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Biofertilizers supply living microorganisms to help plants grow and maintain their health. In this study, we examine the microbiome composition of a commercial biofertilizer that has been proven to promote plant growth. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of the biofertilizer, with 182 fungal species and 964 bacterial genera identified. The biofertilizer contains a variety of microorganisms that had been reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. However, preserving the fungal-inoculated substrate is crucial to maintain fungal diversity in the root fraction. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings indicate that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth.