Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome/Experiment 6

From BugSigDB


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

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
Feces , Stomach , Caecum , Small intestine , Colon Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces,Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach,Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum,Intestinum tenue,Mid intestine,Small bowel,Small intestine,small intestine,Hindgut,Large bowel,Posterior intestine,Colon,colon
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
increased
Chao1 Abundance-based estimator of species richness
increased
Richness Number of species
increased

Signature 1

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

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Atrayees, WikiWorks

Source: Figure 5

Description: LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract

Abundance in Group 1: decreased abundance in PM 2.5 air exposed group

NCBI Quality ControlLinks
Lactobacillus
Staphylococcus
Bacilli

Revision editor(s): Atrayees, WikiWorks

Signature 2

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

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Atrayees, WikiWorks

Source: Figure 5

Description: LEfSe analysis of all samples revealed genera altered with PM exposure throughout the GI tract

Abundance in Group 1: increased abundance in PM 2.5 air exposed group

NCBI Quality ControlLinks
Lactobacillaceae
Rikenellaceae
Bacteroidales

Revision editor(s): Atrayees, WikiWorks