Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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