Whole-genome Shotgun Sequencing for Nasopharyngeal Microbiome in Preschool Children with asthma exacerbation
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AbstractIntroduction: Several studies reported upper airway microbiota in children with bronchiolitis and recurrent wheeze using 16S rRNA-based sequencing approach. However, there has not been any metagenomic study that delineates the high-resolution composition of airway microbiota in these patients. This study characterised nasopharyngeal (NP) microbiome of Chinese children with asthma exacerbation.
Methods: NP secretions were collected in Jan-Apr 2015 from 76 preschool children, which consisted of 24 cases hospitalised for human rhinovirus (HRV)-associated asthma exacerbations, 14 inpatient controls with upper respiratory tract infection (RTI) who were virus-negative, and 38 community controls without any RTI for at least four weeks. Genomic DNA extracted by PowerSoil DNA Isolation Kit (MO BIO Laboratories) was sequenced using Illumina HiSeq X Ten. High-quality reads were mapped to human reference genome Ensembl version GRCh38.87 using Burrows-Wheeler Aligner version 0.7.15-r1140. Following removal of human sequences, these reads underwent microbial taxonomic classification using MetaPhlAn2 version 2.6.0. Heatmaps of relative abundances for bacteria and viruses and cladogram were generated using R version 3.3.1 and MetaPhlAn2’s utility scripts respectively. Linear Discriminant Analysis (LDA) scores for microbial abundances were calculated by LDA Effect Size programme.
Results: The mean (SD) age of cases, inpatient controls and community controls was 3.5 (1.0), 3.5 (1.0) and 4.9 (0.7) years respectively. All groups had low but similar NP biomass (5-7% of all sequence reads). NP biodiversity as represented by Shannon diversity index was lower in cases with asthma exacerbations than community controls (median [IQR]: 3.49 [2.81-3.97] vs 4.17 [3.24-5.84], P=0.029) but similar to inpatient controls (3.44 [2.30-4.46], P=0.674). Detailed microbiome analyses revealed patients with asthma exacerbation to have higher levels of viruses (log LDA score 5.20, P=0.0031) and lower levels of bacteria (log LDA score 5.20, P=0.0032). Bacilli (taxonomy level: class) was lower in cases compared to inpatient and community controls (log LDA score 4.82, P=0.0055), which was accounted for by lower Lactobacillales (order). The class Actinobacteria was higher in community controls than cases and inpatient controls (LDA score 4.47, P=0.00076). Specifically, this difference was due to Bifidobacterium (genus) with (log LDA score 4.24, P=0.021). Community controls also had higher abundances of Clostridium hathewayi, Enterobacter cloaceae and Akkermansia muciniphila, but these were at rare abundance levels.
Conclusion: NP biodiversity is lower in children with asthma exacerbations than community controls. Our results also show high abundance of virus-matched reads in metagenome of most NP samples.
Acknowledgement: Funded by Research Committee’s One-off Fund for Research (3132910) of CUHK
All Author(s) ListLeung Ting Fan, Kwok Jaime, Song Yuping, Tang Man Fung, Tung Christine, Chan Renee Wan-Yi, Leung Agnes Sze-Yin, Tao Kin Pong, Wong Gary Wing-Kin, Tsui Stephen Kwok-Wing
Journal nameClinical and Translational Allergy
Year2018
Month6
Day25
Volume Number8
Issue NumberSupplement 2
PublisherBMC (part of Springer Nature) / BioMed Central
Pages5 - 5
ISSN2045-7022
LanguagesEnglish-United Kingdom
KeywordsAsthma, microbiome, next-generation sequencing

Last updated on 2021-28-11 at 01:02