Mean alpha-diversity indices and mean relative proportions of dominant phyla and genera (>3%) in decreasing order of abundance for ALL samples (NLRI+YLRI), patients with no lower respiratory infections (NLRI) and patients with lower respiratory infections (YLRI).

Linear mixed-effects (LME) models results are shown for alpha-diversity indices and taxa proportions, while permutational multivariate analysis of variance (adonis) results are shown for beta-diversity indices. Significance of LME models analyses was estimated using ANOVA type II or III with Satterthwaite approximation. For each test we report the relevant F statistic (F), degrees of freedom (DF) and significance (P(>F)). Significant associations are indicated in bold.