Sequence #5: Yes, Genomics Can Help With That

Genomics is proving to be a game changer for many resource industries critical to Atlantic Canada’s economic growth.

Nova Scotia’s Minister of Energy Geoff MacLellan recently announced details of his department’s $11.8-million commitment to Phase Two of Nova Scotia’s offshore growth strategy.

MacLellan acknowledged the important role of innovative technologies like genomics in helping to ‘de-risk’ offshore exploration and showed Genome Atlantic’s newly-produced video “Reducing the Risk”, about how genomics is contributing to a better picture of Nova Scotia’s offshore petroleum deposits.

Genomics is helping to tackle another big offshore challenge – microbiologically-influenced corrosion (MIC), which costs the oil and gas industry tens of millions of dollars a year.  Genome Atlantic joined international experts in St. John’s, NL recently for a workshop and research symposium dedicated to better understanding and managing MIC.  Check out Memorial University’s story on the event and the $7.8 million research project managed by Genome Atlantic and Genome Alberta aimed at improving pipeline integrity.  Click here for more information about the MIC research project.

Cannabis is an important emerging industry for Canada, and genomics plays an important role here too. Cultivars and breeders are using genomics to identify desired traits, accelerate breeding and unlock high-value opportunities for developing specialized strains. The Province of New Brunswick has identified cannabis as a major economic driver, and this spring, Genome Atlantic partnered with Opportunities New Brunswick and BioNB to host a panel discussion in Fredericton focused on maximizing cannabis opportunities along the entire value chain, including through genomics technologies.

In aquaculture, another important emerging industry for Atlantic Canada, genomics is driving growth by helping to boost breeding programs, reduce loss from disease and pests, and optimize feed formulas. Better feeds help keep farmed fish healthy, and Genome Atlantic spoke with two leading Ocean scientists at Memorial University who are working with researchers at Cargill Aqua Nutrition and UPEI to develop therapeutic feeds that optimize growth and disease resistance in farmed salmon.

Genomics is also bearing fruit for agricultural researchers like Dalhousie University’s Dr. Sean Myles.  Myles wrote the book – literally – on grapevine breeding programs for the wine industry and was instrumental in leading the development of Canada’s National Apple Breeding Consortium. Check out our conversation with him about the role of genomics in value-added agricultural products, particularly here in Atlantic Canada.

Sequence Issue #4: 163 lives saved….and counting

Ten years ago, Newfoundland researchers cracked the genetic code of a cardiac disease that causes death in seemingly healthy young people. The disease, Type 5 ARVC, is particularly prevalent in Newfoundland and Labrador. Genome Atlantic recently caught up with researchers Drs. Terry-lynn Young and Kathy Hodgkinson to find out what’s happened since their genetic breakthrough – as it turns out, plenty.  More than 500 people have been tested and 163 people fitted with life-saving defibrillators. Watch one patient’s story in the brief, compelling video:

We also checked in with Drs. Chris McMaster and Johane Robitaille on their continuing work in orphan disease discovery and therapies. Seven years ago, McMaster launched a research project called IGNITE to improve our understanding, diagnosis and treatment of orphan diseases.  Multiple gene discoveries and therapies later, this remarkable research team continues to unlock the power of clinical genetics to improve the lives of people with orphan diseases.

Watch this brief video on how the Government of Canada’s recent announcement of $225 million for genomics and precision health research – including on orphan diseases – is bringing new hope for Canadian patients.

Genomics is a powerful tool for many sectors and is one of five pillars of the recently announced Atlantic Canada-based Ocean Supercluster. Genome Atlantic joined a recent Ocean Supercluster celebration in St. John’s, NL, hosted by Petroleum Research Newfoundland and Labrador.  Perhaps Hon. Seamus O’Regan summed it up best when he said, “We came here for the ocean’s riches. We have the expertise that can take on the world. So let’s take it on.”

Oil-eating microbes? They’re real and they may just help unlock the secret of Nova Scotia’s offshore petroleum reserves. We’ve commissioned a video to tell the story, and while it won’t wrap up for a bit, here’s a sneak peek.

Genome Atlantic is helping to “create great things from life” in Atlantic Canada’s bioscience sectors. Find out how in this Opinion Piece published in The Telegram (St. John’s, NL) and Guardian (Charlottetown, PE).

The role of genomics is expanding quickly – not just in traditional sectors but in emerging fields like synthetic biology. Ontario Genomics recently hosted Canada’s first national conference on synthetic biology which combines biology and engineering to design and construct new biological entities – or as one of the speakers put it, “Synthetic biology means engineering biology to make useful stuff.” The conference covered a lot of ground, from developing new therapeutics to reducing our climate footprint – all “useful stuff” indeed!

