Bacterial biogeography of adult airways in atopic asthma/Experiment 2

From BugSigDB


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

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 , Mouth Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,bronchus,Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
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
oral wash specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
oral wash 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

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
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

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 oral wash (OW) specimen types

Abundance in Group 1: increased abundance in oral wash specimens

NCBI Quality ControlLinks
Actinomyces
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 oral wash (OW) specimen types

Abundance in Group 1: decreased abundance in oral wash specimens

NCBI Quality ControlLinks
Corynebacterium
Moraxella
Prevotella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks