The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections

Background: Airway microbiota dynamics during lower respiratory infection (LRI) are still poorly understood due, in part, to insufficient longitudinal studies and lack of uncontaminated lower airways samples. Furthermore, the similarity between upper and lower airway microbiomes is still under debate. Here we compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections. Methods: We prospectively collected 127 tracheal aspirates across four consecutive meteorological seasons (quarters) from 40 patients, of whom 20 developed LRIs and 20 remained healthy. All aspirates were collected when patients had no LRI. We generated 16S rRNA-based microbial profiles (~250 bp) in a MiSeq platform and analyzed them using Mothur and the SILVAv123 database. Differences in microbial diversity and taxon normalized (via negative binomial distribution) abundances were assessed using linear mixed effects models and multivariate analysis of variance. Results and discussion Alpha-diversity (ACE, Fisher and phylogenetic diversity) and beta-diversity (Bray-Curtis, Jaccard and Unifrac distances) indices varied significantly (P<0.05) between NLRI and YLRI microbiotas from tracheostomised patients. Additionally, Haemophilus was significantly (P = 0.009) more abundant in YLRI patients than in NLRI patients, while Acinetobacter, Corynebacterium and Pseudomonas (P<0.05) showed the inverse relationship. We did not detect significant differences in diversity and bacterial abundance among seasons. This result disagrees with previous evidence suggesting seasonal variation in airway microbiotas. Further study is needed to address the interaction between microbes and LRI during times of health and disease

Clinical characteristics of the studied cohort.

<p>NLRI = patients with no lower respiratory infections. YLRI = patients with lower respiratory infections.</p

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).

<p>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 (<i>F</i>), degrees of freedom (<i>DF</i>) and significance (<i>P(>F)</i>). Significant associations are indicated in bold.</p

Alluvial plots of mean relative proportions of most abundant (≥3%) phyla and genera in microbiomes from patients with (YLRI) and without (NLRI) lower respiratory infections (LRI) across meteorological seasons.

<p>Alluvial plots of mean relative proportions of most abundant (≥3%) phyla and genera in microbiomes from patients with (YLRI) and without (NLRI) lower respiratory infections (LRI) across meteorological seasons.</p

Box plots of phylogenetic alpha-diversity of microbiotas from patients with (YLRI) and without (NLRI) lower respiratory infections (LRI) (A) and of microbiotas from YLRI and NLRI patients across meteorological seasons (B).

<p>Box plots of phylogenetic alpha-diversity of microbiotas from patients with (YLRI) and without (NLRI) lower respiratory infections (LRI) (A) and of microbiotas from YLRI and NLRI patients across meteorological seasons (B).</p