Maturation of the gut microbiome and risk of asthma in childhood
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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
Authors
Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H
Journal
Nature communications
Year
2018
The composition of the human gut microbiome matures within the first years of life. It has been hypothesized that microbial compositions in this period can cause immune dysregulations and potentially cause asthma. Here we show, by associating gut microbial composition from 16S rRNA gene amplicon sequencing during the first year of life with subsequent risk of asthma in 690 participants, that 1-year-old children with an immature microbial composition have an increased risk of asthma at age 5 years. This association is only apparent among children born to asthmatic mothers, suggesting that lacking microbial stimulation during the first year of life can trigger their inherited asthma risk. Conversely, adequate maturation of the gut microbiome in this period may protect these pre-disposed children.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Subjects
- Location of subjects
- Denmark
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- no asthma at 5 years old
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with asthma at 5 years old
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 531
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
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
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children
Abundance in Group 1: increased abundance in child with asthma at 5 years old
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Streptococcus |
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in all children
Abundance in Group 1: decreased abundance in child with asthma at 5 years old
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Alistipes | ||
| Flavonifractor | ||
| Faecalibacterium | ||
| Bifidobacterium | ||
| Blautia | ||
| Parabacteroides | ||
| Anaerostipes | ||
| Ruminococcus | ||
| Dialister | ||
| Prevotella |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with asthma at 5 years old among mothers with asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with physician diagnosed asthma based on verified diary recordings of five episodes of troublesome lung symptoms within 6 months, exercise-induced symptoms, prolonged nocturnal cough, and/or persistent cough outside of common colds, need for intermittent rescue use of inhaled β2-agonist, response to a 3-month course of inhaled corticosteroids andrelapse upon ending treatment and mother with asthma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 122
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers
Abundance in Group 1: increased abundance in child with asthma at 5 years old among mothers with asthma
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to asthmatic mothers
Abundance in Group 1: decreased abundance in child with asthma at 5 years old among mothers with asthma
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Differences from previous experiment shown
Subjects
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- child with asthma at 5 years old among mothers without asthma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with asthma at 5 years old among mothers without asthma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 409
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers
Abundance in Group 1: increased abundance in child with asthma at 5 years old among mothers without asthma
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Prevotella | ||
| Streptococcus | ||
| Ruminococcus | ||
| Akkermansia |
Revision editor(s): Atrayees
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
Source: Figure 3
Description: Relative abundances of bacterial genera in 1-year fecal samples associated with asthma at age 5 years in children born to non-asthmatic mothers
Abundance in Group 1: decreased abundance in child with asthma at 5 years old among mothers without asthma
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Bifidobacterium | ||
| Blautia | ||
| Anaerostipes | ||
| Alistipes | ||
| Flavonifractor |
Revision editor(s): Atrayees
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