Figure 3
(A) Venn Diagram of shared and unique KEGG Orthology terms between in vitro (+FUdR) and host-associated E. coli. Counts of KEGG orthologies (KOs) identified within at least one host-associated E. coli or in vitro sample exclusively were quantified to compare shared and unique functional gene counts between the two sample groups. A total of 110 genes were expressed exclusively within host-associated samples, whereas 83 were exclusive to in vitro samples. Over 2500 shared genes were expressed by at least one sample within each group. (B) Significantly differential KEGG orthologies identified between pairwise comparisons of host-associated and in vitro samples mapped to iPath bacterial chemotaxis and fatty acid biosynthesis, elongation and degradation pathways. iPath plots provide a comprehensive overview of the summarized function of significantly differential functional genes between in vitro and host-associated samples. Here, significantly differential KEGG orthologies were mapped onto the KEGG reference Metabolic Pathway map. Regions of the reference pathway highlighted in red are upregulated within in vitro samples, whereas pathways highlighted in blue are increased in expression within host-associated samples. Grey regions are not significantly differential between the two conditions. E. coli upregulation (LDA > 0.5, P < 0.05) of genes related to fatty acid biosynthesis were observed within in vitro samples in comparison to host-associated samples, whereas fatty acid elongation and degradation genes were identified to be overexpressed within host-associated samples. Conserved enrichment of bacterial chemotaxis genes were observed within host-associated samples when compared to in vitro counterparts.
