Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma
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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
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
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
- children who did not experience asthma exacerbation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children who experienced exacerbation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 346
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Zero-Inflated Beta Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.15
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Signature 1
Source: Table E5
Description: Differential microbial abundance between children with exacerbation and children without
Abundance in Group 1: decreased abundance in Children who experienced exacerbation
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Samples with no rhinovirus infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Samples with any rhinovirus infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples with rhinovirus infection assessed by using quantitative PCR and partial sequencing to identify viral strain type
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1883
- Group 1 sample size Number of subjects in the case (exposed) group
- 1239
Lab analysis
Statistical Analysis
Signature 1
Source: Table E5
Description: Differential microbial abundance between samples with rhinovirus and samples without
Abundance in Group 1: increased abundance in Samples with any rhinovirus infection
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table E5
Description: Differential microbial abundance between samples with rhinovirus and samples without
Abundance in Group 1: decreased abundance in Samples with any rhinovirus infection
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Samples that were RV-A negative-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Samples with rhinovirus-A (RV-A)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples with rhinovirus-A
- Group 1 sample size Number of subjects in the case (exposed) group
- 386
Lab analysis
Statistical Analysis
Signature 1
Source: Table E5
Description: Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected
Abundance in Group 1: increased abundance in Samples with rhinovirus-A (RV-A)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table E5
Description: Differential microbial abundance between samples with rhinovirus-A and samples with no rhinovirus detected
Abundance in Group 1: decreased abundance in Samples with rhinovirus-A (RV-A)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- children who did not experience exacerbation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children who experienced exacerbation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children who experienced exacerbation of their asthma (physician-prescribed use of systemic corticosteroids for asthma symptoms, hospitalization for asthma, or both)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 346
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Table I
Description: Differential microbial abundance between children with exacerbation and children without
Abundance in Group 1: increased abundance in Children who experienced exacerbation
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table I
Description: Differential microbial abundance between children with exacerbation and children without
Abundance in Group 1: decreased abundance in Children who experienced exacerbation
| NCBI | Quality Control | Links |
|---|---|---|
| Alloiococcus | ||
| Corynebacterium | ||
| Haemophilus | ||
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 7
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- samples with no rhinovirus infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- samples with any rhinovirus infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples with rhinovirus infection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 1883
- Group 1 sample size Number of subjects in the case (exposed) group
- 1239
Lab analysis
Statistical Analysis
Signature 1
Source: Table I
Description: Differential microbial abundance between samples with any viral infection and samples without
Abundance in Group 1: increased abundance in samples with any rhinovirus infection
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table I
Description: Differential microbial abundance between samples with any viral infection and samples without
Abundance in Group 1: decreased abundance in samples with any rhinovirus infection
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 8
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rhinovirus-negative samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Samples with rhinovirus A
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples with rhinovirus A present
- Group 1 sample size Number of subjects in the case (exposed) group
- 386
Lab analysis
Statistical Analysis
Signature 1
Source: Table I
Description: Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected
Abundance in Group 1: increased abundance in Samples with rhinovirus A
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Table I
Description: Differential microbial abundance between samples infected with rhinovirus-A and samples with no rhinovirus detected
Abundance in Group 1: decreased abundance in Samples with rhinovirus A
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
