The evolution of genetic analysis techniques applied to novel foods is revealing a widening gap between what science is now capable of detecting and what regulatory control systems are actually verifying. It is a gap that is reshaping the meaning of food safety in a market expanding faster than the frameworks designed to oversee it.
Insect flours labelled as “pure” that still contain traces of the insect’s feed. Plant-based products carrying animal contamination somewhere along the supply chain. Botanical supplements in which the detected species does not match the one declared on the label. Complex food mixtures, from spices to processed meat products, containing undeclared ingredients. What emerges from molecular biology laboratories is not simply a collection of isolated anomalies. It points instead to a structural asymmetry between the actual composition of what we eat and the information food labels claim to provide.
Today, the European food industry operates under a dual acceleration. On one side, changing consumption patterns are driving increasingly complex products onto the market, shaped by long supply chains and intensive industrial processing. According to Circana, the European plant-based sector alone reached €16.3 billion in 2025, while insect-based novel foods (regulated under EU Regulation 2015/2283) continue to expand. On the other side, control systems are evolving at a different pace. In 2024, the RASFF (Rapid Alert System for Food and Feed) recorded 5,250 notifications, a 12% increase over the previous year, including roughly 550 reports of suspected food fraud.
It is precisely within this gap, between the speed of innovation and the pace of regulation, that DNA metabarcoding becomes particularly relevant. The technology itself is not new (Tech4Future has already explored it extensively), yet the methodology continues to demonstrate remarkable relevance because it reveals what conventional control procedures, in many cases, still fail to detect.
“I’m not sure whether specific controls for this type of contamination currently exist, but considering how quickly the sector is growing, it would certainly deserve deeper investigation,” says Jessica Frigerio, a researcher working on the application of metabarcoding to novel foods.
The statement is revealing. Researchers working at the forefront of food diagnostics are questioning whether downstream control systems are keeping pace with analytical capabilities. More than the laboratory data itself, this tension captures the core issue at stake.
TAKEAWAYS
A Technique That Redefines What Can Be Seen
Metabarcoding is a molecular biology technique derived directly from DNA barcoding, sharing the same core principle: identifying species through specific regions of the genome, essentially a genetic barcode. The difference, however, fundamentally changes what can actually be detected.
“With standard DNA barcoding, you generally obtain only a single sequence, so you need a clean sample containing one species,” Frigerio explains.
This operational limitation excludes a vast portion of contemporary food products from effective analysis. Spices, processed blends, meat products, and botanical supplements are, by definition, mixtures.
Metabarcoding changes the analytical perspective by relying on advanced sequencing technologies capable of simultaneously identifying all species present within a sample.
“We analyse everything contained in the sample, and this opens up an enormous range of applications.”
From an analytical standpoint, this means moving from a targeted verification model (“is this really species X?”) to a compositional mapping approach capable of reconstructing the actual biological profile of a product.
In the context of food fraud, the implications are significant. The categories most frequently involved in reports from the European Agri-Food Fraud Network (spices, supplements, processed foods) are precisely those where metabarcoding provides the greatest diagnostic advantage.
“Not all cases involve intentional fraud,” Frigerio notes. “Very often they are accidental contaminations caused by failures to properly follow GMP or HACCP procedures.”
In other cases, however, substitution appears deliberate.
“In plant-based supplements, it sometimes happens that the declared species is absent altogether, or replaced with another similar species that has different properties. That cannot simply be accidental.”
What becomes visible for the first time is an intermediate zone between formal compliance and outright adulteration. How many products currently on the market exist within this grey area? How should regulation address systematic but unintended contamination? And how should responsibility be distributed along supply chains where the origin of a defect often becomes impossible to trace retrospectively?
Insect Flours: When the Animal’s Diet Ends Up on the Human Plate
One of the most interesting applications of metabarcoding within the novel food sector concerns insect-based foods, still an emerging category, but already increasingly widespread across several markets.
