Sinonasal Microbiome Sampling: A Comparison of Techniques

Abstract

BackgroundThe role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample.MethodsCross-sectional study with paired design. Mucosal biopsy and swab samples were obtained intra-operatively from the ethmoid sinuses of 6 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8 software package.ResultsAt a maximum subsampling depth of 1,100 reads, the mean observed species richness was 33.3 species (30.6 for swab, versus 36 for mucosa; p > 0.05). There was no significant difference in phylogenetic and non-phylogenetic alpha diversity metrics (Faith’s PD_Whole_Tree and Shannon’s index) between the two sampling methods (p > 0.05). The type of sample also had no significant effect on phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and Bray-Curtis; p > 0.05).ConclusionWe observed no significant difference between the microbiota of mucosal tissue and swab samples. This suggests that less invasive swab samples are representative of the sinonasal mucosa microbiome and can be used for future sinonasal microbiome studies.

A comparison of sampling methods for examining the laryngeal microbiome

“…Exploring this possibility, Bassiouni et al . [7] compared the microbiota of paired mucosal tissue and swab samples collected from six patients with sinus disease and found no difference in sampling methods. Results comparing two sampling techniques used for investigating the esophageal microbiome–secretions collected from a string and mucosal biopsy–also demonstrated similarities in microbial profiles[24].…”

“…Common sampling methods include mucosal biopsy[5], brush[6], and swab[7], as well as lavage[8] and fecal collection [9]. The vocal folds are mucosal tissues housed within the larynx at the junction between the respiratory and gastrointestinal tracts and there is evidence that they have a distinct immunologic role [10] and microbial community[11].…”

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

“…This potentially facilitates the study of the natural history of the disease process, patient-specific contributions to disease, and resilience of the sinus microbiome to perturbation, among many other possibilities. A recent investigation comparing surface swab to tissue biopsy demonstrated no difference in the microbial diversity revealed by the two methods, suggesting that swabs may serve as an adequate sampling method [52], a finding that has since been confirmed by a number of other groups. A recent publication also investigated inter-sinus differences, although only one subject studied had all sinuses from both sides sampled [53].…”

Generalized Hotelling's test for paired compositional data with application to human microbiome studies

“…Given the large number of taxa and relatively small sample sizes, summary statistics, such as -diversity or -diversity, are usually calculated and compared between pairs of samples (Bassiouni et al, 2015;Sinha et al, 2016) for differences in microbiome profiles. Given the large number of taxa and relatively small sample sizes, summary statistics, such as -diversity or -diversity, are usually calculated and compared between pairs of samples (Bassiouni et al, 2015;Sinha et al, 2016) for differences in microbiome profiles.…”