The study by Bulgarelli et al. investigates the microbial communities in the roots and rhizosphere of wild and domesticated barley (Hordeum vulgare). Using 16S rRNA gene profiling and shotgun metagenome analysis, the authors found that a small number of bacterial families, such as Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae, dominate the root-enriched barley microbiota. Host genotype has a minor but significant effect on the diversity of root-associated bacterial communities, possibly reflecting the footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Additionally, genes mediating host, bacteria, and phage interactions show signs of positive selection, indicating co-evolution between the plant and its microbiota. The study highlights that the combined action of microbe-microbe and host-microbe interactions drives the establishment of the root microbiota through physiological processes at the root-soil interface.The study by Bulgarelli et al. investigates the microbial communities in the roots and rhizosphere of wild and domesticated barley (Hordeum vulgare). Using 16S rRNA gene profiling and shotgun metagenome analysis, the authors found that a small number of bacterial families, such as Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae, dominate the root-enriched barley microbiota. Host genotype has a minor but significant effect on the diversity of root-associated bacterial communities, possibly reflecting the footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Additionally, genes mediating host, bacteria, and phage interactions show signs of positive selection, indicating co-evolution between the plant and its microbiota. The study highlights that the combined action of microbe-microbe and host-microbe interactions drives the establishment of the root microbiota through physiological processes at the root-soil interface.