Updates brought by the new Guidance on the characterisation and risk assessment of microorganisms used in the food chain

Following its agenda to regulate the Food and Feed industry with up-to-date regulatory texts, the EFSA published this 4^th November 2025 an update on the guidance on the characterisation and risk assessment of microorganisms used in the food chain. This text aims to follow the industrial mutations and their new research and development advances, but also the state of the art of scientific technics and the new safety discoveries.

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.