Michoacan state has a long history in plant domestication’s. Physalis ixocarpa is a native plant that growth associated to corn crops from this region. Such plants have similar fruits to Physalis philadelphica (husk tomate). Due to the domestication process includes the adaptation to environmental factors, we ask if 1) Does P. ixocarpa has the capacity of association with bacterial communities of the zone where it was domesticated?, and 2) Does the rhizobiome of this plant can increase the potential functions in the soil?. An experiment was established in a traditional milpa system. Samples of rhizobiome from corn, P. ixocarpa, P. philadelphica, and soil were sequenced using Next Generation Sequencing in the region 16S. The potential function, metabolic pathway reconstruction and participation of each bacteria genus was inferred using iVikodak platform. A total of 34 Phyla and 795 genera were identified. Purine metabolism's was the principal function, where all rizhobiomes showed similar metabolic pathways. However, the difference among plant species is the participation of the distinct genera in the purine metabolism. We conclude that rhizobiome of P. ixocarpa shows complementarity for the soil functions, and their utilization can be helpful in zones where the agricultural practices have degraded microbiological soil conditions.