Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children

Background

The nasopharynx is considered an anatomical reservoir from which pathogenic microbes can spread to the lower and upper respiratory airways and cause respiratory infections [1–3]. Culture-independent sequencing methods have shown that some pathogenic bacterial genera associated with asthma (e.g., Moraxella, Streptococcus, Haemophilus, Neisseria, and Staphylococcus) are also present in the nasopharynx [1, 4–6]. Consequently, several recent metataxonomic and metagenomic (see [7] for distinction) studies have investigated how nasopharyngeal microbial communities change during health and disease in relation to clinical variation [1, 3, 5, 8–16]. All these next-generation sequencing (NGS) studies, however, either sampled the nasopharynx as a whole or focused on a particular anatomical area (microenvironment); hence, less is known about the spatial variation (biogeography) in microbial composition of the nasopharynx. The nose has a complicated and diverse anatomical structure, comprised of diverse epithelial cells and glands with different physiologies and functions [17, 18]. Hence, it seems reasonable to expect that different microenvironments in the nose will also harbor distinct microbial communities. However, to our knowledge, only one study has assessed the biogeography of the nasal microbiota [19]. In that study, the authors used 16S rRNA sequence data to compare the microbiotas of three nasal sites (anterior naris, middle meatus, and sphenoethmoidal recess) in healthy subjects and detected significant differences in diversity between the anterior nares and the two inner mucosal sites. No study, so far, has investigated the biogeography of the nasal cavity in asthmatic patients.

In this report, we used targeted 16S rRNA sequencing and two different sampling techniques (nasal washes and nasal brushes) to characterize the nasopharyngeal microbiota in asthmatic children. Nasal brushing is more abrasive than nasal washing and was used to target a particular region of the nasopharynx, the inner portion of the inferior turbinate; nasal washing is assumed to be less spatially specific and to reach the main cavities in the nasopharynx. Hence, given these differences in sampling methodology, we hypothesize that nasal microbiotas collected by nasal washes will be different in alpha- and beta-diversity from those collected by nasal brushes.