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 Uniform resource identifier for web resources.
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
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
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
Needs review
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 | Links |
|---|---|
| unclassified Bacteroidales | |
| unclassified Lactobacillaceae | |
| Lactobacillus | |
| Lactobacillales | |
| Bacteroidaceae | |
| Bacteroidales |
Signature 2
Needs review
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 | Links |
|---|---|
| Lactobacillus | |
| Staphylococcus | |
| unclassified Aerococcaceae |
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Mus musculus
- 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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
Needs review
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 | Links |
|---|---|
| Bacteroidales | |
| Lachnospiraceae | |
| Rickenellaceae | |
| Lachnospira | |
| Bacteroidaceae | |
| Bacteroides | |
| Bacteroidales bacterium | |
| Bacteroidaceae bacterium |
Signature 2
Needs review
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 | Links |
|---|---|
| Bacteroides | |
| Staphylococcus | |
| Lactobacillus | |
| Turicibacter |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Mus musculus
- 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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
| Subject page title: | Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome/Experiment 3/Signature 1 |
|---|---|
| Reviewer: | Rukky |
| Review date: | 2023-3-28 |
| Review state: | Reviewed |
| Quality control tags: |
Needs review
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 | Links |
|---|---|
| Bacteroidales bacterium | |
| Rikenellaceae bacterium |
Signature 2
Needs review
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
| NCBI | Links |
|---|---|
| Bacteroidaceae | |
| Bacteroidaceae bacterium | |
| Bacteroidales | |
| Bacteroidales bacterium | |
| Bacteroides | |
| Oscillospira | |
| Oscillospiraceae | |
| Ruminococcus | |
| Staphylococcaceae | |
| Staphylococcus | |
| Turicibacter |
Experiment 4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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 2
Needs review
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 | Links |
|---|---|
| Lactobacillus |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
- unchanged
- Richness Number of species
- increased
Signature 1
Needs review
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 | Links |
|---|---|
| Parabacteroides | |
| Parabacteroides sp. | |
| unclassified Parabacteroides |
Signature 2
Needs review
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 | Links |
|---|---|
| Anaeroplasma | |
| Clostridium | |
| Turicibacter | |
| Clostridiaceae | |
| Clostridia | |
| Clostridiales bacterium | |
| unclassified Clostridia | |
| unclassified Clostridiaceae |
Experiment 6
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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,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
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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
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