Fig. 2
Microbial colonization of epithelium resulted in gene expression changes that were not phylogenetically conserved. A Phylogenetic tree of microbes used to colonize ALIs. Heatmap of log2 fold change (FC) of A549 epithelial cell IL-8 secretion following exposure to microbial supernatants, relative to vehicle. Grey indicates IL-8 was not measured. B Schematic of the RNA-seq experiment. C PCA plot of genome-wide transcriptional responses of ALIs colonized for 18 h (“x”) or 48 h (“o”) relative to vehicle. Dots were colored based on phylum/genera. D Upset plot of significantly (FDR adjusted P-value < 0.05) differentially expressed genes (DEGs) of ALIs separated by timepoint. Set size indicated total number of up- or downregulated DEGs per timepoint. X-axis was sorted by decreasing set size. Colored dots indicated the timepoints included in the intersection size (number of DEGs). Lines connected the colored dots when the DEGs were shared. E Gene set enrichment analysis of upregulated DEGs. The 20 gene sets with the highest gene ratio (percent of genes within the gene set that were significantly upregulated) from all microbial treatments combined were identified and plotted by timepoint. The size of the dot represented the number of microbial treatments for which that gene set was significantly enriched when examining the microbial treatments separately. The color of the dot represented the FDR adjusted P-value. F Upset plot of DEGs after colonization for 48 h separated by phylum/genus, as described in D. G Gene set enrichment analysis of statistically significant upregulated DEGs at 48 h, separated by phylum/genus. Shown were the 20 gene sets upregulated by the most microbial treatments. “Total” gene set showed the total number of microbial treatments per phylogenetic category. The x-axis represented the number of microbial treatments that were significantly upregulated in each gene set, and the bar was colored based on the number of treatments from each phylogenetic category. Gene sets were colored based on general function