The internship project will aim at identifying micro-organisms fluxes between ecosystems. This work is a part of the TANDEM project, which is an INRAE flagship project that gathers 10 teams. It aims to better understand micro-organisms fluxes in an agri-food cheese production chain. Metagenomic samples have been collected from 10 compartments, from grass to cheese through milk, cow bedding, rumen... Our idea is to identify species present in metagenomic samples and detect if some strains are shared between samples, to infer flows between the various compartments.