Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- 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
- Filtered air group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PM 2.5 air exposed group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice exposed to PM2.5 concentrated from ambient air in Chicago 8 hours per day for 5 days a week for three consecutive weeks in a chamber connected to Versatile Aerosol Concentration Enrichment System (VACES)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
Source: Figure S2
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the stomach
Abundance in Group 1: increased abundance in PM 2.5 air exposed group
NCBI | Quality Control | Links |
---|---|---|
unclassified Lactobacillaceae | ||
unclassified Bacteroidales |
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
Source: Figure S2
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the stomach
Abundance in Group 1: decreased abundance in PM 2.5 air exposed group
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus |
Revision editor(s): WikiWorks