High-Level PM2.5/PM10 Exposure Is Associated With Alterations in the Human Pharyngeal Microbiota Composition/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
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
- Cavity of pharynx Cavitas pharyngealis,Cavitas pharyngis,Lumen of pharynx,Pharyngeal cavity,Cavity of pharynx,cavity of pharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Air pollution air pollution,Air pollution
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pre-smog swabs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-smog swabs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vendors in an open-air farer's market who worked in the same place and were exposed to smog over the same business hours
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 83
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)
- 0.001
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
Source: Figure S3
Description: Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe)
Abundance in Group 1: increased abundance in post-smog swabs
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Bacilli | ||
| Leptotrichia |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
Source: Figure S3
Description: Histogram of unique biomarker bacteria in each group as analyzed by linear discriminant analysis effect size (LefSe)
Abundance in Group 1: decreased abundance in post-smog swabs
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Prevotella |
Revision editor(s): Claregrieve1, WikiWorks
