Fig. 3

Network analysis of interactions between host gene expression, bacterial taxa, bacterial (metatranscriptome) gene expression, and antibiotic resistance. The modules indicated by blue triangles are co-expressed gene clusters in response to influenza virus infection. Direct and indirect interactions between the modules, antibiotic resistance (green diamonds), microbiome expressed functions (orange hexagons), and bacterial families (light blue squares) were identified by correlation analysis. The red edges indicate positive correlations and the grey dashed edges indicate negative correlations. The host modules and the pathways enriched with the genes in the modules are listed. Only the host modules with significantly enriched pathways are shown in the table. o_, p_, f_, and g_ indicate whether the taxonomic assignment was made at the order, phylum, family, or genus level, respectively