This study investigates the root microbiome of *Arabidopsis thaliana* by analyzing the bacterial 16S ribosomal RNA gene sequences from over 600 plants grown in two distinct soils. The researchers aimed to understand how the root microbiome is influenced by soil type and plant genotype. They found that the root microbiome is significantly influenced by soil type, with distinct communities in the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root). The endophytic compartment communities are enriched in Actinobacteria and specific families from other phyla, particularly Proteobacteria. Some bacteria vary between different developmental stages and genotypes. The study also identified a core endophytic compartment microbiome that is consistent across different soils and developmental stages. The findings provide insights into the assembly of the root microbiome and suggest that it may follow similar ecological principles to the mammalian microbiome, with core phyla providing broad metabolic potential and host-genotype-dependent associations contributing to specific functions.This study investigates the root microbiome of *Arabidopsis thaliana* by analyzing the bacterial 16S ribosomal RNA gene sequences from over 600 plants grown in two distinct soils. The researchers aimed to understand how the root microbiome is influenced by soil type and plant genotype. They found that the root microbiome is significantly influenced by soil type, with distinct communities in the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root). The endophytic compartment communities are enriched in Actinobacteria and specific families from other phyla, particularly Proteobacteria. Some bacteria vary between different developmental stages and genotypes. The study also identified a core endophytic compartment microbiome that is consistent across different soils and developmental stages. The findings provide insights into the assembly of the root microbiome and suggest that it may follow similar ecological principles to the mammalian microbiome, with core phyla providing broad metabolic potential and host-genotype-dependent associations contributing to specific functions.