In nature, plants accommodate species-specific microbial communities on their roots that are crucial for host health, development, and protection against pathogens. We have shown in laboratory experiments with Arabidopsis thaliana and the legume Lotus japonicus, that these commensal bacteria exhibit host preference for the plant species from which they were isolated. To identify the molecular mechanisms and assembly dynamics of the root-associated host-specific microbiota, I am using synthetic bacterial communities, gnotobiotic microbiota reconstitution systems, and a combination of next generation sequencing, imaging, and metabolomics. This has relevant implications in sustainable agriculture for the design of stable beneficial field inocula.