Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome/Experiment 4

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Reviewed Marked as Reviewed by Atrayees on 2023-7-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Lwaldron, WikiWorks

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 ControlLinks
unclassified Lactobacillaceae
unclassified Bacteroidales

Revision editor(s): Lwaldron, WikiWorks

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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 ControlLinks
Lactobacillus

Revision editor(s): WikiWorks