Sequence Issue #3: Clustering, Cannabis & Cleaning Up


Recently, Genome Atlantic attended an information session on Canada’s Ocean Supercluster, aimed at small and medium businesses who play a vital role in Atlantic Canada’s ocean economy. The session was well attended by business operators who came to find out more and how they can get involved. It’s exciting to see how the supercluster concept is bringing together ocean companies of every size across our region.

The Ocean Supercluster is one of nine potential superclusters shortlisted recently by the federal government which has committed to invest up to $950 million between 2017-2022 to support up to five business-led supercluster initiatives with the potential to super-charge the economy. Biotechnology and genomics are among the cross-cutting, enabling technologies identified as components of the ocean supercluster vision. (Our last issue of Sequence highlighted several large-scale genomics applications in ocean-related industries.)

This is an unprecedented opportunity for Atlantic Canada and for our ocean industries and businesses. You can find out more at the Canada’s Ocean Supercluster website.

Read more about all nine shortlisted supercluster projects.

Cannabis and public policy

The legalization of recreational cannabis is another huge public policy issue. This Fall, Genome Atlantic co-hosted a panel of experts that included the Honourable Anne McLellan, Chair of Canada’s Task Force on Cannabis Legalization and Regulation, to examine some key topics around the coming legislation, including health and genetics. Check out the full panel discussion video at the end of the article – worthwhile viewing for anyone interested in the issue.

The plunging cost of DNA sequencing has given rise to more genetic tests that help doctors identify best treatments for a range of conditions from genetic disorders to many kinds of cancers.  But genetic tests have a potentially thorny side too.  Recently, Canadian parliamentarians grappled with whether employers, insurance companies, and others could require an employee, client or customer to undergo genetic testing and divulge the results.  To get the inside story, we talked to the man behind Canada’s Genetic Non-Discrimination Act, Senator James Cowan.

Clean up and the power of microbes.

Offshore Technology magazine recently took a deep dive into the role of microorganisms in the offshore oil and gas industry while The Chemical Institute of Canada Magazine focused in on Microbiologically-Influenced Corrosion (MIC), a costly phenomenon that damages pipelines and offshore production and gathering lines. Another recent article, in Canadian Reclamation magazine, highlights three recent examples of how genomics is becoming an increasingly important part of environmental monitoring and cleanup. And speaking of cleanup, a team of Dalhousie University students are using a surprising substance – porcupine scat – to help transform the pulp and paper industry’s cellulose waste into a profitable biofuel on a commercial scale? Genome Atlantic is pleased to be a partner in much of the ground-breaking work highlighted.

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Sequence Issue #2: The Next Big Wave

Recently, Genome Atlantic’s Andy Stone and Stantec’s Marc Skinner teamed up at the monthly Ocean Connector in Halifax to talk about some of the latest genomics-based technologies making waves in ocean research.

Here in Atlantic Canada, we are seeing exciting applications of genomics technologies to solve problems in the offshore oil and gas industry.  One large-scale genomics project is studying microbiologically-influenced corrosion (MIC), a poorly understood phenomenon that accounts for 20% of structural corrosion in oil and gas pipelines.  Predicting how, where and why microbes cause corrosion would be a big win for the oil and gas industry and for the environment. This project has generated considerable attention from the industry and media alike – and this issue of Sequence takes a deeper dive into the project’s offshore component along with some insight from one of the world’s foremost MIC experts on how genomics just might provide the answer.

Genomics is also being used to de-risk offshore petroleum exploration in Nova Scotia’s offshore.   The Play Fairway Analysis completed in 2011 brought $2 billion in exploration activities to the province. Now, genomics is being combined with geology to paint an even clearer picture of petroleum deposits. We’ll have more to report on this exciting story in a future issue of Sequence.

Environmental DNA (eDNA) is another emerging genomics technology that is quickly becoming the Gold Standard for measuring and monitoring species and environmental samples.  eDNA works by collecting and analyzing biological material that organisms leave behind and matching them to specific species.

At the Ocean Connector, Marc Skinner talked about eDNA’s use as an environmental monitoring tool in aquaculture – you can read about it in his blog.  In New Brunswick, the Canadian Rivers Institute has been successfully using eDNA to study wetlands and fish populations in rivers.  Genome BC is leading a project using eDNA to monitor White Sturgeon, an endangered species in Canada.  And earlier this summer, Newfoundland launched the world’s first environmental genomics research centre that will employ eDNA to help industry and researchers monitor the marine environment.  (For a futuristic look at environmental sampling, check out this video Andy shared at the event on the Environmental Sample Processor from the Monterey Bay Aquarium Research Institute.)

