Gestational diabetes-related gut microbiome dysbiosis is not influenced by different Asian ethnicities and dietary interventions: a pilot study
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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
Subjects
- Location of subjects
- Singapore
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gestational diabetes diabetes in pregnancy,GDM,gestational diabetes,gestational diabetes mellitus,maternal gestational diabetes mellitus,Gestational diabetes
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Gestational diabetes mellitus (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gestational diabetes mellitus (GDM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- maternal age, body weight, body height, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 2A
Description: Change in bacterial composition at phylum level between women with and without GDM.
Abundance in Group 1: increased abundance in Gestational diabetes mellitus (GDM)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Fusobacteriota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Figure 2A
Description: Change in bacterial composition at phylum level between women with and without GDM.
Abundance in Group 1: decreased abundance in Gestational diabetes mellitus (GDM)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota | ||
| Verrucomicrobiota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Chinese (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Chinese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- body weight, body height, body mass index, maternal age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: increased abundance in GDM_Chinese
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Figure 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: decreased abundance in GDM_Chinese
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota | ||
| Pseudomonadota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Malay (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Malay
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- body weight, maternal age, body mass index, body height
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: increased abundance in GDM_Malay
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Figure 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: decreased abundance in GDM_Malay
| NCBI | Quality Control | Links |
|---|---|---|
| Acidobacteriota | ||
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Indian (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Indian
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- body height, body mass index, body weight, maternal age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: increased abundance in GDM_Indian
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Figure 2B
Description: Change in bacterial composition at the phylum level between women with and without GDM in the different ethnic groups.
Abundance in Group 1: decreased abundance in GDM_Indian
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Gestational diabetes mellitus (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gestational diabetes mellitus (GDM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women diagnosed with Gestational diabetes mellitus (GDM) using WHO (World Health Organization) 2013 criteria: fasting plasma glucose ≥ 5.1 mmol/L, or a 1-h glucose ≥ 10.0 mmol/L, or a 2-h glucose ≥ 8.5 mmol/L.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Supplementary Table S3
Description: Detailed list of differentially ASVs between GDM and control pregnant women identified through DeSeq2.
Abundance in Group 1: increased abundance in Gestational diabetes mellitus (GDM)
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Table S3
Description: Detailed list of differentially ASVs between GDM and control pregnant women identified through DeSeq2.
Abundance in Group 1: decreased abundance in Gestational diabetes mellitus (GDM)
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Chinese (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Chinese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Chinese ethnicity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Supplementary Figure S1A
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Chinese ethnic group.
Abundance in Group 1: increased abundance in GDM_Chinese
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Figure S1A
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Chinese ethnic group.
Abundance in Group 1: decreased abundance in GDM_Chinese
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Malay (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Malay
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Malay ethnicity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Supplementary Figure S1B
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Malay ethnic group.
Abundance in Group 1: increased abundance in GDM_Malay
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Figure S1B
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Malay ethnic group.
Abundance in Group 1: decreased abundance in GDM_Malay
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control_Indian (non-GDM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM_Indian
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women with gestational diabetes mellitus (GDM) of Indian ethnicity.
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Supplementary Figure S1C
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Indian ethnic group.
Abundance in Group 1: increased abundance in GDM_Indian
Revision editor(s): Rahila, Aleru Divine, WikiWorks
Signature 2
Source: Supplementary Figure S1C
Description: Differentially abundant ASVs identified from DeSeq2 based analysis between GDM and non GDM mothers belonging to the Indian ethnic group.
Abundance in Group 1: decreased abundance in GDM_Indian
Revision editor(s): Rahila, Aleru Divine, WikiWorks
