The EU's stance on genetically modified microorganisms (GMMs)

Genetically modified microorganisms (GMMs) are widely used to produce food products in the EU. Examples of such products include valuable molecules such as enzymes, amino acids, vitamins or sugars. The contained use of such GMMs is common practice. This raises the question: are the final products labelled as genetically modified foods and what kinds of products would require that in the EU?

What counts as a genetically modified food product in the EU when it comes to micro-organisms?

The products of microbial fermentation in the EU market are generally not genetically modified products and therefore labelling requirements do not apply. Currently, the main principle is that if the final product (e.g. purified protein) does not contain viable cells of the production microorganism or detectable amounts of its DNA, with a detection limit of 10 ng DNA/1 g product, the product falls outside the scope of the European regulation on genetically modified food and feed (EC) 1829/2003. The vast majority of companies have been able to meet these requirements.

How are new genomic techniques regulated in the EU?

New genomic techniques (NGTs) is an umbrella term for a variety of techniques that can alter the genetic material of an organism and which have emerged since 2001, when the existing Directive 2001/18/EC on the deliberate release into the environment of genetically modified organisms (the GMO Directive) was adopted.

The use of NGTs has made significant progress over the last decade making it possible to modify the genetic material of an organism so that the product does not contain any foreign genetic material at all. Genetically modified microbes, plants, and even animals can be developed faster, with less cost and with more accuracy. New genomic techniques are as safe as traditional breeding or old ways of genetic modification. NGTs are used in health biotechnology, industrial biotechnology and plant biotechnology, and they are rapidly replacing old cloning techniques.

Although in many cases it is impossible to distinguish NGT products from those developed through conventional breeding, the Court of Justice of the European Union clarified in 2018 that organisms from new mutagenesis techniques fall within the scope of the GMO Directive. For products of microbial fermentation, when NGTs are used in the development of the production organism, the GMO Directive would be applied if the final product contains viable cells of the genetically modified microorganism. Viable GMMs would thus count as deliberate release, meaning the intentional, uncontained introduction into the environment of a GMO.

Specific challenges for genetically modified microorganisms and their products

If it is not technologically feasible to purify the fermentation product from the DNA of the production strain, the product will fall under the Regulation on genetically modified food and feed. There is an EFSA GMO panel guidance on GMMs in foods from 2011, but all other necessary guidance documents thereafter have been written for genetically modified plants. With the increasing number of companies using microbial fermentation to produce foods, there is a need to develop proper guidance and regulatory pathways for GMMs, too.

Proposals for changes

On December 16 2025, the EU Commission proposed a new Biotech Act and changes to the Directive on deliberate release of GMOs into the environment. The 2025 proposal acknowledges that GMMs are significantly different from GM plants in their biology, applications, and regulatory needs. The proposal proposes tailored rules for GMMs, including adapted risk assessment for GMMs, unlimited validity of market consent for GMMs, introduction of “low-risk” GMMs with simplified authorisation and reduced post-market monitoring, and adapted detection method requirements. In addition, EFSA would be allowed to provide scientific advice to applicants, and regulatory sandboxes would be introduced for GMOs subject to authorisation under the GMO Directive 2001/18/EC, excluding genetically modified food and feed under Regulation (EC) No 1829/2003.

At the same time, simplification of legislation in the form of a Food and Feed Safety Simplification Package was also proposed by the Commission.

There is movement towards clarifying that fermentation products made with GMMs, where no viable cells are present, and reasonable efforts are made to minimise residues, may be explicitly excluded from the scope of Regulation 1829/2003. The proposal would rely on the processing aid status of the GMM, meaning that if DNA is merely a residue and not a safety concern, the product would not be considered genetically modified food/feed. This would harmonise the interpretation across Member States and reduce market fragmentation.

To clarify the concept of residues being “unintentional but technically unavoidable”, EFSA provided a technical report to assess the existing processes to remove recombinant DNA from fermentation products produced with GMMs. As a conclusion, EFSA could not determine a definitive list of purification steps or other processes and conditions that reliably remove the residual DNA from production GMMs in fermentation-derived products.

However, the final legal texts and implementation details are still pending. The scope and timelines for these changes are not yet fully clear. On the positive side, we support EFSA giving scientific advice to reduce the uncertainty related to specific requirements. We also welcome that fermentation products containing trace amounts of residual DNA from the production organism are excluded from Regulation 1829/2003, and the intent to introduce specific requirements for GMMs in Directive 2001/18. On the other hand, regulatory sandboxes should be allowed to novel foods, for the same reason as the Commission justifies not allowing them: regulatory sandboxes could alleviate ethical and cultural concerns regarding their acceptability.

Genetic modification and food products made with the help of new genomic techniques can make our foods safer, more abundant, and less demanding of resources. There is an ongoing discussion in the political sphere of what the actual risks are and hopefully regulators will abide by the findings of the scientific community. Biotechnology holds great potential to make global food systems more sustainable and further the objectives of the European Green Deal. Our work continues to advance science-based regulations that are proportionate to actual risks and designed to foster both innovation and safety.

Edit: This 2023 article was updated in January 2026 to include the recent changes to the EU's stance on genetically modified microorganisms (GMMs).