Fig. 3

Significant associations between nasal microbiome taxonomic and functional composition and subject phenotypes in feature-wise testing. Significant associations (q < 0.25) between individual taxonomic and functional features and phenotypic covariates using a MaAsLin multivariable linear model. a Of note, first attendance at daycare (during the preceding month) was an extremely strong determinant of initial microbiome colonization by several taxa (M. catarrhalis, H. influenzae), and the nasal microbiome exhibited a much weaker time dependence than does the gut during infant development (i.e., few taxa were consistently temporally variable between months 0 and 12). The presence of a number of oral-associated species (i.e., Streptococcus and Veillonella species) was a mild correlate of S. aureus gain. S. aureus relative abundance was included as a positive control. b After applying a species dominance filter, we found the association of many gene families (grouped by Enzyme Commission (EC) number) in infants with daycare attendance, while many functions in mothers were associated with time and infant “ever” acquisition of S. aureus