Bacterial biogeography of adult airways in atopic asthma/Experiment 6

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Sputum , Bronchus Expectoration,Sputum,sputum,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

bronchial brush specimens

Group 1 name Corresponds to the case (exposed) group for case-control studies

induced sputum specimens

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

induced sputum specimen type

Group 0 sample size Number of subjects in the control (unexposed) group

27

Group 1 sample size Number of subjects in the case (exposed) group

27

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).

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

Pielou Quantifies how equal the community is numerically

unchanged

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Richness Number of species

increased

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and induced sputum (IS) specimen types

Abundance in Group 1: increased abundance in induced sputum specimens

NCBI	Quality Control	Links
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks