Barley root microbiota is dominated by a small number of bacterial families, including Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae. Host genotype influences the diversity of root-associated bacterial communities, possibly reflecting the effects of barley domestication. Functional traits relevant to host interactions are enriched in root-associated taxa, and genes involved in host, bacteria, and phage interactions show signs of positive selection. Microbial communities in the root interior and surrounding soil contribute to plant growth. The study used 16S rRNA gene profiling and shotgun metagenome analysis to investigate the structure and function of the barley root microbiota in wild and domesticated accessions. The results indicate that the combined action of microbiome-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface. The structure of the barley bacterial microbiota is dominated by Actinobacteria, Bacteroidetes, and Proteobacteria. The rhizosphere and root microbiota show distinct community compositions, with the rhizosphere being more enriched in certain bacterial families. The study also found that the host genotype has a small but significant effect on the diversity of root-associated bacterial communities. Functional analysis revealed that traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. The study also identified positive selection in proteins involved in these traits. The results suggest that the barley rhizosphere and root are two microhabitats colonized by communities with taxonomically distinct profiles, which emerge from the soil biota through progressive differentiation. The study also found that the root microbiota of the model plant Arabidopsis thaliana is dominated by members of Actinobacteria, Bacteroidetes, and Proteobacteria. The study compared the bacterial microbiota of barley and Arabidopsis and found similar taxonomic compositions. The study also found that the root microbiota of barley is enriched in certain bacterial families, such as Microbacteriaceae. The study also identified positive selection in proteins involved in pathogen-host interactions, including bacterial secretion and phage defense. The study found that the T3SS, a system used by bacteria to suppress plant immune responses, is under positive selection in the barley rhizosphere. The study also found that the T6SS, a contact-dependent transport system mediating microbe-microbe interactions, is under positive selection. The study also identified positive selection in proteins involved in plant immunity, including elicitors and effectors. The study found that the CRISPR system, which provides protection against phages in bacteria and archaea, is under positive selection in the barley rhizosphere. The study also found that the host genotype has a small but significant effect on the diversity of root-associated bacterial communities. The study suggests that the host innate immune system and the supply and demand of functions of root metabolism are relevant host factors for bacterialBarley root microbiota is dominated by a small number of bacterial families, including Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae. Host genotype influences the diversity of root-associated bacterial communities, possibly reflecting the effects of barley domestication. Functional traits relevant to host interactions are enriched in root-associated taxa, and genes involved in host, bacteria, and phage interactions show signs of positive selection. Microbial communities in the root interior and surrounding soil contribute to plant growth. The study used 16S rRNA gene profiling and shotgun metagenome analysis to investigate the structure and function of the barley root microbiota in wild and domesticated accessions. The results indicate that the combined action of microbiome-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface. The structure of the barley bacterial microbiota is dominated by Actinobacteria, Bacteroidetes, and Proteobacteria. The rhizosphere and root microbiota show distinct community compositions, with the rhizosphere being more enriched in certain bacterial families. The study also found that the host genotype has a small but significant effect on the diversity of root-associated bacterial communities. Functional analysis revealed that traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. The study also identified positive selection in proteins involved in these traits. The results suggest that the barley rhizosphere and root are two microhabitats colonized by communities with taxonomically distinct profiles, which emerge from the soil biota through progressive differentiation. The study also found that the root microbiota of the model plant Arabidopsis thaliana is dominated by members of Actinobacteria, Bacteroidetes, and Proteobacteria. The study compared the bacterial microbiota of barley and Arabidopsis and found similar taxonomic compositions. The study also found that the root microbiota of barley is enriched in certain bacterial families, such as Microbacteriaceae. The study also identified positive selection in proteins involved in pathogen-host interactions, including bacterial secretion and phage defense. The study found that the T3SS, a system used by bacteria to suppress plant immune responses, is under positive selection in the barley rhizosphere. The study also found that the T6SS, a contact-dependent transport system mediating microbe-microbe interactions, is under positive selection. The study also identified positive selection in proteins involved in plant immunity, including elicitors and effectors. The study found that the CRISPR system, which provides protection against phages in bacteria and archaea, is under positive selection in the barley rhizosphere. The study also found that the host genotype has a small but significant effect on the diversity of root-associated bacterial communities. The study suggests that the host innate immune system and the supply and demand of functions of root metabolism are relevant host factors for bacterial