On November 4 2025, the European Food Safety Authority (EFSA) published the “Guidance on the characterisations of microorganisms in support of the risk assessment of products used in the food chain” (EFSA Journal 2025;23(11):9705).

Scope and Application

The Guidance defines the criteria and methods for characterising microorganisms and is designed to support applicants in preparing the risk assessment dossier whenever a product:

• contains live or inactivated microorganisms,
• is constituted by microorganisms;
• is produced by microorganisms (genetically modified or not), for example, via fermentation.

The document focuses primarily on the initial phase of risk assessment – characterisation and hazard identification– providing detailed instructions on which data to generate, the correct methodologies for interpretation.

Relevance for Novel Food applications

For operators developing Novel Foods involving microorganisms or microbial processes, this Guidance represents a key reference that must be applied in conjunction with the existing Novel Food regulatory framework to ensure a successful submission,

In Novel Food applications (Reg. EU 2015/2283), the microorganisms represent:

• the Novel Food itself,
• an ingredient intentionally present in the final product (e.g. probiotics), or
• a production strain used to obtain food or ingredients.

Unlike other regulatory areas, Novel Food applications have historically relied on case-by-case scientific justifications, with limited harmonisation of methodological expectations.

The 2025 Guidance effectively marks a transition towards a harmonized and structured framework that EFSA will now apply to ensure consistency across all food domains. Consequently, any incomplete or inaccurate characterisation now fundamentally compromises the entire risk assessment process.

Key Points
The guidance places the genomic approach at the center as the preferred tool for risk identification

1.WGS (Whole Genome Sequencing) as the central tool
WGS is now the reference method for strain-level characterisation of bacteria, yeasts, filamentous fungi and viruses. It is used to confirm identity and screen for traits of concern such as toxins or virulence factors.

2.Antimicrobial resistance (AMR): a genomic – first approach
AMR assessment follows a “Genomics‑First” workflow: a bioinformatic screen of WGS data identifies resistance genes; if acquired genes are detected, complementary phenotypic evidence (e.g., MIC) is required.

3.Strict purity for production strains
For strains used in fermentation but not present in the final product, applicants must demonstrate the absence of viable cells (testing at least 9 samples from 3 independent batches) and assess residual DNA via sensitive molecular assays (PCR) according to matrix‑specific criteria

What to do now

The Guidance sets the scientific standard EFSA follows when reviewing dossiers.
To ensure a successful evaluation process, applicants should consider the following:

• Assess compliance: non-alignment with these recommendations carries a high risk of “clock-stops” or formal rejection during the suitability check.
• Review legacy data: dossiers developed using older characterisation approaches may require revision or data integration to meet the new requirements.
• Strategic integration: early inclusion of these scientific expectations into development and regulatory planning is essential for a robust and efficient submission.

>>> Complife Group supports applicants through integrated regulatory consulting, scientific support and testing activities, assisting in the alignment of Novel Food dossiers involving microorganisms with the expectations outlined in the 2025 EFSA Guidance.

 

Reference:

Guidance on the characterisation of microorganisms in support of the risk assessment of products used in the food chain.”