*** PROJECT UPDATES ***  We want to share with you a couple of agriculture stories too.  One is about a unique genomics research project that could turn an oilseed wonder into a more sustainable feed ingredient for farmed fish – a potential win-win for both our regional aquaculture and agriculture sectors. We also sat down recently for a one-on-one with Kelci Miclaus, a leading genomics software developer with JMP Genomics/SAS. Kelci was the keynote speaker at an agriculture and genomics conference that Genome Atlantic hosted in New Brunswick in June. Her perspective on how genomics is transforming agriculture is fascinating. Enjoy!

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Newfoundland’s offshore set to help unlock mysteries of microbial corrosion

Newfoundland’s offshore is expected to yield significant data for a four-year, $7.8 million collaborative genomics research project focusing on microbiologically-influenced corrosion (MIC) of oil and gas pipelines. MIC is believed to account for roughly 20 percent of corrosion failures in oil and gas pipelines, costing the oil and gas industry billions of dollars a year on control, repair and prevention measures to avoid oil spills directly related to MIC.

Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production is using genomics to better predict how, where and why MIC occurs and how to mitigate it. Funded under Genome Canada’s Large-Scale Applied Research Project Competition (LSARP), the project is co-led by an interdisciplinary team of scientists at the University of Calgary, the University of Alberta and Memorial University in Newfoundland and is co-managed by Genome Alberta and Genome Atlantic.

“MIC is an important issue in offshore operations. It often goes undetected and causes failure,” says Memorial University’s Dr. Faisal Khan, one of the project co-leads and head of the project’s Memorial University team whose main focus is uncovering how microbes cause corrosion. “This project will develop the mechanisms to detect early MIC occurrence and model MIC-induced failure.”

A Canada Research Chair (Tier I) in Safety and Risk Engineering and a chemical engineer, Khan works with the oil and gas industry on safety and asset integrity and is well-acquainted with Atlantic Canada’s offshore. He explains that while MIC is well documented, it is poorly understood.

“We know that microbes cause corrosion but we are examining how they cause corrosion. We will do this by identifying the chemical source and how it reacts to the surface of the metal to cause corrosion. The risk models we’re developing will link the corrosion process to the outcome,” Khan explains. “This will be very important for industry when evaluating their level of corrosion intervention and control and where to focus their resources on corrosion mitigation.”

Dr. Lisa Gieg of the University of the University of Calgary and the overall project lead, explains that sampling will be key to the research team’s examination of corrosion. A microbiologist, Gieg studies anaerobic hydrocarbon metabolism and specializes in environmental and petroleum microbiology, and is responsible for the genomics aspects of the project.

“By using field samples from both offshore Newfoundland and onshore pipelines across Canada, we hope to build a comprehensive picture that will help us understand the microbial effects on the industry,” Gieg says. “Investigators will be collecting biofilm sludge in field samples provided by the energy sector for genomic analysis.” By identifying the micoorganisms present, the study hopes to pinpoint the interactions among different microbial populations that cause pipelines to corrode and leak.

Rounding out the trio of project leads is Dr. John Wolodko, the Alberta Innovates Technology Futures Strategic Chair in Bio and Industrial Materials at the University of Alberta. He will perform the materials evaluation, testing and design.

The idea for the project, says Wolodko, came from the oil and gas industry itself. “They don’t want to spend money on replacing systems all the time. It’s a cost that trickles down to the consumer.”

In addition to being a costly problem and an environmental risk, MIC is also a major safety hazard with implications that go well beyond the oil and gas industry. The phenomenon also affects major infrastructure such as bridges and vessels – any type of product or infrastructure made with metal and exposed to the elements.

Even for the oil and gas industry, “It’s not just about pipelines,” says Gieg. “The research will look at all points of contact between oil and steel in extraction, production and processing. This work can help make the industry safer.”

Practical implications are high on the investigators’ agendas and one of the project’s main goals is to integrate the results into corrosion management frameworks and standards to reduce oil spills, improve asset integrity worker safety, and environmental compliance.

Unique in its multi-disciplinary approach, Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production brings the combined expertise of genomics, electrochemistry, degradation modeling, risk assessment and management and practical applications to bear on MIC. The project leads have cited collaboration as key to the project’s success. Genomics will play a large role in facilitating the cross-disciplinary nature of the investigation.

