School of Medicine and Health Sciences Poster Presentations

Title

Nasopharyngeal Microbiome Diversity Changes Over Time in Children with Asthma

Poster Number

126

Document Type

Poster

Publication Date

3-2016

Abstract

Background

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome in asthmatic infants and adults; less is known, however, about microbiome core composition and temporal dynamics in children and adolescents, which poses an obstacle to identifying microbial biomarkers of pediatric asthma (pulmotypes) and establishing associations between microbial succession and disease. Here we use NGS technology to characterize the nasopharyngeal microbiome of asthmatic children and determine its stability over time.

Methods

Two nasopharyngeal washes collected ~6 months apart were taken from 40 asthmatic children living in the Washington D.C. area. Samples were sequenced for the 16S-V4 rRNA gene region (~250 bp) in a MiSeq platform. Raw data were processed in mothur (SILVA reference database) and Operational Taxonomic Units (OTU)-based alphaand beta-diversity metrics were estimated. Relatedness among samples was assessed using Procrustes, PCoA ordination and neighbor-joining clustering analyses. Differences in microbial diversity between patient time points and seasons were assessed in both rarefied and non-rarefied OTU datasets. Core microbiome analyses were also performed to identify potential biomarkers of asthma.

Results and Discussion

A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both asthmatic infants and adults, but in different proportions. Five OTUs (genus* above) defined the nasopharyngeal core microbiome at the 95% level. Microbial OTU abundance significantly varied between time points in 35 of the 40 patients analyzed, but no significant differences in diversity were observed seasonally. Future cross-sectional studies of the nasopharyngeal microbiome need to be aware of potential intra-patient longitudinal variation

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Open Access

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Comments

Presented at: GW Research Days 2016

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Nasopharyngeal Microbiome Diversity Changes Over Time in Children with Asthma

Background

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome in asthmatic infants and adults; less is known, however, about microbiome core composition and temporal dynamics in children and adolescents, which poses an obstacle to identifying microbial biomarkers of pediatric asthma (pulmotypes) and establishing associations between microbial succession and disease. Here we use NGS technology to characterize the nasopharyngeal microbiome of asthmatic children and determine its stability over time.

Methods

Two nasopharyngeal washes collected ~6 months apart were taken from 40 asthmatic children living in the Washington D.C. area. Samples were sequenced for the 16S-V4 rRNA gene region (~250 bp) in a MiSeq platform. Raw data were processed in mothur (SILVA reference database) and Operational Taxonomic Units (OTU)-based alphaand beta-diversity metrics were estimated. Relatedness among samples was assessed using Procrustes, PCoA ordination and neighbor-joining clustering analyses. Differences in microbial diversity between patient time points and seasons were assessed in both rarefied and non-rarefied OTU datasets. Core microbiome analyses were also performed to identify potential biomarkers of asthma.

Results and Discussion

A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both asthmatic infants and adults, but in different proportions. Five OTUs (genus* above) defined the nasopharyngeal core microbiome at the 95% level. Microbial OTU abundance significantly varied between time points in 35 of the 40 patients analyzed, but no significant differences in diversity were observed seasonally. Future cross-sectional studies of the nasopharyngeal microbiome need to be aware of potential intra-patient longitudinal variation