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Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity

To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collecte...

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Autores principales: De Boeck, Ilke, Wittouck, Stijn, Wuyts, Sander, Oerlemans, Eline F. M., van den Broek, Marianne F. L., Vandenheuvel, Dieter, Vanderveken, Olivier, Lebeer, Sarah
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712567/
https://www.ncbi.nlm.nih.gov/pubmed/29238339
http://dx.doi.org/10.3389/fmicb.2017.02372
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author De Boeck, Ilke
Wittouck, Stijn
Wuyts, Sander
Oerlemans, Eline F. M.
van den Broek, Marianne F. L.
Vandenheuvel, Dieter
Vanderveken, Olivier
Lebeer, Sarah
author_facet De Boeck, Ilke
Wittouck, Stijn
Wuyts, Sander
Oerlemans, Eline F. M.
van den Broek, Marianne F. L.
Vandenheuvel, Dieter
Vanderveken, Olivier
Lebeer, Sarah
author_sort De Boeck, Ilke
collection PubMed
description To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collected paired nasal and nasopharyngeal swabs from 100 healthy participants in a citizen-science project. High-throughput 16S rRNA gene V4 amplicon sequencing was performed and samples were processed using the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm. This allowed us to identify the bacterial richness and diversity of the samples in terms of amplicon sequence variants (ASVs), with special attention to intragenus variation. We found both niches to have a low overall species richness and uneven distribution. Moreover, based on hierarchical clustering, nasopharyngeal samples could be grouped into some bacterial community types at genus level, of which four were supported to some extent by prediction strength evaluation: one intermixed type with a higher bacterial diversity where Staphylococcus, Corynebacterium, and Dolosigranulum appeared main bacterial members in different relative abundances, and three types dominated by either Moraxella, Streptococcus, or Fusobacterium. Some of these bacterial community types such as Streptococcus and Fusobacterium were nasopharynx-specific and never occurred in the nose. No clear association between the nasopharyngeal bacterial profiles at genus level and the variables age, gender, blood type, season of sampling, or common respiratory allergies was found in this study population, except for smoking showing a positive association with Corynebacterium and Staphylococcus. Based on the fine-scale resolution of the ASVs, both known commensal and potential pathogenic bacteria were found within several genera – particularly in Streptococcus and Moraxella – in our healthy study population. Of interest, the nasopharynx hosted more potential pathogenic species than the nose. To our knowledge, this is the first large-scale study using the DADA2 algorithm to investigate the microbiota in the “healthy” adult nose and nasopharynx. These results contribute to a better understanding of the composition and diversity of the healthy microbiome in the URT and the differences between these important URT niches. Trial Registration: Ethical Committee of Antwerp University Hospital, B300201524257, registered 23 March 2015, ClinicalTrials.gov Identifier: NCT02 933983.
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spelling pubmed-57125672017-12-13 Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity De Boeck, Ilke Wittouck, Stijn Wuyts, Sander Oerlemans, Eline F. M. van den Broek, Marianne F. L. Vandenheuvel, Dieter Vanderveken, Olivier Lebeer, Sarah Front Microbiol Microbiology To improve our understanding of upper respiratory tract (URT) diseases and the underlying microbial pathogenesis, a better characterization of the healthy URT microbiome is crucial. In this first large-scale study, we obtained more insight in the URT microbiome of healthy adults. Hereto, we collected paired nasal and nasopharyngeal swabs from 100 healthy participants in a citizen-science project. High-throughput 16S rRNA gene V4 amplicon sequencing was performed and samples were processed using the Divisive Amplicon Denoising Algorithm 2 (DADA2) algorithm. This allowed us to identify the bacterial richness and diversity of the samples in terms of amplicon sequence variants (ASVs), with special attention to intragenus variation. We found both niches to have a low overall species richness and uneven distribution. Moreover, based on hierarchical clustering, nasopharyngeal samples could be grouped into some bacterial community types at genus level, of which four were supported to some extent by prediction strength evaluation: one intermixed type with a higher bacterial diversity where Staphylococcus, Corynebacterium, and Dolosigranulum appeared main bacterial members in different relative abundances, and three types dominated by either Moraxella, Streptococcus, or Fusobacterium. Some of these bacterial community types such as Streptococcus and Fusobacterium were nasopharynx-specific and never occurred in the nose. No clear association between the nasopharyngeal bacterial profiles at genus level and the variables age, gender, blood type, season of sampling, or common respiratory allergies was found in this study population, except for smoking showing a positive association with Corynebacterium and Staphylococcus. Based on the fine-scale resolution of the ASVs, both known commensal and potential pathogenic bacteria were found within several genera – particularly in Streptococcus and Moraxella – in our healthy study population. Of interest, the nasopharynx hosted more potential pathogenic species than the nose. To our knowledge, this is the first large-scale study using the DADA2 algorithm to investigate the microbiota in the “healthy” adult nose and nasopharynx. These results contribute to a better understanding of the composition and diversity of the healthy microbiome in the URT and the differences between these important URT niches. Trial Registration: Ethical Committee of Antwerp University Hospital, B300201524257, registered 23 March 2015, ClinicalTrials.gov Identifier: NCT02 933983. Frontiers Media S.A. 2017-11-29 /pmc/articles/PMC5712567/ /pubmed/29238339 http://dx.doi.org/10.3389/fmicb.2017.02372 Text en Copyright © 2017 De Boeck, Wittouck, Wuyts, Oerlemans, van den Broek, Vandenheuvel, Vanderveken and Lebeer. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
De Boeck, Ilke
Wittouck, Stijn
Wuyts, Sander
Oerlemans, Eline F. M.
van den Broek, Marianne F. L.
Vandenheuvel, Dieter
Vanderveken, Olivier
Lebeer, Sarah
Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title_full Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title_fullStr Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title_full_unstemmed Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title_short Comparing the Healthy Nose and Nasopharynx Microbiota Reveals Continuity As Well As Niche-Specificity
title_sort comparing the healthy nose and nasopharynx microbiota reveals continuity as well as niche-specificity
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712567/
https://www.ncbi.nlm.nih.gov/pubmed/29238339
http://dx.doi.org/10.3389/fmicb.2017.02372
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