Understanding how plants distinguish between commensal and pathogenic microorganisms is one of the major challenges in the plant microbe interaction research. We previously identified a gene encoding CYP71A27 connected to camalexin, which is necessary for a plant growth promoting (PGP) activity of a number of bacterial strains. To dissect its function, we compared multilevel responses in roots of wild type Arabidopsis and the cyp71A27 mutant to two bacterial strains, a PGP Pseudomonas fluorescens CH267 and a pathogen Burkholderia glumeae PG1. We showed that the pathogen induces a greater reprogramming of the transcriptome, proteome, and metabolome than the PGP strain.