Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Mutlu EA, Comba IY, Cho T, Engen PA, Yazıcı C, Soberanes S, Hamanaka RB, Niğdelioğlu R, Meliton AY, Ghio AJ, Budinger GRS, Mutlu GM
Journal
Environmental pollution (Barking, Essex : 1987)
Year
2018
Keywords:
Air pollution, Feces, Gastrointestinal, Intestine, Microbiota
Recent studies suggest an association between particulate matter (PM) air pollution and gastrointestinal (GI) disease. In addition to direct deposition, PM can be indirectly deposited in oropharynx via mucociliary clearance and upon swallowing of saliva and mucus. Within the GI tract, PM may alter the GI epithelium and gut microbiome. Our goal was to determine the effect of PM on gut microbiota in a murine model of PM exposure via inhalation. C57BL/6 mice were exposed via inhalation to either concentrated ambient particles or filtered air for 8-h per day, 5-days a week, for a total of 3-weeks. At exposure's end, GI tract tissues and feces were harvested, and gut microbiota was analyzed. Alpha-diversity was modestly altered with increased richness in PM-exposed mice compared to air-exposed mice in some parts of the GI tract. Most importantly, PM-induced alterations in the microbiota were very apparent in beta-diversity comparisons throughout the GI tract and appeared to increase from the proximal to distal parts. Changes in some genera suggest that distinct bacteria may have the capacity to bloom with PM exposure. Exposure to PM alters the microbiota throughout the GI tract which maybe a potential mechanism that explains PM induced inflammation in the GI tract.
Experiment 1
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
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine,small intestine
- 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 ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Differences from previous experiment shown
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,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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Differences from previous experiment shown
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,caecum
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
Reviewed Marked as Reviewed by Rukky on 2023-3-28
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Differences from previous experiment shown
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,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
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
Experiment 5
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-19
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
Differences from previous experiment shown
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,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
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
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
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
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 |
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