Table 1.

Mean alpha-diversity indices, beta-diversity indices, and mean relative proportions of dominant genera (>3%) in decreasing order of abundance in a cohort of 20 patients with a tracheostomy

	Total	D0	D1	W1	W2	W3	W4	F	DF	P(>F)
Alpha-diversity index
ACE	76.7	87.4	65.9	86.3	71.3	77.0	71.5	0.6	78.7	0.435
Shannon	2.1	2.3	2.0*	2.2	1.9*	2.1	2.0*	4.4	75.9	0.042
Fisher	9.3	10.9	8.8*	10.2	7.9*	9.1	8.2*	4.1	77.1	0.045
PD	6.6	7.5	6.2*	7.2	6.2*	6.5	6.2*	4.1	77.1	0.044
Beta-diversity
Unifrac-unw								1.4	2	0.045
Unifrac-w								0.7	2	0.401
Genus
Streptococcus	20.8	21.8	19.2	25.3	17.7	16.3	24.8	0.5	90.0	0.477
Haemophilus	10.1	5.4	14.8*	4.5	7.9	5.6	22.5*	5.0	67.8	0.035
Corynebacterium	8.9	6	4.5	9.4	20.8	5.8	6.7	0.5	44.1	0.484
Neisseria	8.5	6.6	6.7	8.8	8.4	10.6	9.9	1.8	80.1	0.183
Moraxella	7.8	6.9	11.3*	5.9	8.6	13.8*	6.6	4.6	119.2	0.046
Stenotrophomonas	4.1	2.7	4.7	3.7	3.7	5.9	4	0.2	77.1	0.667
Prevotella	3.9	3.1	3.7	7.2	4.1	3.2	2	0.05	83.1	0.833
Pseudomonas	3.4	2.4	2.6	3.2	3.7	5.2	3.3	3.9	81.2	0.063

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 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. If overall LME tests were significant we also compared the pre-ARI group against each post-ARI group and those pairwise comparisons resulting significant are marked with an * (= P≤0.05).

Abbreviations: ARI, acute respiratory infection. D0, day 0 or pre-ARI; D1, day 1 of ARI; W1, week 1 post-ARI, W2–4, week 2–4 post-ARI.