Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
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
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 Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): WikiWorks
Experiment 2
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
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 Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09
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
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 Control | Links |
|---|---|---|
| Prevotella | ||
| Alkanindiges | ||
| Gardnerella |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Lucy Mellor on 2021/02/09
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 Control | Links |
|---|---|---|
| Dialister |
Revision editor(s): WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Atrayees on 2023-7-18
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
Source: Figure 4, text
Description: Species differentially abundant between asthmatics and health controls
Abundance in Group 1: increased abundance in asthma
| NCBI | Quality Control | Links |
|---|---|---|
| Hoylesella buccalis | ||
| Dialister invisus | ||
| Gardnerella vaginalis | ||
| Alkanindiges hongkongensis |
Revision editor(s): WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Fatima on 2021/07/16
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
Source: Figure 5
Description: Difference in fold change between asthmatics and healthy controls
Abundance in Group 1: increased abundance in asthma
| NCBI | Quality Control | Links |
|---|---|---|
| Hoylesella buccalis | ||
| Gardnerella vaginalis |
Revision editor(s): WikiWorks
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