Sex-specific effects of PM2.5 maternal exposure on offspring's serum lipoproteins and gut microbiota
-
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
- China
- 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
- mice dams exposed to filtered blanks PND 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR male mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5 air
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- 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
- V3-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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7a & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
Roseburia | |
Alistipes | |
Lachnospiraceae | |
Rikenellaceae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7a & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
Aerococcaceae | |
Facklamia ⚠ | |
Neisseria | |
Neisseriaceae | |
Neisseriales | |
Staphylococcaceae | |
Escherichia/Shigella sp. |
Experiment 2
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 10
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR male mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7b & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
Clostridiaceae | |
Proteus | |
Pseudonocardiales | |
g__clostridium sensu strictog__clostridium sensu stricto |
Experiment 3
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 21
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR male mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7c & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
g__clostridium xivag__clostridium xiva | |
Bacillales Family X. Incertae Sedis | |
Gemella | |
Oscillibacter | |
Roseburia | |
Bacillales |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7c & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
Bacteroides | |
Bacteroidaceae | |
Desulfovibrio | |
Anaerotruncus |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 35
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR male mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 7d& text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR male mice exposed to PM 2.5
NCBI | Links |
---|---|
Streptococcus | |
Streptomycetaceae |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 10
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR female mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7f & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
k__bacteriak__bacteria |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7f & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
Coriobacteriales | |
Enterorhabdus | |
Prevotellaceae | |
g__entemoacterg__entemoacter | |
Coriobacteriaceae |
Experiment 6
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 21
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR female mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Subject page title: | Sex-specific effects of PM2.5 maternal exposure on offspring's serum lipoproteins and gut microbiota/Experiment 6/Signature 1 |
---|---|
Reviewer: | Rukky |
Review date: | 2023-3-28 |
Review state: | Reviewed |
Quality control tags: |
Source: Figure 7g & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
Deltaproteobacteria | |
Desulfovibrionaceae | |
Desulfovibrionales | |
Verrucomicrobiaceae | |
Verrucomicrobiae | |
Verrucomicrobiales | |
Verrucomicrobiota | |
Anaerostipes sp. |
Signature 2
Source: Figure 7g & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
Lactobacillaceae | |
Lactobacillus | |
f__chloroplastf__chloroplast | |
p__cyanobacteria_Chloroplastp__cyanobacteria_Chloroplast | |
c__chloroplastc__chloroplast | |
Streptophyta |
Experiment 7
Subjects
- Location of subjects
- China
- 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
- mice dams exposed to filtered blanks PND 35
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ICR female mice exposed to PM 2.5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ICR mice exposed to PM 2.5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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)?
- No
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 7h & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: increased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
Oscillospiraceae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 7h & text
Description: LEfSe analysis of male offspring on PND 3 (a), PND 10 (b), PND 21 (c), PND 35 (d). LEfSe analysis of female offspring on PND 3 (e), PND 10 (f), PND 21 (g), PND 35 (h). N = 8/group/gender/time.
Abundance in Group 1: decreased abundance in ICR female mice exposed to PM 2.5
NCBI | Links |
---|---|
Peptostreptococcaceae | |
g__clostridium_XIg__clostridium_XI |
Revision editor(s): WikiWorks