In the era of metagenomics, more and more studies consider ecosystems rather than individual organisms to elucidate biological mechanisms. This enabled to associate two previously independent research fields: genomics and ecology. A host organism can be highly dependent on its microbial environment and new methods are needed to decipher the interactions occurring at this level. The microbiome is an interesting support from the ecological and evolutionary point of view as it may impact the growth ability, the fitness and even the survival of the host. Theories about holobionts suggest that the microbiome is faster to adapt than the host, further emphasizing the need to focus on this cornerstone of ecosystems studies. A major concern is to understand the reasons determining the diversity of the communities as well as the mechanisms underlying the general ecosystem functionalities. Here we focus on Ectocarpus subulatus str. BFT along with its bacterial community. Multi-omics studies were performed to gain better insights into the organization of the holobiont. Functional annotation, metabolic network modeling and biological pathway completion inform on potential interaction mechanisms at the metabolic scale. The hypothesis according to which microbial communities gather preferentially in order to optimize functional complementarity can explain the metabolic richness and diversity of the microbiome observed in the algal holobiont.