As the movement among consumers for more information about the products they’re purchasing and consuming continues to grow, the food industry will experience persistent pressure from both advocacy groups and the government on disclosure of product safety information and ingredients. Top of mind as of late has been the debate over GMOs. “Given all of the attention on GMOs on the legislative side, there is huge demand from consumers to have visibility and transparency into whether products have been genetically modified or not,” says Mahni Ghorashi, co-founder of Clear Labs.
Mahni Ghorashi, co-founder of Clear Labs
Today Clear Labs announced the availability of its comprehensive next-generation sequencing (NGS)-based GMO test. The release comes at an opportune time, as the GMO labeling bill, which was passed by the U.S. House of Representatives last week, heads to the desk of President Obama.
Clear Labs touts the technology as the first scalable, accurate and affordable GMO test. NGS enables the ability to simultaneously screen for multiple genes at one time, which could companies save time and money. “The advantage and novelty of this new test or assay is the ability to screen for all possible GMO genes in a single universal test, which is a huge change from the way GMO testing is conducted today,” says Ghorashi.
The PCR test method is currently the industry standard for GMO screening, according to the Non-GMO Project. “PCR tests narrowly target an individual gene, and they’re extremely costly—between $150–$275 per gene, per sample,” says Ghorashi. “Next-generation sequencing is leaps and bounds above PCR testing.” Although he won’t specify the cost of the Clear Labs assay (the company uses a tiered pricing structure based on sample volume), Ghorashi says it’s a fraction of the cost of traditional PCR tests.
The new assay screens for 85% of approved GMOs worldwide and targets four major genes used in manufacturing GMOs (detection based on methods of trait introduction and selection, and detection based on common plant traits), allowing companies to determine the presence and amount of GMOs within products or ingredient samples. “We see this test as a definitive scientific validation,” says Ghorashi. The company’s tests integrate software analytics to enable customers to verify GMO-free claims, screen suppliers, and rank suppliers based on risk.
Screenshot of the Clear Labs GMO test, which is based on next-generation sequencing technology.
Clear Labs isn’t targeting food manufacturers of a specific size or sector within the food industry but anticipates that a growing number of leading brands will be investing in GMO testing technology. “We expect to see adoption across the board in terms of company size, related more to what their stance is on food transparency and making that information readily available to their end consumers,” says Ghorashi.
How safe is a raw diet? Could sterilizing our food actually make us more prone to sickness? Are vegans healthier than carnivores? In the last few decades, global food poisoning scares from beef to peanut butter have kept food scientists and researchers around the world asking these questions and searching for improved methods of handling and testing what we eat.
It’s been more than 150 years since Louis Pasteur introduced the idea of germ theory—that bacteria cause sickness—fundamentally changing the way we think about what makes our food safe to eat. While we’ve advanced in so many other industrial practices, we’re still using pasteurization as the standard for the global food industry today.
Although pasteurization effectively controls most organisms and keeps the food supply largely safe, we continue to have foodborne outbreaks despite additional testing and more sophisticated techniques. The potential health promise of genomics, and the gut microbiome genetics and bacterial ecosystems, could be the key to the next frontier in food safety.
The scientific community is once again at the cusp of a new era with the advent of metagenomics and its application to food safety.
What is metagenomics? Metagenomics is the study of the bacterial community using genetics by examining the entire DNA content at once. Whole genome sequencing of a single bacterium tells us about the DNA of a specific organism, whereas metagenomic testing tells us about the interaction of all the DNA of all the organisms within a sample or an environment. Think of the vast quantity of genetic material in the soil of a rice patty, a lettuce leaf, your hand, a chicken ready for cooking, or milk directly from a cow. All of them have thousands of bacteria that live together in a complex community called the microbiome that may contain bacteria that are sometimes harmful to humans—and possibly also other bacteria that help to keep the potentially harmful bacteria in check.
