Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects/Experiment 6
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-4
Subjects
- Location of subjects
- China
- 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
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- contralateral non-cancerous site with no antibiotics (TNo)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cancerous site with no antibiotics (To)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cancerous site samples from lung cancer patients who received no antibiotics in the prior three months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- 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
- V3-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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-4
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and To (cancerous site samples of lung cancer patients who received no antibiotics prior to 3 months)
Abundance in Group 1: increased abundance in Cancerous site with no antibiotics (To)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacteriaceae | ||
| Acidaminococcaceae | ||
| Phascolarctobacterium |
Revision editor(s): Folakunmi
