Dataset Information

A comparison of sampling methods for examining the laryngeal microbiome.

ABSTRACT: Shifts in healthy human microbial communities have now been linked to disease in numerous body sites. Noninvasive swabbing remains the sampling technique of choice in most locations; however, it is not well known if this method samples the entire community, or only those members that are easily removed from the surface. We sought to compare the communities found via swabbing and biopsied tissue in true vocal folds, a location that is difficult to sample without causing potential damage and impairment to tissue function. A secondary aim of this study was to determine if swab sampling of the false vocal folds could be used as proxy for true vocal folds. True and false vocal fold mucosal samples (swabbed and biopsied) were collected from six pigs and used for 454 pyrosequencing of the V3-V5 region of the 16S rRNA gene. Most of the alpha and beta measures of diversity were found to be significantly similar between swabbed and biopsied tissue samples. Similarly, the communities found in true and false vocal folds did not differ considerably. These results suggest that samples taken via swabs are sufficient to assess the community, and that samples taken from the false vocal folds may be used as proxies for the true vocal folds. Assessment of these techniques opens an avenue to less traumatic means to explore the role microbes play in the development of diseases of the vocal folds, and perhaps the rest of the respiratory tract.

SUBMITTER: Hanshew AS

PROVIDER: S-EPMC5375147 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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A comparison of sampling methods for examining the laryngeal microbiome.

Hanshew Alissa S AS Jetté Marie E ME Tadayon Stephanie S Thibeault Susan L SL

PloS one 20170331 3

Shifts in healthy human microbial communities have now been linked to disease in numerous body sites. Noninvasive swabbing remains the sampling technique of choice in most locations; however, it is not well known if this method samples the entire community, or only those members that are easily removed from the surface. We sought to compare the communities found via swabbing and biopsied tissue in true vocal folds, a location that is difficult to sample without causing potential damage and impai ...[more]

PMID: 28362810

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Project description:BackgroundUnderstanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome.ResultsThe microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members.ConclusionsOverall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research.

Dataset Information

A comparison of sampling methods for examining the laryngeal microbiome.

Publications

A comparison of sampling methods for examining the laryngeal microbiome.

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