Integration of microbiome aspects in food and feed safety risk assessment: regulatory readiness, methodological and data gaps, and stakeholder perspectives

The integration of microbiome science into food and feed safety risk assessment marks a critical regulatory turning point. Long perceived as passive, the gut microbiome is now understood as a metabolically active organ influencing host immunity, nutrient metabolism, and neurological functions. It interacts dynamically with xenobiotics such as food additives, contaminants, and pesticides, altering their toxicity and bioavailability through microbial metabolism—sometimes detoxifying, but in other cases generating harmful metabolites. This challenges conventional toxicology models and demands a paradigm shift from host-centric to host–microbiome integrated assessments. Mounting scientific evidence, such as EFSA’s review of glyphosate and concerns regarding emulsifiers and sweeteners, highlights microbiome effects but exposes the absence of validated regulatory guidelines. At the same time, the EU’s Food 2030 strategy identifies “The Microbiome World” as a priority pathway to achieve nutrition, sustainability, and resilience goals, reinforcing a top-down mandate to strengthen EFSA’s capacity to assess these interactions in line with the European Green Deal and Farm to Fork Strategy. This deep dive maps the regulatory, scientific, and stakeholder landscape, addressing gaps in methodological standardisation, data harmonisation, and multi-actor convergence, and offers strategic insight to support the adoption of microbiome-informed regulatory frameworks.