Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
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
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
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
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
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
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
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