Metagenomics uses laboratory methods to break up cells and extract many millions of DNA molecular fragment, and sequencing instruments to measure the sequences of A’s, C’s, G’s, and T’s that represent the genetic information in each of those fragments. Then scientists use computer programs to take the information from millions or billions of fragments to determine from what bacteria they came. The process is a little like mixing up many jigsaws, grabbing some pieces from the mix, and figuring out what was in the original pictures. The “pictures” are the genomes of bacteria, which in some cases carry enough unique information to associate a given bacterium with a previously seen colony of the same species.
Genomics of single bacterial cultures, each from a single species, is well established as a way to connect samples of contaminated foods with reported cases of foodborne illnesses. With metagenomics, which essentially looks for all known species simultaneously, one hopes to do a better job of early detection and prevention. For example, if a machine malfunction causes pasteurization or cleaning to be incomplete, the metagenomics measurement will likely show compositional shifts in which bacterial phyla are abundant. This can make it possible to take remedial action even before there are signs of pathogens or spoilage that would have led to a costly recall.
Up until now, keeping food safe has meant limiting the amount of harmful bacteria in the community. That means using standard methods such as pasteurization, irradiation, sterilization, salt and cooking. To determine whether food is actually safe to eat, we test for the presence of a handful of specific dangerous organisms, including Listeria, E. coli, and Salmonella, to name a few. But what about all the “good” bacteria that is killed along with the “bad” bacteria in the process of making our food safe?
Nutritionists, doctors and food scientists understand that the human gut is well equipped to thrive unless threatened by particularly dangerous contaminants. The ability to determine the entire genetic makeup within a food could mean being able to know with certainty whether it contains any unwanted or unknown microbial hazards. Metagenomic testing of the food supply would usher in an entirely new approach to food safety—one in which we could detect the presence of all microbes in food, including previously unknown dangers. It could even mean less food processing that leaves more of the healthful bacteria intact.
More than 150 years ago, Pasteur pointed us in the right direction. Now the world’s brightest scientific minds are primed to take the food industry the next leap toward a safer food supply.
By Steven Guterman, Sarah McMullin, Steve Phelan No Comments
The combination of improved digital tracking along the food supply chain, as well as fast, accurate DNA testing will provide modern, state-of-the-art tools essential to guarantee accurate labeling for the ever-increasing quantities of foods and ingredients shipped globally.
The sheer scale of the international food supply chain creates opportunities for unscrupulous parties to substitute cheaper products with false labels. We know fraud is obviously a part of the problem. Some suppliers and distributors engage in economically motivated substitution. That is certain.
It’s equally true, however, that some seafood misidentification is inadvertent. In fact, some species identification challenges are inevitable, particularly at the end of the chain after processing. We believe most providers want to act in an ethical manner.
Virtually all seafood fraud involves the falsification or manipulation of documents created to guarantee that the label on the outside of the box matches the seafood on the inside. Unfortunately, the documents are too often vague, misleading or deliberately fraudulent.
Oceana, an international non-profit focused solely on protecting oceans and ocean resources, has published extensively on seafood fraud and continues to educate the public and government through science-based campaigns.
Seafood fraud is not just an economic issue. If the product source is unknown, it is possible to introduce harmful contamination into the food supply. By deploying two actions simultaneously, we can help address this problem and reduce mistakes and mishandling:
Improved digital tracking technologies deployed along the supply chain
Faster, DNA-based in-house testing to generate results in hours
Strategic collaborations can help industry respond to broad challenges such as seafood fraud. We partner with the University of Guelph to develop DNA-based tests for quick and accurate species identification. The accuracy and portability produced by this partnership allow companies to deploy tests conveniently at many points in the supply chain and get accurate species identification results in hours.
Our new collaboration with SAP, the largest global enterprise digital partner in the world, will help ensure that test results can be integrated with a company’s supply chain data for instant visibility and action throughout the enterprise. In fact, SAP provides enterprise-level software to customers who distribute 78% of the world’s food and accordingly its supply chain validation features have earned global acceptance.