The project’s Atlantic Canada partners include Dalhousie University, Husky Energy, Suncor Energy, LumniUltra, Petroleum Research Newfoundland and Labrador, Research and Development Corporation of Newfoundland and Labrador and Mitacs.

Written with files from The Globe and Mail; U Today (University of Calgary); The Gazette (Memorial University); Genome Atlantic; and Genome Alberta.


For more on this project

Connecting the dots: the elderly, frailty and the microbiome

A pilot study of microbial genes in pensioners living in an assisted care facility in Atlantic Canada has shed new light – and more than a few surprises – on the state of residents’ microbiome.

There is a known link between the gut microbiome and factors like diet, immune development, infectious diseases, and even living conditions. But little is known about the relationship between gut microbes and frailty.

Frail individuals are more vulnerable to poor health and are at a greater risk for accidents and illness. Could the microbiome of aging and frail individuals provide information that could contribute to better health outcomes?

This was a key question of a recent pilot study conducted with 47 pensioners in Northwoodcare, an assisted living facility in Halifax. The study, led by Dr. Rob Beiko and Dr. Kenneth Rockwood of Dalhousie University, looked at the changing composition of the community of bacteria that live in the gastrointestinal tract – collectively known as the gut microbiome – in relation to the participants’ age, health and lifestyles.

Beiko and Rockwood set out to explore how age and frailty affect the gut microbiome, specifically pinpointing what bacteria are present or absent and determining whether the microbiome in aging and frail individuals changes over time. Their hope was that the information gathered from the study could ultimately help in developing better techniques for frailty assessment and inform health care and quality of life decisions for frail individuals.

Study participants, aged 65-98, were scored on the Clinical Frailty Scale, a global clinical measure of fitness and frailty in elderly people. In the process, extensive information was gathered on their health and lifestyles. Then, subjects’ stool samples were collected once a week for five weeks and microbial genes were analyzed to see if their gut microbiomes showed associations with frailty.

Obtaining both high- and low-resolution sequencing through Dalhousie University’s Integrated Microbiome Resource (IMR) “made life a lot easier for us,” says Beiko, the Canada Research Chair in Bioinformatics, at the university’s Faculty of Computer Science. The study relied on the IMR’s Illumina MiSeq and NextSeq sequencers to identify the bacteria and the functions they play.

‘we can look for specific things that can influence critical decision making’ – Dr. Rob Beiko

A unique feature of the study was that Northwood’s subjects shared the same type of housing, environment and diet, although they differed widely in their health status and prescribed drugs. A surprising finding, says Beiko, was that “living in the same facility does not lead to anyone having the same or even similar (microbe) species profiles.”

Contrary to previous studies carried out by others, the research showed that older adults and frailer subjects had as much bacterial diversity as their younger and less frail counterparts. Furthermore, with few exceptions, most subjects’ microbiomes were relatively stable during the five-week period of the study.

Exceptions, though, were sometimes dramatic. One subject showed wild instability with Pseudomonas, a potentially opportunistic pathogen, and with Akkermansia, a bacterium associated with weight loss and anti-inflammation. The Pseudomonas appeared in week one but disappeared by week two, never to return for the rest of the sampling period. Meanwhile, Akkermansia turned up in week two and grew in abundance each week until it became dominant in week five.

“We don’t know if there is any sort of casual relationship, but it’s interesting that the pathogen goes away and then other things that might be good, actually bloom afterwards,” says Beiko. This observation, and others like it, have become key motivators for expanding the study to see if more examples of these phenomena can be found.

Another important finding in a few individuals was the presence of bacterial genes that confer resistance to certain antibiotics. These results dovetail with a new Genome Canada study, headed by Beiko and managed by Genome Atlantic, which is developing a quick and practical way to identify antimicrobial-resistant genes in patients’ samples. In the hands of a clinician, the resulting information would take the guesswork out of prescribing effective antibiotics in an era of increasing bacterial resistance.

For Beiko, the most encouraging takeaway was confirmation of the potential for harnessing microbiome analysis for clinical application. “One of the most immediate benefits of screening the microbiome is that we can look for specific things that can influence critical decision making,” he says.

The results from the pilot study are now driving applications for multi-year studies to characterize explore the relationship between frailty and the microbiome for subjects living in a wider array of environments. Beiko and his informatics lab team continue to probe sequencing data, and develop more complex models and tools to uncover the patterns buried in enormous bacterial diversity. “The relationship between aging, frailty and the microbiome is very complicated,” he says, “but we’re starting to see the big picture and we know where to look next.”