ABSTRACT: Escherichia coli is a diverse species, ranging from commensal strains that are part of the gut microbiome, to virulent strains that cause a variety of different infections. Much of this genomic diversity is attributable to horizontally-acquired elements, including bacteriophages. RNA sequencing has helped to reveal how pathogenic and laboratory-adapted strains respond to the gut environment, but relatively few studies have been conducted in commensal strains. Further, traditional transcriptomic data analysis techniques are not tailored to capture changes in horizontally-acquired elements, leaving them relatively understudied. Here we performed RNA sequencing on commensal E. coli MP1, which was recently isolated from mice. We analyzed the transcriptomes of MP1 grown in standard laboratory conditions or in simulated intestinal fluid (SIF), in strains that either carry or lack the vB_EcoP_Kapi1 prophage. We find that both lysogeny and growth media cause broad transcriptional changes in MP1, with growth media playing a larger role. Functional enrichment analysis revealed up-regulation of aerobic respiration, purine biosynthesis, and xenobiotic export, and down-regulation of flagellar motility and chemotaxis, acid stress response, fatty acid beta oxidation, and transport processes in SIF. In Kapi1 lysogens, transport processes were also down-regulated. Hypothesizing that horizontally-acquired genes may have been missed by traditional functional enrichment analyses, we next performed an in-depth analysis of these elements. Some genes on all identified elements were expressed, and many were differentially expressed; sugar uptake and contact-dependent inhibition systems were down-regulated in SIF, while the pathogenicity island PAI-X and multiple dynamin family proteins were strongly up-regulated in Kapi1 lysogens. Finally, we analyzed the Kapi1 transcriptome, revealing expression of λ-like regulatory genes and a putative novel accessory gene during lysogeny. Our results demonstrate that growth media and lysogeny have profound impacts on the host transcriptome. Many of the processes differentially regulated in SIF have been previously shown to be differentially regulated in the gut. In Kapi1 lysogens, the only genes consistently up-regulated were encoded by horizontally-acquired elements, suggesting cross-talk. Importantly, these genes were completely missed in traditional functional enrichment analyses, highlighting a significant gap in our knowledge of the transcriptional landscape of horizontally-acquired elements.
