Different functional genes of upper airway microbiome associated with natural course of childhood asthma

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-2-4

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29052232

DOI Digital object identifier for electronic documents.

10.1111/all.13331

URI

Authors

Kim BS, Lee E, Lee MJ, Kang MJ, Yoon J, Cho HJ, Park J, Won S, Lee SY, Hong SJ

Journal

Allergy

Year

2018

Keywords:

airway, childhood asthma, function, microbiome

BACKGROUND: Microbial colonization of the airway plays a role in the pathogenesis of asthma; however, the effect of the upper airway microbiome on childhood asthma is not fully understood. We analyzed the metagenome of airway microbiome to understand the associated role of upper airway microbiome with the natural course of childhood asthma. METHODS: Nasopharyngeal swabs were collected from children with asthma, those in asthma remission, and control groups. High-throughput sequencing was used to examine the structure and functional dynamics of the airway microbiome with respect to asthma phenotypes. RESULTS: The composition of microbiota differed among healthy control, asthma, and remission groups. The relative abundance of Streptococcus was negatively associated with FEV1% predicted (P = .023) and that of Staphylococcus was negatively associated with methacholine PC20 (P = .013). Genes related to arachidonic acid metabolites, lysine residues, and glycosaminoglycans in the microbiome could be associated with airway inflammation. In particular, genes related to synthesis of anti-inflammatory prostaglandin E2 (PGE2 ) were not detected from the airway microbiome in the asthma group. CONCLUSIONS: These data suggest that alterations in the composition and function of the upper airway microbiome could be related with the natural course of asthma in children.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-4

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Subjects

Location of subjects: South Korea

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Nasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy control

Group 1 name Corresponds to the case (exposed) group for case-control studies: asthma

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: asthma

Group 0 sample size Number of subjects in the control (unexposed) group: 31

Group 1 sample size Number of subjects in the case (exposed) group: 31

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Dunn's test

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

Source: Figure 2

Description: Relative abundance of bacterial genera in patients with asthma and healthy controls

Abundance in Group 1: increased abundance in asthma

NCBI	Quality Control	Links
Staphylococcus
Prevotella

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Signature 2

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Curated date: 2021/01/10

Curator: Lucy Mellor

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Source: Figure 2

Description: Relative abundance of bacterial genera in patients with asthma and healthy controls

Abundance in Group 1: decreased abundance in asthma

NCBI	Quality Control	Links
Haemophilus

Revision editor(s): WikiWorks

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-4

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: asthma remission

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: asthma remission