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Environmental Genomics Firm eDNAtec Harnesses NGS for Biodiversity Surveillance

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BALTIMORE – Canadian environmental genomics company eDNAtec is harnessing high-throughput next-generation sequencing to provide environmental DNA (eDNA) solutions at an industrial scale.

The St. John's, Newfoundland-based company currently offers biodiversity assessment and monitoring services primarily through its NGS-based environmental metabarcoding workflow, while it is also advancing research for eDNA applications through its dedicated R&D arm, Centre for Environmental Genomics Applications (CEGA).

"The ​​company is formed around the commercialization and application development of environmental DNA procedures and methodologies," said Mehrdad Hajibabaei, a professor at the University of Guelph in Canada and the founder and CSO of eDNAtec.

Hajibabaei, whose research interests include molecular biodiversity and genomics technologies, said that despite recent advancements in the environmental genomics field, most research has been focusing on discovery science but less on developing real-world applications.

"The mandate of eDNAtec has been to basically fill this gap," he said, adding that the goal for the company was to develop eDNA technologies that are robust, scalable, and cost-effective for commercial use and to start offering these tools to a wider community of environmental researchers.

After an incubation period starting around 2015, eDNAtec was officially launched in 2017. Setting its primary focus on the marine ecosystem, the company placed its headquarters and laboratory in St. John's, a seaside city with abundant marine environmental research opportunities related to oil and gas productions as well as fisheries, Hajibabaei said.

Since its inception, eDNAtec has been able to garner support from industry — such as funding set aside by energy production companies for environmental research and stewardship — as well as government grants, Hajibabaei said. Together, these funding opportunities have added up to close to C$18 million of investment for the company.

One of eDNAtec's flagship products is EnviroSeq, an end-to-end, NGS-based eDNA workflow optimized for biodiversity monitoring. According to Hajibabaei, EnviroSeq has three main categories of environmental applications.

One, he said, is to survey the general biodiversity of an environment, offering a baseline analysis. Another application is to survey the so-called bioindicator organisms, such as certain species of fish, amphibians, and macroinvertebrates, that can reflect the dynamics of an environment. The third application is to examine rare targets, for example endangered species, that are typically less abundant in an environment but need to be monitored with very high sensitivity.

EnviroSeq, which is built on the backbone of environmental metabarcoding, comprises seven steps: program design, local environment assessment, sample collection, DNA extraction, sequencing, analysis, and interpretation. Each of these has been optimized for biodiversity monitoring applications, Hajibabaei said.

For instance, the company offers custom-assembled sample collection kits, using mostly off-the-shelf components, to better preserve specific substrate types.

"Most of our samples come from remote sites … so the big challenge is how to get the samples in a DNA-friendly, RNA-friendly fashion," Hajibabaei said. "A lot of efforts [from the company] has gone into developing these kits in such a way that they can provide optimal results in conditions that are suboptimal." In addition, depending on the client's needs, the company is staffed with a team of ecologists and field technologists that can be deployed to help collect the samples, he added.

In terms of sample type, Hajibabaei, who referred to eDNA sampling as a "liquid biopsy for the environment," said water has been the main workhorse. Studies have shown that even terrestrial organisms can shed their DNA into the surrounding environment, he said, and eventually end up in a watershed.

Beyond sampling, Hajibabaei said, EnviroSeq also "meticulously" incorporated a series of quality control procedures, such as control reagents and compartmentalized lab space, during its DNA extraction and library prep stage in order to boost the accuracy of the results while minimizing the chance of contamination. In addition, the workflow also adopts various biological and technical replicates to ensure the reproducibility of the data.

EnviroSeq is an amplicon-based assay, Hajibabaei added, noting that the technology mostly focuses on eukaryote markers, such as CO1, 18S RNA, and ITS. Outside of EnviroSeq, the company also works with other genomic technologies such as metagenomics, transcriptomics, and shallow genome sequencing, he said.

For sequencing, the company uses the Illumina NovaSeq platform, which can generate over a million reads for each amplicon. "In the typical metabarcoding workflow, you barely get 200,000 reads through MiSeq," Hajibabaei said, adding that the additional sequencing depth can help uncover more rare targets. Furthermore, he said company researchers have developed mitigations to curb index hopping during sequencing.

After analyzing the sequencing data with tailored bioinformatics pipelines, the end product of EnviroSeq is interpretable, and executive reports include various standardized visualizations of the results and analysis.

While Hajibabaei did not disclose the price for EnviroSeq, he said that with sequencing costs significantly shrinking, the assay is "quite cost competitive" compared with conventional metabarcoding protocols. As for its turnaround time, he said that without a queue, the company can typically return a report to customers a week after the samples arrived in the lab.

In addition to offering EnviroSeq, eDNAtec has also forged partnerships with environmental engineering and consulting companies, which incorporate its services as part of their offerings, Hajibabaei said. The company is also collaborating with regulatory agencies as well as academic and industry partners to carry out individualized R&D projects.

He noted that eDNAtec has a wide customer base, which includes researchers from both the public and private sectors. He also highlighted the company's existing partners, which include Fisheries and Oceans Canada and ExxonMobil.

In terms of IP, Hajibabaei said most of the company's current offerings are based on know-how and are not patented. However, he said the company is in the process of developing an intellectual property portfolio for potential future products and services.

As for competition, he said that although there are other companies emerging in the environmental DNA space, each of them has its own flavor, and eDNAtec seemingly has the unique position of specializing in high-throughput eDNA applications, especially for the ocean, at an industrial scale. Still, "I am actually quite happy to see these companies bubbling up because then it shows the market is developing," he said, adding that healthy competition will likely galvanize more progress for the entire field.

Moving forward, Hajibabaei said that eDNAtec, which currently has about 20 employees, is in the middle of "a very big expansion plan," aiming to double its workforce within a year. As the company continues to expand, he also expects it to generate more service and R&D contracts, bringing in more revenue.

"My vision, and I think that [is] what we are working towards in our company, is to work with the partners, both in the public sector and in the private sector, to showcase the usefulness of having biodiversity data through eDNA," he said.

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