The gut microbiota provides number of beneficial functions to its host, including nutrition, immune system regulation and niche protection against pathogens. In return, the host shapes the environment to ensure commensal bacteria provide benefit. To maintain this ecosystemic symbiotic interactions at the organ scale, a myriad of microscale interactions occurs, between bacteria, or between the host and the microbiota. To decipher these ecosystem-wide regulation mechanisms, data at different scale and resolution must be articulated. This project aims at building an appropriate multidisciplinary methodology enhancing data integration to identify new mechanisms involved in the gut microbiota homeostasis.