Subgingival Microbiota during Healthy Pregnancy and Pregnancy Gingivitis
-
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
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pregnancy Gestation,PREGN,Pregnancies,pregnancy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women sampled between 21 to 24 wk of gestation without gingivitis
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- increased
Signature 1
Source: Appendix Figure 1, 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: increased abundance in pregnant women without gingivitis
NCBI | Links |
---|---|
Bacteroides | |
Fusobacteriia | |
Fusobacterium | |
Spirochaetota | |
Treponema | |
Candidatus Saccharibacteria |
Signature 2
Source: Appendix Figure 2, text
Description: Phylum and Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: decreased abundance in pregnant women without gingivitis
NCBI | Links |
---|---|
Bergeyella | |
Gemella | |
Haemophilus | |
Streptococcus | |
Terrahaemophilus |
Experiment 2
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women with gingivitis
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Appendix Figure 1, 2, text
Description: Genera showing significant differential abundance in subgingival samples.
Abundance in Group 1: increased abundance in pregnant women with gingivitis
NCBI | Links |
---|---|
Bacteroides | |
Campylobacter | |
Candidatus Saccharibacteria | |
Filifactor ⚠ | |
Fretibacterium | |
Spirochaetota | |
Tannerella | |
Treponema |
Experiment 3
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- gingivitis acute gingivitis,chronic gingivitis,gingiva inflammation,gingivitis,inflammation of gingiva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pregnant women without gingivitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women with gingivitis
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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)
- .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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: increased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: Linear discriminant analysis effect size. Differentially abundant taxonomic profile of subgingival plaque (SGP) microbiota in pregnant women with gingivitis versus pregnant women without gingivitis
Abundance in Group 1: decreased abundance in pregnant women with gingivitis
Revision editor(s): Tislam
Experiment 4
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- pregnancy Gestation,PREGN,Pregnancies,pregnancy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non pregnant women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pregnant women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pregnant women
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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)
- .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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Source: Figure 3, text
Description: Linear discriminant analysis effect size. pregnant women without gingivitis versus nonpregnant women without gingivitis
Abundance in Group 1: increased abundance in pregnant women
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: pregnant women without gingivitis versus nonpregnant women without gingivitis
Abundance in Group 1: decreased abundance in pregnant women
NCBI | Links |
---|---|
Bergeyella sp. oral taxon 322 | |
Gemella morbillorum | |
Haemophilus sp. | |
Neisseria bacilliformis | |
Rothia aeria | |
Streptococcus sp. | |
Terrahaemophilus aromaticivorans |
Revision editor(s): Tislam