The food fraud and safety digital tracking innovations being developed by SAP will be critical in attacking fraud. Linking paper documents with definitive test results at all points in the supply chain is no longer a realistic solution. Paper trails in use today do not go far enough. Product volume has rendered paper unworkable. Frustrated retailers voice concerns that their customers believe they are doing more testing and validation than they can actually undertake.
We must generate more reliable data and make it available everywhere in seconds in order to protect and strengthen the global seafood supply chain.
Catfish will become the first seafood species to be covered by United States regulations as a result of recent Congressional legislation. This change will immediately challenge the capability of supply chain accuracy. Catfish are but one species among thousands.
Increasingly, researchers and academics in the food industry recognize fast and reliable in-house and on-site testing as the most effective method to resolve the challenges of seafood authentication.
DNA-based analyses have proven repeatedly to be the most effective process to ensure accurate species identification across all food products. Unfortunately, verifying a species using DNA sequencing techniques typically takes one to two weeks to go from sample to result. With many products, and especially with seafood, speed on the production line is essential. In many cases, waiting two weeks for results is just not an acceptable solution.
Furthermore, “dipstick” or lateral-flow tests may work on unprocessed food at the species level, however, DNA testing provides the only accurate test method to differentiate species and sub-species in both raw and processed foods.
Polymerase chain reaction (PCR), which analyzes the sample DNA, can provide accurate results in two to three hours, which in turn enhances the confidence of producers, wholesalers and retailers in the products they sell and minimizes their risk of recalls and brand damage.
New technology eliminates multi-day delays for test results that slow down the process unnecessarily. Traditional testing options require sending samples to commercial laboratories that usually require weeks to return results. These delays can be expensive and cumbersome. Worse, they may prevent fast, accurate testing to monitor problems before they reach a retail environment, where brand and reputational risk are higher.
Rapid DNA-based testing conducted in-house and supported by sophisticated digital tracking technologies will improve seafood identification with the seafood supply chain. This technological combination will improve our global food chain and allow us to do business with safety and confidence in the accuracy and reliability of seafood shipments.
When it comes to preventing foodborne illness, staying ahead of the game can be an elusive task. In light of the recent outbreaks affecting Chipotle (norovirus, Salmonella, E. coli) and Dole’s packaged salad (Listeria), having the ability to identify potentially deadly outbreaks before they begin (every time) would certainly be the holy grail of food safety.
One year ago IBM Research and Mars, Inc. embarked on a partnership with that very goal in mind. They established the Consortium for Sequencing the Food Supply Chain, which they’ve touted as “the largest-ever metagenomics study…sequencing the DNA and RNA of major food ingredients in various environments, at all stages in the supply chain, to unlock food safety insights hidden in big data”. The idea is to sequence metagenomics on different parts of the food supply chain and build reference databases as to what is a healthy/unhealthy microbiome, what bacteria lives there on a regular basis, and how are they interacting. From there, the information would be used to identify potential hazards, according to Jeff Welser, vice president and lab director at IBM Research–Almaden.
“Obviously a major concern is to always make sure there’s a safe food supply chain. That becomes increasingly difficult as our food supply chain becomes more global and distributed [in such a way] that no individual company owns a portion of it,” says Welser. “That’s really the reason for attacking the metagenomics problem. Right now we test for E. coli, Listeria, or all the known pathogens. But if there’s something that’s unknown and has never been there before, if you’re not testing for it, you’re not going to find it. Testing for the unknown is an impossible task.” With the recent addition of the diagnostics company Bio-Rad to the collaborative effort, the consortium is preparing to publish information about its progress over the past year. In an interview with Food Safety Tech, Welser discusses the consortium’s efforts since it was established and how it is starting to see evidence that using microbiomes could provide insights on food safety issues in advance.
Food Safety Tech:What progress has the Consortium made over the past year?
