The data in this project is part of CIRCLES: Controlling mIcRobiomes CircuLations for bEtter food Systems. CIRCLES is a European Union Horizon 2020 research and innovation programme-funded project. It aims to unlock the potential of natural microbiomes for the sustainable production of high-quality food, with the ultimate objective of delivering new and healthier food applications. The data in this project was collected from Atlantic salmon, both farmed and wild, across different tissues and developmental stages. The microbiomes and resistomes from the samples have been used as a reference for interpreting microbiome data from farmed specimens, as well as for developing microbiome-tailored “circular” actions. CIRCLES has modeled the link between fish production in open-sea cages and marine environmental quality, with a focus on the marine microbiome and resistome.