Maturation of the gut microbiome and risk of asthma in childhood

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-20
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Atrayees

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 ControlLinks
Veillonella
Streptococcus

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Atrayees

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 ControlLinks
Roseburia
Alistipes
Flavonifractor
Faecalibacterium
Bifidobacterium
Blautia
Parabacteroides
Anaerostipes
Ruminococcus
Dialister
Prevotella

Revision editor(s): WikiWorks, Atrayees

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Veillonella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks, Suwaiba, Atrayees

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

NCBI Quality ControlLinks
Alistipes
Bifidobacterium
Dialister
Faecalibacterium
Roseburia
Ruminococcus
Lachnospiraceae incertae sedis
Blautia
Parabacteroides
Streptococcus
Prevotella
Flavonifractor
Akkermansia

Revision editor(s): WikiWorks, Suwaiba, Atrayees

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2023/07/20

Curator: Atrayees

Revision editor(s): Atrayees

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

Curated date: 2023/07/20

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Veillonella
Prevotella
Streptococcus
Ruminococcus
Akkermansia

Revision editor(s): Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-20

Curated date: 2023/07/20

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Faecalibacterium
Bifidobacterium
Blautia
Anaerostipes
Alistipes
Flavonifractor

Revision editor(s): Atrayees