November 4, 2025 — On November 4, 2025, the European Food Safety Authority (EFSA) officially released its updated Guidance on the Characterisation of Microorganisms Used in the Food and Feed Chain. This new guidance consolidates and replaces several previous documents, providing a unified framework for the safety assessment of all products containing or produced by microorganisms (including non-GM microorganisms) that require pre-market evaluation within the EU.

Expanded Scope, Including New Microbial Categories

The updated guidelines now cover a broader range of microorganisms, including bacteria, fungi, yeasts, microalgae, protozoa, and viruses (including bacteriophages). This marks the first time that viruses and microalgae are included in EFSA's risk assessment framework, with clear requirements for their characterisation and evaluation.

Enhanced Microbial Characterisation: Whole Genome Sequencing Required

The new guidelines impose strict requirements for microbial identification:

• Bacteria, yeasts, filamentous fungi, and viruses must be identified using whole genome sequencing at both species and strain levels.
• For microalgae and protozoa, identification should combine morphological features with multi-gene marker sequences.
• The guidelines emphasize distinguishing between intrinsic antimicrobial resistance and acquired resistance, and the presence of transferable acquired resistance genes constitutes a safety concern.

Clarification of Product Composition and Risk Assessment Boundaries

The guidelines also provide clear boundaries for assessing the microbial composition of end products:

• Live microorganism products (such as biomass) require a full risk assessment.
• If the product is produced by microorganisms but contains no live cells (e.g., purified fermentation products), the risk assessment focuses on the final product itself.
• For non-living microbial products, it must be demonstrated that they do not contain viable cells or transferable DNA.

Expanded Environmental Risk Assessment to All Relevant Microorganisms

The new guidelines require environmental risk assessments for all microorganisms that may be directly exposed to the environment, including non-GMO microorganisms. These assessments should evaluate the microorganism's survival, reproductive capacity, gene transfer potential, and its potential impact on plants, animals, and ecological processes.

Simplified Assessment Pathway for "Non-concern" Microorganisms

Microorganisms meeting the following criteria may be considered safe and eligible for a simplified assessment pathway:

• Species listed on EFSA's “Presumed Safe” list with no acquired resistance genes.
• The final product contains no detectable live microorganisms or recombinant DNA.
• The microorganisms are non-pathogenic, do not produce toxins, and have no adverse environmental impact.

Implementation Timeline and Industry Impact

The guidelines are effective immediately upon their publication on November 4, 2025. They are expected to have a significant impact on the development and approval processes for food enzymes, novel foods, feed additives, and plant protection products. Affected companies must adjust their research and registration strategies promptly to meet the new data requirements and avoid delays in market access.

Source

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9705