Jeff Welser: For the first project with Mars, we decided to focus around pet food. Although they might be known for their chocolates, at least half of Mars’ revenue comes from the pet care industry. It’s a good area to start because it uses the same food ingredients as human food, but it’s processed very differently. There’s a large conglomeration of parts in pet food that might not be part of human food, but the tests for doing the work is directly applicable to human food. We started at a factory of theirs and sampled the raw ingredients coming in. Over the past year, we’ve been establishing whether we can measure a stable microbiome (if we measure day to day, the same ingredient and the same supplier) and [be able to identify] when something has changed.
At a high level, we believe the thesis is playing out. We’re going to publish work that is much more rigorous than that statement. We see good evidence that the overall thesis of monitoring the microbiome appears to be viable, at least for raw food ingredients. We would like to make it more quantitative, figure out how you would actually use this on a regular basis, and think about other places we could test, such as other parts of the factory or machines.
Sequencing the food supply chain. Click to enlarge infographic (Courtesy of IBM Research)
FST: What are the steps to sequencing a microbiome?
Welser: A sample of food is taken into a lab where a process breaks down the cell walls to release the DNA and RNA into a slurry. A next-generation sequencing machine identifies every snippet of DNA and RNA it can from that sample, resulting in huge amounts of data. That data is transferred to IBM and other partners for analysis of the presence of organisms. It’s not a straightforward calculation, because different organisms often share genes or have similar snippets of genes. Also, because you’ve broken everything up, you don’t have a full gene necessarily; you might have a snippet of a gene. You want to look at different types of genes and different areas to identify bad organisms, etc. When looking at DNA and RNA, you want to try to determine if an organism is currently active.
The process is all about the analysis of the data sequence. That’s where we think it has a huge amount of possibility, but it will take more time to understand it. Once you have the data, you can combine it in different ways to figure out what it means.
FST: Discuss the significance of the sequencing project in the context of recent foodborne illness outbreaks. How could the information gleaned help prevent future outbreaks?
Welser: In general, this is exactly what we’re hoping to achieve. Since you test the microbiome at any point in the supply chain, the hope is that it gives you much better headlights to a potential contamination issue wherever it occurs. Currently raw food ingredients come into a factory before they’re processed. If you see the problem with the microbiome right there, you can stop it before it gets into the machinery. Of course, you don’t know whether it came in the shipment, from the farm itself, etc. But if you’re testing in those places, hopefully you’ll figure that out as early as possible. On the other end, when a company processes food and it’s shipped to the store, it goes onto the [store] shelves. It’s not like anyone is testing on a regular basis, but in theory you could do testing to see if the ingredient is showing a different microbiome than what is normally seen.
The real challenge in the retail space is that today you can test anything sitting on the shelves for E. coli, Listeria, etc.— the [pathogens] we know about. It’s not regularly done when [product] is sitting on the shelves, because it’s not clear how effectively you can do it. It still doesn’t get over the challenge of how best to approach testing—how often it needs to be done, what’s the methodology, etc. These are all still challenges ahead. In theory, this can be used anywhere, and the advantage is that it would tell you if anything has changed [versus] testing for [the presence of] one thing.
FST: How will Bio-Rad contribute to this partnership?
Welser: We’re excited about Bio-Rad joining, because right now we’re taking samples and doing next-generation sequencing to identify the microbiome. It’s much less expensive than it used to be, but it’s still a fairly expensive test. We don’t envision that everyone will be doing this every day in their factory. However, we want to build up our understanding to determine what kinds of tests you would conduct on a regular basis without doing the full next-gen sequencing. Whenever we do sequencing, we want to make sure we’re doing the other necessary battery of tests for that food ingredient. Bio-Rad has expertise in all these areas, and they’re looking at other ways to advance their testing technology into the genomic space. That is the goal: To come up with a scientific understanding that allows us to have tests, analysis and algorithms, etc. that would allow the food industry to monitor on a regular basis.
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