Humans are vessels for thousands of microbial species, and the same is true for higher plants. These microbes have the potential to profoundly impact the health of their hosts, raising the tantalizing possibility that hosts control the structure of resident microbial communities. We use GWAS mapping to determine the host factors that shape microbial communities growing within Arabidopsis thaliana, and use controlled experiments to test the importance of candidate host factors in shaping these microbial communities. We also explore species interactions with the aim of understanding community assembly across host genotypes. Ultimately, our goal is to enhance plant resistance by identifying conditions that favor protective microbes.