Tag Archives: DNA barcoding

Blockchain

Future Of Food Safety: Next-Gen Technologies On The Rise

By Steve Orth
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Blockchain

Food safety is one of the biggest health concerns worldwide. The World Health Organization estimates that about one in 10 people contract an illness from contaminated food, with more than 400,000 dying each year as a result. Food contamination leads to illness, death, lost productivity, and wasted money.

Fortunately, technology to improve food safety continues to advance. The shift moves toward automation and system monitoring to improve accuracy and decrease the time that workers must attend to routine tasks. With the use of these developing technologies, commercial and industrial organizations can help to prevent foodborne illness and provide greater transparency to the consumer.

Smart Devices

The Internet of Things (IoT) provides several opportunities to improve food safety in commercial and industrial spaces. The premise behind IoT is that each device or appliance can connect to a larger hub, providing information about the contents or function of the equipment in real-time. These tools can improve food safety by performing safety checks, recording data like food temperatures, and allowing centralized monitoring of the entire system. In kitchens, restaurants and food processing plants with fewer employees, the ability to get information at a touch can simplify routine tasks and improve accuracy.

Sensors

Advanced sensor technology improves old technology by centralizing data collection and providing real-time updates. Sensors work by assessing factors like temperature or humidity within a controlled space. Older systems required workers to visually inspect the temperatures and adjust as needed. The latest models provide integrated data with the capacity to send immediate alerts when the conditions fall below safe levels. The technology minimizes food waste by prompting quick action, while giving operators the ability to confirm that the food always remains at safe levels.

3D Printing

Testing materials can be expensive, proprietary, and difficult to fit to every application, which highlights the benefits of 3D printing. 3D printing relies on the slow accumulation of material into a specific 3D design. The broad availability of designs allows organizations to contract out 3D printing of testing tools or bring the entire production in-house. The technology is revolutionizing various industries for its ability to provide custom products at a fraction of the cost of traditional manufacturing, often for much less investment.

Automated Sanitation

Automated sanitation systems improve the speed of cleaning and decrease the risk of human error. UV light systems gained notoriety for their ability to dramatically reduce the spread of pathogens like SARS CoV-2, creating benefits for commercial and industrial applications. UV and ozone sanitation improve results over liquid disinfectants and provide better results for surfaces that need to be sterilized.

The automation of these and other sanitation systems significantly cut down on the time workers must spend cleaning up. Industrial automation solutions minimize the risk of contamination, as well as shortening equipment downtime.

Blockchain

Blockchain is best known for its use in cryptocurrency, but the premise offers potential to decrease the effects of food contamination. The United States Food and Drug Administration notes that traceability presents the biggest problem for handling outbreaks of listeria or E. coli. The United Nations Development Programme argues that blockchain’s decentralized organization allows for the accurate presentation of information that cannot be misrepresented or deleted. This technology can provide detailed tracking of a food’s journey from farm to table to reduce time and money spent determining the source of a contaminated food.

DNA Barcoding

Preventing foodborne illness and the spread of pathogens involves greater effort to inspect during every step of the food’s journey. DNA barcoding presents interesting opportunities to quickly evaluate foods to classify their species and identify the presence of foreign bodies. The method highlights parts of the genome that identify a specific species, creating a barcode of sorts that can be used to verify the species. This level of detail in inspection can increase the accuracy of labeling, as well as providing a way to track the origin at a molecular level.

Automated Inspections

Human inspection can fail, especially for workers who may be operating in understaffed conditions. The increase in automated systems provides a viable solution. Visual systems can inspect each item for signs of damage or faulty production, immediately removing them from possible use. The latest technology can identify faults that are beyond human observation, increasing the accuracy of the equipment and minimizing the use of defective products.

Artificial Intelligence

Artificial intelligence (AI) has the potential to revolutionize all of these systems and more. AI uses the collection and processing of data to identify trends and highlight risks within a contained environment. The system can handle automated checks, maintenance, and other tasks that were once performed by humans. AI can use data to predict failures of systems or the likelihood of contamination, so that workers can address them in advance. With access to real-time data, AI can also provide immediate alerts to changes in food preparation or storage, to minimize food loss and the growth of foodborne illness.

Handling food in any capacity requires attention to food safety to minimize illness and death among the most vulnerable populations. In the interest of increasing food safety, researchers and manufacturers are investing in technology to automate food safety tasks such as sanitation and tracking food temperatures. While some technologies represent the vanguard of the food industry, others are gaining relevance worldwide. Exploring these technologies helps food safety professionals to evaluate the best systems to protect consumers throughout the use of their commercial and industrial spaces.

