Plant growth-promoting rhizobacteria (PGPRs) are bacteria that colonize the plant roots. These beneficial bacteria have an influence on plant development through multiple mechanisms, such as nutrient availability, alleviating biotic and abiotic stress, and secrete phytohormones. Therefore, their inoculation constitutes a powerful tool towards sustainable agriculture and crop production. To understand plant-PGPRs interaction we present the classification of PGPR using machine learning and meta-learning classifiers namely Support Vector Machine (SVM), Kernel Logistic Regression (KLR), meta-SVM and meta-KLR to predict the presence ofBacillus megateriuminoculated in tomato root tissues using publicly available transcriptomic data. The original dataset presents 36 significantly differentially expressed genes. As the meta-KLR achieved near-optimal performance considering all the relevant metrics, this meta learner was afterwards used to identify the informative genes (IGs). The outcomes showed 157 IGs, being present all significantly differentially expressed genes previously identified. Among the IGs, 113 were identified as tomato genes, 5 asBacillus subtilisproteins, 1 asEscherichia coliprotein and 6 were unidentified. Then, a functional enrichment analysis of the tomato IGs showed 175 biological processes, 22 molecular functions and 20 KEGG pathways involved inB. megaterium–tomato interaction. Furthermore, the biological networks study of theirArabidopsis thalianaorthologous genes identified the co-expression, predicted interaction, shared protein domains and co-localization networks.Supplementary InformationThe online version contains supplementary material available at 10.1007/s13205-023-03690-0.