The nasal microbiome in asthma

From BugSigDB
Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, Grishin A, Bunyavanich S
Journal
The Journal of allergy and clinical immunology
Year
2018
Keywords:
16S rRNA sequencing, Nasal, asthma, microbiome, upper airway, upper respiratory tract
BACKGROUND: Nasal microbiota may influence asthma pathobiology. OBJECTIVE: We sought to characterize the nasal microbiome of subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls to identify nasal microbiota associated with asthma activity. METHODS: We performed 16S ribosomal RNA sequencing on nasal swabs obtained from 72 primarily adult subjects with exacerbated asthma (n = 20), nonexacerbated asthma (n = 31), and healthy controls (n = 21). Analyses were performed using Quantitative Insights into Microbial (QIIME); linear discriminant analysis effect size (LEfSe); Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; and Statistical Analysis of Metagenomic Profiles (PICRUSt); and Statistical Analysis of Metagenomic Profiles (STAMP). Species found to be associated with asthma activity were validated using quantitative PCR. Metabolic pathways associated with differentially abundant nasal taxa were inferred through metagenomic functional prediction. RESULTS: Nasal bacterial composition significantly differed among subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls (permutational multivariate ANOVA, P = 2.2 × 10-2). Relative to controls, the nasal microbiota of subjects with asthma were enriched with taxa from Bacteroidetes (Wilcoxon-Mann-Whitney, r = 0.33, P = 5.1 × 10-3) and Proteobacteria (r = 0.29, P = 1.4 × 10-2). Four species were differentially abundant based on asthma status after correction for multiple comparisons: Prevotella buccalis, Padj = 1.0 × 10-2; Dialister invisus, Padj = 9.1 × 10-3; Gardnerella vaginalis, Padj = 2.8 × 10-3; Alkanindiges hongkongensis, Padj = 2.6 × 10-3. These phyla and species were also differentially abundant based on asthma activity (exacerbated asthma vs nonexacerbated asthma vs controls). Quantitative PCR confirmed species overrepresentation in asthma relative to controls for Prevotella buccalis (fold change = 130, P = 2.1 × 10-4) and Gardnerella vaginalis (fold change = 160, P = 6.8 × 10-4). Metagenomic inference revealed differential glycerolipid metabolism (Kruskal-Wallis, P = 1.9 × 10-4) based on asthma activity. CONCLUSIONS: Nasal microbiome composition differs in subjects with exacerbated asthma, nonexacerbated asthma, and healthy controls. The identified nasal taxa could be further investigated for potential mechanistic roles in asthma and as possible biomarkers of asthma activity.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-7-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Subjects

Location of subjects
United States of America
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
Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Asthma Airway hyperreactivity,asthma,Asthma (disorder),Asthma NOS,Asthma NOS (disorder),ASTHMA NOS W (AC) EXAC,Asthma unspecified,Asthma unspecified (disorder),Asthma, Bronchial,Asthma, unspecified,Asthma, unspecified type, with acute exacerbation,Asthma, unspecified type, without mention of status asthmaticus,Asthmas,Asthmatic,BHR - Bronchial hyperreactivity,Bronchial asthma,Bronchial Hyperreactivities,Bronchial hyperreactivity,bronchial hyperreactivity,Bronchial hyperresponsiveness,Bronchial hypersensitivity,chronic obstructive asthma,chronic obstructive asthma with acute exacerbation,chronic obstructive asthma with status asthmaticus,DUST PNEUMONOPATHY NEC,Exercise induced asthma,exercise induced asthma,Exercise-induced asthma,exercise-induced asthma,Exercise-induced asthma (disorder),Hyperreactive airway disease,Hyperreactive airways disease,Hyperreactivities, Bronchial,Hyperreactivity, Bronchial,Other forms of asthma,Pneumonopathy due to inhalation of other dust,Pneumopathy due to inhalation of other dust,Pneumopathy due to inhalation of other dust (disorder),Pneumopathy due to inhalation of other dust NOS,Pneumopathy due to inhalation of other dust NOS (disorder),Asthma
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
exacerbated asthma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
20

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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)?
No

Alpha Diversity

Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-18

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

Source: Figure 2

Description: Distinct bacterial composition in subjects with exacerbated asthma and healthy controls (phylum level)

Abundance in Group 1: increased abundance in exacerbated asthma

NCBI Quality ControlLinks
Bacteroidota
Pseudomonadota

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
non-exacerbated asthma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care.
Group 1 sample size Number of subjects in the case (exposed) group
31

Lab analysis

Statistical Analysis

Alpha Diversity

Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-18

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

Source: Figure 2

Description: Distinct bacterial composition in subjects with non-exacerbated asthma and healthy controls (phyum level)

Abundance in Group 1: increased abundance in non-exacerbated asthma

NCBI Quality ControlLinks
Bacteroidota
Pseudomonadota

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
non-exacerbated asthma
Group 1 name Corresponds to the case (exposed) group for case-control studies
exacerbated asthma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
physician-diagnosed current asthma presenting with an encounter diagnosis of asthma exacerbation
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
20

Lab analysis

Statistical Analysis

Statistical test
LEfSe
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2

Alpha Diversity

Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Figure 3

Description: Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma

Abundance in Group 1: increased abundance in exacerbated asthma

NCBI Quality ControlLinks
Prevotella
Alkanindiges
Gardnerella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Figure 3

Description: Linear discriminant analysis (LDA) demonstrated distinct bacterial genera enriched in exacerbated and non-exacerbated asthma

Abundance in Group 1: decreased abundance in exacerbated asthma

NCBI Quality ControlLinks
Dialister

Revision editor(s): WikiWorks

Experiment 4


Reviewed Marked as Reviewed by Atrayees on 2023-7-18

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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
physician-diagnosed current asthma presenting for routine, non-urgent, asthma followup care or with an encounter diagnosis of asthma exacerbation
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
51

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified


Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-18

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

Source: Figure 4, text

Description: Species differentially abundant between asthmatics and health controls

Abundance in Group 1: increased abundance in asthma

NCBI Quality ControlLinks
Hoylesella buccalis
Dialister invisus
Gardnerella vaginalis
Alkanindiges hongkongensis

Revision editor(s): WikiWorks

Experiment 5


Reviewed Marked as Reviewed by Fatima on 2021/07/16

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Lab analysis

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
RT-qPCR

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
T-Test
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No


Signature 1

Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Figure 5

Description: Difference in fold change between asthmatics and healthy controls

Abundance in Group 1: increased abundance in asthma

NCBI Quality ControlLinks
Hoylesella buccalis
Gardnerella vaginalis

Revision editor(s): WikiWorks