“We conducted an exploratory study specifically on these products,” says Frigerio. “We purchased both 100% insect flours and more processed products such as pasta, protein bars, crackers, and pet food. First we used barcoding to verify the insect species, then metabarcoding to analyse everything else present in the sample.”
The findings highlighted an unexpected dimension. “Even in flours labelled as 100% insect, we detected numerous plant species. These were not adulterants, they were simply remnants of what the insect had eaten.”
The insect’s diet can therefore leave detectable traces in the final product. “We were able to identify a clear dietary pattern and detect it again even in highly processed foods.”
This introduces a significant food safety issue. “Insect feed may contain allergens relevant to humans, and this is not necessarily being considered. Metabarcoding can provide an initial indication of the presence of such allergens.”
The technique also enables relative quantitative estimates. “It is not a perfectly quantitative measurement because DNA concentration is not directly proportional to biomass, but it still provides an indication of relative percentages.”
To assess the real-world implications, the research group complemented the genetic analyses with protein testing. “We carried out targeted tests and found that, in many cases, soy levels exceeded European labelling thresholds. This means that allergic consumers could potentially be exposed without knowing it.”
According to Frigerio, the issue is not necessarily intentional misconduct. “I do not think there is deliberate fraud involved. Rather, this is a new sector where regulation and control systems may not yet be fully adequate.”
Plant-Based Foods and the Fragility of Ethical Choice
Within the plant-based sector, the problem shifts but remains equally significant. Here, the central issue concerns consistency with consumer expectations and ethical commitments.
“The most important point is verifying the possible presence of animal material,” Frigerio explains. “For many consumers, this is an ethical choice. If I buy a plant-based product and traces of meat are present, that becomes a serious issue.”
Again, contamination may originate from the production chain itself. “It can happen through oversight or because procedures are not followed correctly. It is not necessarily intentional.”
The key issue, however, is that the sensitivity of metabarcoding reveals what production systems are unable to guarantee as truly absent. “It is a technique capable of detecting extremely small DNA fragments, meaning it can identify contaminations that would otherwise remain invisible.”
On one side, diagnostics are advancing faster than operational control systems. On the other, they are establishing new expectations around what “purity” means for plant-based products.
Regulation Still Chasing Diagnostics
For the moment, regulation has not kept pace. “I’m not sure whether specific controls for this type of contamination already exist, but given the growth of the sector, this deserves much deeper attention.”
This uncertainty raises broader questions involving consumer rights, supply-chain accountability, and information governance. What happens when ethical purchasing decisions rely on labels that control systems cannot verify with the same resolution science can now provide? What level of accidental contamination should be considered acceptable in products aimed at consumers who deliberately avoid animal-derived materials? And who is operationally responsible for closing this gap — not only at the regulatory level, but in everyday industrial practice?
In practice, metabarcoding does not replace other analytical methods. It complements them. It functions as a high-resolution screening tool capable of rapidly producing a complex compositional snapshot of a food product. “With a single analysis we can obtain much more information,” says Frigerio. “Clearly, further investigation with more specific techniques is still necessary, but it provides an excellent starting point.”
The problem is that this starting point has not yet become operationally widespread. The technique exists, is extensively documented in scientific literature, and is already used in specialised studies, but to what extent has it actually entered the routine protocols of public and private laboratories? How systematically are food surveillance systems integrating it into their procedures? And is its adoption occurring evenly across EU member states, or following the familiar asymmetries of technical capacity and investment?
These questions move the discussion beyond the availability of technology and into the governance of technology itself. The existence of a tool does not guarantee its use; and its use within a limited number of research laboratories does not automatically translate into a recognised control standard. Between scientific discovery and institutional adoption lies a long chain of economic, political, and regulatory decisions.
One fundamental question therefore remains open. If technology is already capable of detecting contaminations, potential allergens, and discrepancies between labels and actual composition, how aligned are current control systems with these capabilities? In a market where novel foods are evolving faster than regulation, and diagnostics faster than both, who assumes responsibility for closing the gap? And perhaps most importantly: what does “food safety” concretely mean in a context where our ability to see what we eat has advanced beyond our collective ability to regulate it?