Sources

World Health Organization (WHO). (2022, May 19). Food safety. Who.int; World Health Organization: WHO. https://www.who.int/news-room/fact-sheets/detail/food-safety

Brous, P., Janssen, M., & Herder, P. (2019). The dual effects of the Internet of Things (IoT): A systematic review of the benefits and risks of IoT adoption by organizations. International Journal of Information Management, 51(1), 101952. https://doi.org/10.1016/j.ijinfomgt.2019.05.008

Pangarkar, T. (2024, May 7). 3D Printing Statistics 2024 By New Technology, Filaments, Types. Market Scoop. https://scoop.market.us/3d-printing-statistics/

US EPA, O. (2021, January 14). Disinfecting Surfaces with UV Light to Reduce Exposure to SARS-CoV-2. Www.epa.gov. https://www.epa.gov/emergency-response-research/disinfecting-surfaces-uv-light-reduce-exposure-sars-cov-2

NEW ERA OF SMARTER FOOD SAFETY FDA’s Blueprint for the Future. (n.d.). https://www.fda.gov/media/139868/download

Blockchain for Agri-Food Traceability | United Nations Development Programme. (n.d.). UNDP. https://www.undp.org/publications/blockchain-agri-food-traceability

DNA Barcoding – an overview | ScienceDirect Topics. (n.d.). Www.sciencedirect.com. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/dna-barcoding

Susanne Kuehne, Decernis
Food Fraud Quick Bites

The Root Causes Of A Botanical Fraud

By Susanne Kuehne
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Susanne Kuehne, Decernis
Eleuthero, Decernis
Find records of fraud such as those discussed in this column and more in the Food Fraud Database, owned and operated by Decernis, a Food Safety Tech advertiser. Image credit: Susanne Kuehne

Eleuthero root and root extract are used for herbal over-the-counter medicinal supplements with anti-inflammatory, anti-stress, energy boosting and antioxidant properties. Eleuthero (Eleutherococcus senticosus), also known as Siberian Ginseng, can be adulterated by adding Eleuthero aerial parts, the use of alternate species of Eleutherococcus or by declaring Periploea sepium (Chinese Silk) as Eleuthero. Variances in nomenclature in different parts of the world contribute to adulteration and mislabeling. The use of correct Latin names and comparison to authentic botanical material, as well as analytical methods to authenticate Eleuthero, for example, DNA barcoding and spectrometric methods, help to avoid that fraudulent Eleuthero products show up in medicinal supplements.

Resource

  1. Coskun, S.H., and Brinckmann, J. (November 2021). “Adulteration of Eleuthero (Eleutherococcus senticosus) Root and its Extracts”. American Botanical Council.
Susanne Kuehne, Decernis
Food Fraud Quick Bites

All Bison, No Bull

By Susanne Kuehne
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Susanne Kuehne, Decernis
Bison
Find records of fraud such as those discussed in this column and more in the Food Fraud Database. Image credit: Susanne Kuehne

Bison and other game meats have become increasingly popular over the course of the past years, and these products have enjoyed an increase in pricing as a result. Bison, deer and beef meats have very similar appearances; in addition, bison and domestic cattle can cross-breed and therefore the meat cannot be distinguished by DNA barcoding alone. To ensure that bison meat was not mixed with other red meat species, a specific polymerase chain reaction method (PCR-SFLP) was used in a recently published study. Out of 45 commercial bison meat samples, three samples showed other meat species, which were not identified on the label.

Resource

  1. Scales, Z.M., et al. (February 3, 2021). “Use of DNA Barcoding Combined with PCR-SFLP to Authenticate Species in Bison Meat Products”. MDPI.

 

DNA sequencing

Whole Sample Next-Generation DNA Sequencing Method: An Alternative to DNA Barcoding

By Casey Schlenker, Jenna Brooks, Kent Oostra, Ryan McLaughlin
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DNA sequencing

This article discusses a non-targeted method for whole sample next generation DNA sequencing (NGS) that does not rely on DNA barcoding. DNA barcoding requires amplification of a specific gene region, which introduces bias. Our non-targeted method removes this bias by eliminating the amplification step. The applications of this method are broad and we have begun optimizing workflows for numerous materials, both processed and unprocessed. Some of the materials we have been able to successfully identify at the species level are fish tissue, fish meal, unrefined fish oil, unrefined plant-based oils (nuts, seeds, and fruits), specific components of cooked and processed products such as cookies and powders, and processed meats. Non-targeted NGS is also a very powerful tool to comprehensively identify constituents of microbial communities in probiotics and fermented products like kombucha. Additionally, this non-targeted technique is applicable to detection and identification of microbial contamination at various levels of manufacturing including equipment surfaces, processing water and assaying intermediate processing steps. In this communication we briefly review a current issue in the botanicals industry, discuss the methods that have been used in the past to tackle that problem, and present preliminary results from a pilot study we performed to determine the utility of non-targeted NGS in high-throughput identification of botanical raw materials.

