Lower respiratory tract microbiome composition and community interactions in smokers/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-2-16

Curated date: 2023/10/09

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

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
Lung Pulmo,Lung,lung
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Smoking status measurement Smoking status measurement,smoking status measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Active smokers & former smokers
Group 1 name Corresponds to the case (exposed) group for case-control studies
Never smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants who have never smoked
Group 0 sample size Number of subjects in the control (unexposed) group
46
Group 1 sample size Number of subjects in the case (exposed) group
9
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
use of antibiotics within 12weeks prior to study

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V6-V8
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2.5

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
decreased

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-13

Curated date: 2023/10/09

Curator: OdigiriGreat

Revision editor(s): OdigiriGreat, Folakunmi

Source: Fig 5

Description: Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using LEFse.

Abundance in Group 1: increased abundance in Never smokers

NCBI Quality ControlLinks
Alphaproteobacteria
Bacillota
Bacteroidales
Bacteroidia
Eubacteriaceae
Eubacterium
Haemophilus
Hyphomicrobiales
Lautropia
Megasphaera
Methylobacteriaceae
Methylobacterium
Mogibacterium
Negativicutes
Pasteurellaceae
Pasteurellales
Prevotella
Prevotellaceae
Selenomonadales
Veillonella
Veillonellaceae

Revision editor(s): OdigiriGreat, Folakunmi