Sex-specific effects of PM 2.5 maternal exposure on offspring's serum lipoproteins and gut microbiota

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Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Lwaldron, WikiWorks

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.

Revision editor(s): Lwaldron, WikiWorks

Experiment 2

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Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Levitest, WikiWorks

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

Revision editor(s): Levitest, WikiWorks

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks, Atrayees

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

Revision editor(s): WikiWorks, Atrayees

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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 PM_2.5 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:

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks, Rukky

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.

Revision editor(s): WikiWorks, Rukky

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): Aiyshaaaa, WikiWorks

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

Revision editor(s): Aiyshaaaa, WikiWorks

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Needs review

Curated date: 2021/01/10

Curator: Zyaijah Bailey

Revision editor(s): WikiWorks

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