The value of the global herbal dietary supplement (botanical) market was estimated to be greater than $90 billion in 2016, with a projected compound annual growth rate of 5-6%. Currently, regulators and manufacturers in this rapidly expanding market seek to confirm the veracity of label claims, investigate fraud, identify adulterants and ensure product quality.1 These products are often dried and ground, making visual identification difficult, time consuming and sometimes impossible.2 It is critical to this market that botanical identification be high-throughput, accurate and cost effective. Historically, various chromatography techniques have been used to meet this need, but those techniques rely on identification of molecules that can vary significantly due to storage conditions, which has led to the use of DNA barcoding as an analytical technique. However, DNA barcoding is not without significant challenges.1

For quite some time, scientists have had the ability to identify biological samples by sequencing their DNA.3 Currently DNA sequencing-based identification methods rely heavily on a technique called DNA barcoding, which functions analogously to the barcodes found on products in a grocery store. DNA barcoding amplifies a distinct small gene region that serves as a unique identifier and “scans” it by DNA sequencing.4 The advantages of this amplification are high sensitivity and simplification of data analysis. However, this amplification is not completely reliable and in practice can create biases and false positives.5 There is also the possibility that the amplification may fail, causing false negatives.6 When using DNA barcoding to identify botanical raw materials, numerous labs have observed notably high levels of apparent contamination.7 While it is certainly likely that some or even many botanical raw material samples contain contamination, it is also possible that the amplification-based method of DNA barcoding is itself contributing to the levels of contamination that are being observed.

We have partnered with Practical Informatics and Pacific Northwest Genomics to develop comprehensive whole sample DNA screening methods that don’t rely on amplification. To achieve this we are utilizing a non-targeted metagenomics workflow. Non-targeted metagenomic analysis is a powerful tool for examining the entire genetic content of a sample, instead of just one particular gene region (if a gene is a word or phrase, then a genome is the entire book, and the metagenome is the library). Unlike DNA barcoding, which requires PCR amplification, non-targeted metagenomic analysis requires no prior knowledge of a sample’s source and does not introduce the biases that plague PCR initiated methods. All of the DNA extracted from a sample is analyzed without targeting any particular gene region, relying instead on complex data analysis to identify the constituents (Figure 1). This is accomplished with the use of advanced molecular biology techniques and sophisticated computational methods, combined with a highly-curated database of species-identifying DNA sequences. Our research and development team has completed several experiments demonstrating the utility of a non-targeted DNA sequencing method.

DNA sequencing
Figure 1. The traditional targeted method, or DNA barcoding uses a PCR amplification step prior to sequencing. Non-target whole sample sequencing skips the amplification step and all present DNA is sequenced and used in analysis.

Our research endeavors to solve the issues of DNA sequence analysis that originate with the PCR step by simply eliminating amplification from our process entirely. PCR amplification as a prelude to DNA sequencing traces to traditional technologies that were lower throughput and required large amounts of material. Current generation high-throughput DNA sequencing technologies do not require large amounts of starting material, and therefore amplification can be avoided. Many DNA barcoding methods require universal primers, which, during PCR, can amplify some products but not others, leading to false negatives. A solution to that issue is to use specific primers, however this is also inherently problematic as a certain foreknowledge of the sample identity is required. What is the advantage to our non-targeted sequencing method? There is no need to direct the analysis to any particular identification before sequencing, decreasing the introduction of bias and false negatives. As an added bonus, we don’t need to know what the sample is prior to analysis—we can tell you what it is rather than you telling us.

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magnifying glass

Next-Generation DNA Sequencing Finds Unexpected Contaminants

By Food Safety Tech Staff
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magnifying glass

With more regulatory and consumer scrutiny being placed on the authenticity of food products, companies must use technologies that can verify products and ingredients, and detect contaminants. NSF International recently acquired AuthenTechnologies, a testing laboratory that provides DNA-species identification services to improve authenticity, safety and quality of natural products. Using shorter segments and validated reference materials, AuthenTechnologies employs a DNA sequencing method that can identify “almost any” species and detect contaminants that cannot be distinguished morphologically or chemically. The method also screens for allergens, GMOs, fillers and filth.

“As the food supply chain becomes more complex and regulations continue to evolve and become more rigorous, this technology is becoming essential to achieving regulatory compliance and brand protection while preventing issues associated with fraud, mislabeling and adulteration,” said Lori Bestervelt, Ph.D, international executive vice president and chief technology officer at NSF, in a company release. AuthenTechnologies’ co-founder Danica Harbaugh Reynauld, Ph.D., adds, “We’ve developed a more highly specific DNA methodology capable of identifying a single organism to a complex blend of unlimited ingredients.” Reynauld, who will join NSF as global director of scientific innovation, will lead the NSF AuthenTechnologies center of excellence with NSF’s global network of labs.

In comparison to DNA barcoding, next-generation DNA sequencing is highly specific and can identify species in highly processed materials and complex mixtures. DNA barcoding is unable to differentiate between closely related species and is less suitable in detecting extracts as well.