It has been shown that bacterial communities in the rhizosphere of crops have profound influence on plant performance including productivity, pathogen resistance, and nutrient and heavy metal uptake. Due to cadmium (Cd) contamination in agricultural lands, understanding the mechanisms underlying the dynamics of bacterial communities under Cd stress is essential to achieve sustainable agroecosystems. However, the composition of soil bacterial communities co-shaped by plant species and soil properties including Cd concentration is still obscure. The high complexity of the communities is a challenge for studying the mechanisms of community dynamics. The present study is to identify representative and culturable bacterial communities associated with rice roots under Cd stress using the newly developed gnotobiotic system. Bacterial assemblages in paddy soil will be collected and the culturable members will be obtained through host-mediated selection under Cd stress simulating the actual Cd concentration in paddy fields. It is expected that the obtained simplified, culturable and repeatable bacterial community shall facilitate future studies on the detailed experiments to define the mechanisms underlying the dynamics of community assemblages and the beneficial effects of such microbiomes on rice.