Fig. 4: Gene and metabolite abundance during airway epithelial development.

a Global gene expression was measured 7 times over 28 days in an air-liquid model of epithelial differentiation (monolayer to ciliated epithelium). A total of 2,553 transcripts, summarised by 8 core temporal profiles, showed significant variation in abundance during mucociliary development. Hallmark functional roles are shown for each cluster. Clusters CL2, CL3, CL4 and CL5 show late peaks of expression and contain genes that can interact with the microbiome. Upregulated chemokines and immune-function genes are also noted within the clusters. b Metabolites (square) measured in the supernatant of the fully differentiated airway cells were linked to genes (circle) identified in bacterial isolates. Arrows indicate if the reactions were reversible or irreversible, with metabolites as substrates and products. These networks were built based on KEGG pathways. c Binary heatmap displaying the presence (1) or absence (0) of genes (columns) identified in the genomic sequences of bacterial isolates (rows). Bacterial isolates are organised into Kegg Ontology phylogeny clusters (see Fig. 2). Gene annotations (top) indicate the frequency of the gene: ‘frequent’ for genes in >75% of isolates, ‘intermediate’ for genes in 25–75% of isolates and ‘rare’ for those in <25% of isolates.