Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
Source: Figure S3
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.
Abundance in Group 1: increased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Bacteroidales | ||
| unclassified Lactobacillaceae | ||
| Lactobacillus | ||
| Lactobacillales | ||
| Bacteroidaceae | ||
| Bacteroidales |
Signature 2
Source: Figure S3
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the small intestine.
Abundance in Group 1: decreased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Staphylococcus | ||
| unclassified Aerococcaceae |
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces 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
Lab analysis
Statistical Analysis
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
Source: Figure S6
Description: Individual abundance histograms of bacterial lineages changing particularly in the fecal samples
Abundance in Group 1: increased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Lachnospiraceae | ||
| Rickenellaceae | ||
| Lachnospira | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Bacteroidales bacterium | ||
| Bacteroidaceae bacterium |
Signature 2
Source: Figure S6
Description: Individual abundance histograms of bacterial lineages changing particularly in the fecal samples
Abundance in Group 1: decreased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Staphylococcus | ||
| Lactobacillus | ||
| Turicibacter |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum
Lab analysis
Statistical Analysis
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
Source: Figure S4
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.
Abundance in Group 1: increased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales bacterium | ||
| Rikenellaceae bacterium |
Signature 2
Source: Figure S4
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the cecum.
Abundance in Group 1: decreased abundance in PM 2.5 air exposed group
Experiment 4
Subjects
- 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
Lab analysis
Statistical Analysis
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
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
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
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure S5
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the colon
Abundance in Group 1: increased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Parabacteroides sp. | ||
| unclassified Parabacteroides |
Signature 2
Source: Figure S5
Description: Histograms of relative abundance of selected statistically differentially abundant genera in the colon
Abundance in Group 1: decreased abundance in PM 2.5 air exposed group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Clostridium | ||
| Turicibacter | ||
| Clostridiaceae | ||
| Clostridia | ||
| Clostridiales bacterium | ||
| unclassified Clostridia | ||
| unclassified Clostridiaceae |
Experiment 6
Subjects
- 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,Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,Intestinum tenue,Mid intestine,Small bowel,Small intestine,Hindgut,Large bowel,Posterior intestine,Colon
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
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
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 Control | Links |
|---|---|---|
| Lactobacillus | ||
| Staphylococcus | ||
| Bacilli |
Signature 2
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 Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Rikenellaceae | ||
| Bacteroidales |
