This proposal mainly aims to share scientific evidence‐based knowledge, data and methods relevant for risk assessment to account for effects on/by gut microbiomes in humans and domestic animals. In addition, where current evidence may not be existing or not sufficient, this proposal includes several experimental case‐studies and trials focused on: i) the ability of prebiotics for human gut modulation; ii) the metabolic capacity of human gut microbiota in relation to dietary threads (food allergens); iii) the effects of feed additives on the poultry and pig gut microbiome in relation with Campylobacter and Salmonella and welfare/health indicators. The ultimate goal will be to delineate a roadmap to advance research to address specific risk assessment needs. This proposal will provide a unique opportunity for experts on a wide range of disciplines (i.e., bibliometrics and science analysis, microbiology, food science and technology, analytical chemistry, bioinformatics, genomics, transcriptomics, metabolomics, systems biology, food allergy, immunology, food safety, animal health and welfare, and human and animal gut microbiota) to collaborate and foster mutual understanding on their respective expertise and risk evaluations. The international consortium of this proposal is formed by 22 researchers and 8 technicians belonging to two public institutions (CSIC and ANSES) and whose technical and financial involvement is fully in line with EFSA’s requirements for the above referenced LOT.