Fig. 4
Difference in nasopharyngeal microbial community composition between healthy and RSV-infected individuals is strongly characterized by an overrepresentation of Haemophilus. The strongest differentially abundant microbial taxa for healthy versus RSV-infected individuals are shown in a graphical Cytoscape visualization (a) [51]. Nodes represent taxa (node size represents average relative abundance (i.e., dominance) for both experimental groups combined); edges (dashed lines) link the different taxonomic levels. The weighed fold-change (node color) is calculated as the 2log of the ratio of the relative abundance between healthy and RSV (0 = no difference between disease state, 1 = twice as abundant in RSV, etc.). So, yellow to red indicates an overrepresentation during RSV infection, hence an underrepresentation in healthy infants and vice versa for light to dark blue. The significance (node border width) is expressed as the p value of a Mann–Whitney U test, FDR-corrected for multiple testing. The genus-level p values are listed on the right of the genera nodes. We observe a strong and significant overrepresentation of Haemophilus genus during RSV infection (p = 0.011) (b) and of Achromobacter (p = 0.001) (Additional file 2: Figure S4A). For recovery versus RSV samples, significance was determined using Wilcoxon signed rank test