Table 2. 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.

Taxon	ALL	NLRI	YLRI	F	DF	P(>F)
Alpha-diversity
ACE	75.1	64.1	87.1	6.61	39	0.017
Fisher	8.7	7.1	10.4	6.22	40	0.014
PD	6.7	5.9	7.5	9.74	40	0.003
Shannon	2.1	2.0	2.1	0.20	40	0.655
Beta-diversity
Unifrac-unw				2.75	2	0.023
Unifrac-w				7.85	2	0.006
Bray-Curtis				3.40	2	0.011
Jaccard				2.46	2	0.018
Phyla
Proteobacteria	48.8	47.1	50.5	1.28	41	0.265
Firmicutes	26.5	28.7	24.1	1.22	41	0.277
Bacteroidetes	12.5	10.6	14.5	1.11	38	0.298
Actinobacteria	8.3	9.1	7.5	2.02	42	0.163
Fusobacteria	3.2	3.5	2.9	0.65	45	0.424
Genus
Streptococcus	16.5	16.7	16.2	0.69	36	0.411
Neisseria	11.0	9.1	13.6	2.13	37	0.153
Haemophilus	8.7	5.9	11.5	4.13	37	0.009
Moraxella	8.1	9.1	7.0	1.85	36	0.171
Pseudomonas	7.8	9.0	6.5	3.70	40	0.025
Corynebacterium	6.6	7.4	5.6	3.46	41	0.034
Staphylococcus	4.4	6.0	2.7	1.72	34	0.199
Acinetobacter	3.3	4.9	1.5	3.21	37	0.030
Prevotella	3.0	2.6	3.3	0.11	35	0.746
Stenotrophomonas	3.0	2.6	3.5	0.07	37	0.797