Effects of sex and chronic cigarette smoke exposure on the mouse cecal 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
Tam A, Filho FSL, Ra SW, Yang J, Leung JM, Churg A, Wright JL, Sin DD
Journal
PloS one
Year
2020
RATIONALE: Chronic smoke exposure is associated with weight loss in patients with Chronic Obstructive Pulmonary Disease (COPD). However, the biological contribution of chronic smoking and sex on the cecal microbiome has not been previously investigated. METHODS: Adult male, female and ovariectomized mice were exposed to air (control group) or smoke for six months using a standard nose-only smoke exposure system. DNA was extracted from the cecal content using the QIAGEN QIAamp® DNA Mini Kit. Droplet digital PCR was used to generate total 16S bacterial counts, followed by Illumina MiSeq® analysis to determine microbial community composition. The sequencing data were resolved into Amplicon Sequence Variants and analyzed with the use of QIIME2®. Alpha diversity measures (Richness, Shannon Index, Evenness and Faith's Phylogenetic Diversity) and beta diversity (based on Bray-Curtis distances) were assessed and compared according to smoke exposure and sex. RESULTS: The microbial community was different between male and female mice, while ovariectomy made the cecal microbiome similar to that of male mice. Chronic smoke exposure led to significant changes in the cecal microbial community in both male and female mice. The organism, Alistipes, was the most consistent bacteria identified at the genus level in the cecal content that was reduced with chronic cigarette exposure and its expression was positively related to the whole-body weight of these mice. CONCLUSION: Chronic smoke exposure is associated with changes in the cecal content microbiome; these changes may play a role in the weight changes that are observed in cigarette smokers.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- Canada
- 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
- all other mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- male mice exposed to cigarette smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- male mice exposed to smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 7
Description: Differentially abundant taxa in the smoke-exposed male mice versus all other mice
Abundance in Group 1: increased abundance in male mice exposed to cigarette smoke
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- Canada
- 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
- all other mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- female mice exposed to cigarette smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- female mice exposed to cigarette smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- 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
- Illumina
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 7
Description: Differentially abundant taxa in the smoke-exposed female mice versus all other mice
Abundance in Group 1: increased abundance in female mice exposed to cigarette smoke
| NCBI | Links |
|---|---|
| Bacteroidaceae | |
| Bacteroides | |
| Muribaculaceae |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- Canada
- 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
- all other mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ovariectomized female mice exposed to cigarette smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ovariectomized female mice exposed to smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- 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
- Illumina
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 7
Description: Differentially abundant taxa in the smoke-exposed ovariectomized female mice versus all other mice
Abundance in Group 1: increased abundance in ovariectomized female mice exposed to cigarette smoke
| NCBI | Links |
|---|---|
| Butyrivibrio | |
| Prevotellaceae | |
| Rikenella ⚠ | |
| g__prevotellaceae_NK3B1_groupg__prevotellaceae_NK3B1_group | |
| g__ruminococcaceae_UCG_007g__ruminococcaceae_UCG_007 |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- Canada
- 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
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mice exposed to smoke
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- male, female or ovariectomized females mice exposed to smoke
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 2
Description: Differential microbial taxa between the control and smoke-exposed groups
Abundance in Group 1: increased abundance in mice exposed to smoke
Revision editor(s): WikiWorks743, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/7
Source: Figure 2
Description: Differential microbial taxa between the control and smoke-exposed groups
Abundance in Group 1: decreased abundance in mice exposed to smoke
| NCBI | Links |
|---|---|
| Alistipes | |
| Lachnospiraceae | |
| Muribaculaceae | |
| Rikenellaceae | |
| g__f__Xll_UGC_001g__f__Xll_UGC_001 | |
| uncultured Bacteroidales bacterium |
Revision editor(s): WikiWorks743, Claregrieve1
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