Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

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
Bronchus Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,bronchus
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Atopic asthma allergic asthma,Atopic 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
Patients who have 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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

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

NCBI Quality ControlLinks
Actinomyces
Alloprevotella tannerae
Anaerovorax
Campylobacter
Fusobacterium
Haemophilus
Kingella
Lactobacillus iners
Neisseria
Neisseria subflava
Porphyromonas
Prevotella
Segatella copri
Sphingopyxis
Sphingopyxis alaskensis
Treponema
Treponema amylovorum
Veillonella
Veillonella dispar

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

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 Quality ControlLinks
Actinobacillus
Kocuria palustris
Lacticaseibacillus zeae
Lactobacillus
Leptotrichia
Methylobacterium
Peptostreptococcus

Revision editor(s): Claregrieve1, WikiWorks