Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment
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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 Uniform resource identifier for web resources.
Authors
Durack J, Lynch SV, Nariya S, Bhakta NR, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, Sharp-King T, White SR, Woodruff PG, Avila PC, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Moore WC, Peters SP, Que L, Smith LJ, Sorkness CA, Wechsler ME, Wenzel SE, Boushey HA, Huang YJ
Journal
The Journal of allergy and clinical immunology
Year
2017
BACKGROUND: Compositional differences in the bronchial bacterial microbiota have been associated with asthma, but it remains unclear whether the findings are attributable to asthma, to aeroallergen sensitization, or to inhaled corticosteroid treatment. OBJECTIVES: We sought to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, subjects with atopy but no asthma, and nonatopic healthy control subjects and to determine relationships of the bronchial microbiota to phenotypic features of asthma. METHODS: Bacterial communities in protected bronchial brushings from 42 atopic asthmatic subjects, 21 subjects with atopy but no asthma, and 21 healthy control subjects were profiled by using 16S rRNA gene sequencing. Bacterial composition and community-level functions inferred from sequence profiles were analyzed for between-group differences. Associations with clinical and inflammatory variables were examined, including markers of type 2-related inflammation and change in airway hyperresponsiveness after 6 weeks of fluticasone treatment. RESULTS: The bronchial microbiome differed significantly among the 3 groups. Asthmatic subjects were uniquely enriched in members of the Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and the Sphingomonodaceae family and depleted in members of the Mogibacteriaceae family and Lactobacillales order. Asthma-associated differences in predicted bacterial functions included involvement of amino acid and short-chain fatty acid metabolism pathways. Subjects with type 2-high asthma harbored significantly lower bronchial bacterial burden. Distinct changes in specific microbiota members were seen after fluticasone treatment. Steroid responsiveness was linked to differences in baseline compositional and functional features of the bacterial microbiome. CONCLUSION: Even in subjects with mild steroid-naive asthma, differences in the bronchial microbiome are associated with immunologic and clinical features of the disease. The specific differences identified suggest possible microbiome targets for future approaches to asthma treatment or prevention.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic 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
- atopic asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic asthma
- 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
- 42
- 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
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2a, Supplemental Table S4
Description: Differentially abundant microbial taxa in atopic asthmatic (AA) subjects compared with healthy controls (HC)
Abundance in Group 1: increased abundance in atopic asthma
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2a, Supplemental Table S4
Description: Differential microbial abundance between atopic asthmatic (AA) subjects compared with healthy controls (HC)
Abundance in Group 1: decreased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Actinobacillus | |
| Kocuria palustris ⚠ | |
| Lacticaseibacillus zeae | |
| Lactobacillus | |
| Leptotrichia | |
| Methylobacterium ⚠ | |
| Peptostreptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic 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
- atopic no asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic nonasthmatic subjects
- 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
- 21
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2b, Supplemental Table S5
Description: Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC)
Abundance in Group 1: increased abundance in atopic no asthma
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2b, Supplemental Table S5
Description: Differential microbial abundance between atopic nonasthmatic (ANA) subjects compared with healthy controls (HC)
Abundance in Group 1: decreased abundance in atopic no asthma
| NCBI | Links |
|---|---|
| Helicobacter | |
| Lacticaseibacillus zeae | |
| Lactobacillus | |
| Leptotrichia | |
| Parvimonas | |
| Porphyromonas | |
| Prevotella | |
| Pseudomonas ⚠ | |
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- atopic no asthma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- atopic asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic asthma
- 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
- 42
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2c, Supplemental Table S6
Description: Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects
Abundance in Group 1: increased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Dialister | |
| Fusobacterium | |
| Haemophilus | |
| Leptotrichia | |
| Mycoplasma | |
| Neisseria subflava | |
| Prevotella | |
| Prevotella intermedia | |
| Selenomonas |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 2c, Supplemental Table S6
Description: Differential microbial abundance between atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA) subjects
Abundance in Group 1: decreased abundance in atopic asthma
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- nonresponder
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- inhaled corticosteroid responder
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- inhaled corticosteroid (ICS) responder
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Figure 6b
Description: Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma
Abundance in Group 1: increased abundance in inhaled corticosteroid responder
Revision editor(s): Claregrieve1, WikiWorks, Merit
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Figure 6b
Description: Differential relative taxon abundance in inhaled corticosteroid (ICS) responders versus nonresponders among those with atopic asthma
Abundance in Group 1: decreased abundance in inhaled corticosteroid responder
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline (corticosteroid treatment group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post inhaled corticosteroid treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- asthma patients after inhaled corticosteroid treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment
Abundance in Group 1: increased abundance in post inhaled corticosteroid treatment
| NCBI | Links |
|---|---|
| Microbacteriaceae | |
| Neisseria | |
| Moraxella | |
| Spirochaetaceae | |
| Actinomycetaceae | |
| Mycoplasmataceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects who responded to treatment after inhaled corticosteroid (ICS) treatment
Abundance in Group 1: decreased abundance in post inhaled corticosteroid treatment
| NCBI | Links |
|---|---|
| Acholeplasmataceae | |
| Lactobacillaceae | |
| Prevotellaceae | |
| Lachnospiraceae | |
| Peptostreptococcaceae | |
| Fusobacterium | |
| Dialister |
Revision editor(s): WikiWorks
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline (placebo group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post placebo treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- placebo treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects after placebo treatment
Abundance in Group 1: increased abundance in post placebo treatment
| NCBI | Links |
|---|---|
| Eikenella | |
| Spirochaetaceae | |
| Mycoplasmataceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Text, Figure 6d
Description: Taxa differentially expressed in asthmatic subjects after placebo treatment
Abundance in Group 1: decreased abundance in post placebo treatment
| NCBI | Links |
|---|---|
| Acinetobacter ⚠ | |
| Actinomycetaceae | |
| Prevotellaceae | |
| Peptostreptococcaceae |
Revision editor(s): WikiWorks
Experiment 7
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic 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
- atopic asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic asthma
- 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
- 42
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4a
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC)
Abundance in Group 1: increased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Actinomycetota | |
| Bacteroidota | |
| Fusobacteriota | |
| Pseudomonadota | |
| Spirochaetota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4a
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with healthy controls (HC)
Abundance in Group 1: decreased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Bacillota |
Revision editor(s): WikiWorks
Experiment 8
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic 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
- atopic no asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic no asthma
- 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
- 21
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4b
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC)
Abundance in Group 1: increased abundance in atopic no asthma
| NCBI | Links |
|---|---|
| Actinomycetota | |
| Bacillota | |
| Pseudomonadota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4b
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic nonasthmatic (ANA) subjects compared with healthy controls (HC)
Abundance in Group 1: decreased abundance in atopic no asthma
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Fusobacteriota | |
| Spirochaetota |
Revision editor(s): WikiWorks
Experiment 9
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- atopic asthma allergic asthma,atopic asthma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- atopic no asthma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- atopic asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- atopic asthma
- 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
- 42
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Negative Binomial Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4c
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA)
Abundance in Group 1: increased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Bacteroidota | |
| Fusobacteriota |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/14
Source: Supplemental Figure E4c
Description: Bacterial phylum significantly enriched or depleted in relative abundance in atopic asthmatic (AA) subjects compared with atopic nonasthmatic (ANA)
Abundance in Group 1: decreased abundance in atopic asthma
| NCBI | Links |
|---|---|
| Actinomycetota | |
| Bacillota | |
| Pseudomonadota | |
| Spirochaetota |
Revision editor(s): WikiWorks
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