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<div>The recognition of conserved Pathogen-Associated Molecular Patterns (PAMPs), such as bacterial flagellin, by Pattern Recognition Receptor (PRRs) membrane proteins activates an immune response that confers broad defense against many microbes. When pre-induced, PAMP triggered immunity (PTI) restricts the growth of pathogenic bacteria such as <i>Pseudomonas syingae</i> pv. <i>tomato</i> (<i>Pto</i>) in the apoplastic space. Although the plant cellular processes involved in flagellin/FLS2 signaling have been well studied, the mechanisms by which PTI suppresses further colonization of the apoplastic space by <i>Pto</i> are poorly understood. The objective of this study is to use <i>Pto</i> as a probe to better understand the mechanism(s) of PTI. <i> Pto </i>was exposed to pre-induced immune activated (Flg22) and naïve (Mock) <i>Arabidopsis</i> leaves for 1, 3, and 5 hours before extraction using a newly developed method to access the <i>Pto </i>transcriptome <i>in planta</i>. Principal component analysis of transcriptome profiles between treatments show separation of Flg22 and Mock samples after one hour of exposure. Differential expression of genes in <i>Pto</i> exposed to these two conditions reveal that virulence genes and sugar metabolism are downregulated whereas chemotaxis, motility, and nutrient uptake are upregulated by exposure to immune defenses. Expression profile of <i>Pto</i> exposed to immune defenses is suggestive of entering stationary phase with consistent levels of expression for major cellular processes.</div>