in 62 phyla, a 40-percent decline in bacterial richness compared to the non-plume samples. At the same time, the researchers identified 16 distinct taxa that were "significantly" enriched in the plume samples, all of which were known to degrade hydrocarbons or have been observed in previous investigations to thrive in the presence of crude oil in cold waters.

According to the study authors, the presence of hydrocarbon-degrading microbial communities provides "a potential for intrinsic bioremediation of oil contaminants" in the Gulf of Mexico. Researchers from Lawrence Livermore National Laboratory, the University of the Pacific, and the University of Oklahoma also took part in the study.

The Science paper is one of more than 10 published this year that have highlighted the use of the PhyloChip platform. In a May Applied and Environmental Microbiology study, researchers used the array to assess the diversity of anaerobic microbes in spacecraft assembly clean rooms.

The same month, a Microbial Ecology paper highlighted the use of the chip to study bacterial diversity of weathered terrestrial Icelandic volcanic glasses. And last week a study appeared in The ISME Journal that used the array to investigate the structure of the human gastric bacterial community in relation to Helicobacter pylori status.

"Detecting and measuring changes in bacteria communities has come into its own, and the time is right for advancing this type of research," said Warrington. Since PhyloTech began offering the PhyloChip assay as a service in July, the firm's main customers have been researchers interested in using the array to survey microbial populations in disease research as well as in environmental samples, she said.

That month, PhyloTech closed a $1.2 million seed financing round to support its operations (BAN 7/6/2010). The firm's current goal is to offer its assay and analysis products available as a service. Researchers who submit samples to PhyloTech are provided with a web link to a data-analysis report that includes graphical representations "like those you would see in journal publications," Warrington said. The firm's turnaround time is typically "a few weeks," depending on the study.

"We want to work with anyone who wants to look at changes in microbial communities," said Warrington. "These are geologists in environmental positions, industry looking at sources of contamination, people who want to manage agricultural products, as well as those in the disease-research community who are interested in correlating microbial community changes with disease of interest."

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PhyloTech is considering making the PhyloChip assay available in kits for customers to run in their own labs, but has no plans in the near term to do so, according to Warrington. The firm also plans to introduce other products beyond PhyloChip, but at a later date.

Additionally, while Warrington and PhyloTech CEO Thane Kreiner are both former employees of Affymetrix, Warrington stressed the firm is not married to the Affy platform. An Affymetrix spokesperson this week also confirmed that the GeneChip maker has no stake in PhyloTech.

"No doubt there will be other products, other assays, and it is not certain that they will be array-based," she said. "We are agnostic when it comes to platforms."

Whatever new products emerge from PhyloTech, the company will continue to focus on human disease and environmental testing, Warrington added.

Arrays and Sequencing

PhyloTech has been advancing its core service into a marketplace that at times can seem more interested in next-generation sequencing technologies. Indeed, one of the frequently asked questions on the firm's website is, "Isn’t next generation sequencing more sensitive? Faster? Better for discovery?"

Warrington said that the PhyloChip platform has benefitted from the adoption of next-gen sequencing technologies. Developed in the lab of Gary Andersen at LBNL in 2005, the chip is now in its third generation and contains more sequences than it originally did.

"There is much more sequence information available today than there was [available] back then," said Warrington. "That is in no small part due to the fact that sequencing technologies have advanced."
She cited the Human Microbiome Project, a National Institutes of Health-funded initiative that seeks to identify and characterize microorganisms found in healthy and diseased humans, as one effort that has led to the availability of more information that could later be harnessed by the PhyloChip.

At the same time, the firm is staunch in its belief that its assay offers advantages over sequencing.
"A lot of it has to do with the depth you would have to sequence to get the equivalent sensitivity of the PhyloChip," said Warrington. Using next-gen sequencing "would be extremely expensive."

She also said that contemporary next-gen sequencing suffers from a "higher error rate" due to its digital output format. Sequencing "can fool people" because analyzing a digital output is different than looking at sequence traces, which can be ambiguous, she said. So, "when researchers go back to do Sanger sequencing to identify what they think are novel strains, they aren't novel; they are misreads."

While the company touts its advantages over sequencing today, it has not ruled out potentially adopting that technology in the future. Warrington added that the firm's PhyloChip is currently based on Affy's older cartridge-format arrays, and could in the future upgrade to the company's GeneAtlas or GeneTitan systems, which support its newer array strip format.

"We are keeping an eye on Affymetrix's new products as well as other companies'," said Warrington. "We are interested in what will make sense in different applications in different markets."

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