New EFSA Guidance for microorganisms (2025) : What changes and how GenoScreen help you stay fully compliant
Following its agenda to regulate the Food and Feed industry with up-to-date regulatory texts, the EFSA significantly raised the technical expectations for the characterisation and risk assessment of microorganisms used in food and feed. As of November 4th, 2025, dossiers that rely on outdated genomic analysis, incomplete resistance screening or legacy databases may no longer meet regulatory expectations.
At GenoScreen, we have been supporting industrial stakeholders and regulatory teams in generating regulatory-grade genomic data and building EFSA-compliant dossiers. Our experts actively monitor regulatory updates, enabling us to provide immediate and reliable interpretation of new requirements.
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What are the new features of the EFSA 2025 guide for microorganisms in the food chain?
EFSA 2025: Harmonization of regulations and new categories of microorganisms
This new version makes significant changes in EFSA regulation.
First, it unifies several individual regulations, that is, it brings in one guidance those of the Food Enzymes, the Feed Additives and the Novel Food. By unifying the guidances, it homogenises the analyses needed for the characterisation and risk assessment of microorganisms used in the food (and feed) chain.
This new version, also widen the use cases of microorganisms in food/feed processes by adding the case of “Active Agent”, GM or non-GM microorganisms capable of multiplications used directly in (or as) the product.
Another great feature in this guidance, is the consideration of microalgae, protists and bacteriophages, which increase the categories of microorganisms used in Food/Feed processes. It surely will affect positively the respective markets of Food Enzymes, Feed Additives and Novel Food.
Strengthening microbial risk assessment standards
This Guidance also increase its standards in matters of risk assessment, by including new resistance tests, as antifungal ones. It also increases the specificity of outcomes. The Guidance on the characterisation of microorganisms applies to Plant Protection Products (PPPs) in a supplementary capacity. For products under the PPP Regulation, the risk assessment is conducted by the Member States and EFSA according to the relevant, existing regulatory framework. In this context, the new guidance covers the scientific requirements supporting the characterisation of the microorganism (specifically sections “Characterisation of the Microorganism” and “Presence of viable cells and DNA in the final product”), and should be considered in addition to other existing PPP guidance documents.
How GenoScreen helps you stay compliant with the new update?
Our analysis and bioinformatics pipelines have already been fully updated to meet these new requirements, ensuring immediate compliance and optimal support for the new regulatory framework.
What are the key differences between the EFSA 2025 Guidance and the previous version?
Scope of microoraganisms
Scope of microoraganisms
2025 Guidance
Explicitly includes bacteriophages, microalgae, protists, viruses.
Old Guidance
Applies to bacteria, yeasts, filamentous fungi, and the products derived from them.
Antimicrobial Resistance (AMR) and antifungal resistance
Antimicrobial Resistance (AMR) and antifungal resistance
2025 Guidance
Explicit discrimination between intrinsic vs acquired resistance; applies to bacteria and bacteriophage hosts.
Introduces antifungal resistance testing for yeasts/fungi.
Old Guidance
AMR genes inquired only for bacteria.
Antifungal resistance not investigated.
Production of Antimicrobial Substances
Production of Antimicrobial Substances
2025 Guidance
Explicit WGS + phenotypic screening for production of antimicrobial compounds.
Systematically assessed for active agents, biomasses, and production strains.
Old Guidance
Less detailed; focused mainly phenotypic screening for antimicrobial production by the organism.
Not systematically addressed across all microorganisms.
Toxigenicity and Pathogenicity
Toxigenicity and Pathogenicity
2025 Guidance
Requires WGS-based screening for virulence genes + supporting literature and phenotypic tests (e.g., cytotoxicity tests, toxin assays).
Studies extended to other types of microorganisms, with some species-specific extra-care testing frameworks (e.g., Enterococcus faecium vs lactis, Bacillus cereus group.
Old Guidance
Literature review + phenotypic testing for known toxins/pathogenicity; WGS is not systematically required.
Special attention on species from Bacillus and Enterococcus species; applied generic screening elsewhere.
Genetic Modification
Genetic Modification
2025 Guidance
Add the possibility to have GMM strains as active agents.
Explicitly extends to GM viruses (phages), GM microalgae, synthetic biology constructs.
Old Guidance
Active agent could not be GMM.
Focused mainly on GM bacteria, yeasts, fungi.
Presence of Viable Cells and DNA
Presence of Viable Cells and DNA
2025 Guidance
Introduces extended sampling protocol and explicit spiking/recovery controls. Much more detailed procedural requirements to ensure reproducibility and sensitivity.
Old Guidance
Less prescriptive on protocols.
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What does it mean for your activity if nothing is updated ?
If dossiers are submitted under the previous framework without the new required analyses and justification, the risks are clear:
• immediate dossier rejection or suspension
• mandatory resubmission with new genomic and analytical data
• loss of several months of market access, delaying product launch
• significantly higher costs when issues are discovered after submission rather than before
How to make your microbial product EFSA-compliant in 2025?
The regulatory landscape has changed — and industrial players developing microbial products now need deeper and more structured genomic justification than ever, but with the right partner, regulatory compliance becomes a competitive advantage.
GenoScreen helps you:
• update and strengthen existing EFSA dossiers
• generate regulatory-grade genomic data suitable for submission
• validate or upgrade internal pipelines to make them EFSA-proof
• anticipate reviewer questions and avoid costly delays at the submission stage
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