Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum
-
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
- Denmark
- 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
- Normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gestational diabetes mellitus (GDM) pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) pregnancy (third trimester) during the first visit
- Group 0 sample size Number of subjects in the control (unexposed) group
- 161
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- 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
- 2.0
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: FIG 2 (B)
Description: Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: increased abundance in gestational diabetes mellitus (GDM) pregnancy
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: decreased abundance in gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerosporobacter | ||
| Acetivibrio | ||
| Marvinbryantia |
Revision editor(s): Rahila
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Previous normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Previous GDM pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) pregnancy Postpartum (average of nine months) during second visit
- Group 0 sample size Number of subjects in the control (unexposed) group
- 82
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Signature 1
Source: FIG 2 (D)
Description: Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: increased abundance in Previous GDM pregnancy
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (D)
Description: Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: decreased abundance in Previous GDM pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Pseudomonadales | ||
| Ruminococcus2Ruminococcus2 |
Revision editor(s): Rahila
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Preceding normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Preceding gestational diabetes mellitus (GDM) pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) during third trimester pregnancy within genus-level OTUs
- Group 0 sample size Number of subjects in the control (unexposed) group
- 79
Lab analysis
Statistical Analysis
- Statistical test
- Wald Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Table S5
Description: Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level
Abundance in Group 1: increased abundance in Preceding gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Blautia | ||
| Ruminococcus2Ruminococcus2 |
Revision editor(s): Rahila
Signature 2
Source: Table S5
Description: Operational taxonomic units differentially abundant in women with and without gestational diabetes during third trimester pregnancy at the genus level
Abundance in Group 1: decreased abundance in Preceding gestational diabetes mellitus (GDM) pregnancy
Revision editor(s): Rahila
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Previous normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Previous gestational diabetes mellitus (GDM) pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) average of 8.8 months postpartum pregnancy within genus-level OTUs
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level
Abundance in Group 1: increased abundance in Previous gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Clostridium sensu strictoClostridium sensu stricto | ||
| Collinsella | ||
| Anaerovorax | ||
| Alistipes | ||
| Phreatobacter |
Revision editor(s): Rahila
Signature 2
Source: Table S5
Description: Operational taxonomic units differentially abundant in women with and without gestational diabetes at postpartum pregnancy at the genus level
Abundance in Group 1: decreased abundance in Previous gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae incertae sedis | ||
| Clostridium IVClostridium IV | ||
| Isobaculum | ||
| Bacteroides | ||
| Eggerthella | ||
| Faecalibacterium |
Revision editor(s): Rahila
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal pre-pregnancy BMI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight pre-pregnancy BMI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women that shows overweight pre-pregnancy BMI
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S12
Description: Taxonomic biomarkers of overweight down to genus level identified by linear discriminant analysis (LDA) using LEfSe.
Abundance in Group 1: increased abundance in Overweight pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Porphyromonas |
Revision editor(s): Rahila
Signature 2
Source: Figure S12
Description: Taxonomic biomarkers of overweight down to genus level identified by linear discriminant analysis (LDA) using LEfSe.
Abundance in Group 1: decreased abundance in Overweight pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiaceae | ||
| Verrucomicrobiales | ||
| Verrucomicrobiia | ||
| Verrucomicrobiota | ||
| Akkermansia | ||
| Eggerthella | ||
| Clostridium XVIIIClostridium XVIII | ||
| Sporobacter | ||
| Ethanoligenens | ||
| Oscillibacter |
Revision editor(s): Rahila
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obesity pre-pregnancy BMI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Pregnant women that shows obesity pre-pregnancy BMI
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S12
Description: Taxonomic biomarkers of Obesity down to genus level identified by linear discriminant analysis (LDA) using LEfSe.
Abundance in Group 1: increased abundance in obesity pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Acidaminococcus | ||
| Ruminococcus2Ruminococcus2 |
Revision editor(s): Rahila
Signature 2
Source: Figure S12
Description: Taxonomic biomarkers of Obesity down to genus level identified by linear discriminant analysis (LDA) using LEfSe.
Abundance in Group 1: decreased abundance in obesity pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Ethanoligenens | ||
| Sporobacter | ||
| Eggerthella | ||
| Erysipelotrichaceae incertae sedis |
Revision editor(s): Rahila
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Overweight women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Operational taxonomic units differentially abundant in women with Overweight body mass index during third trimester of pregnancy
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
Lab analysis
Statistical Analysis
- Statistical test
- Wald Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S10
Description: Operational taxonomic units differentially abundant in pregnant women between Overweight and Lean pre-pregnancy body mass index
Abundance in Group 1: increased abundance in Overweight women
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium |
Revision editor(s): Rahila
Signature 2
Source: Table S10
Description: Operational taxonomic units differentially abundant in pregnant women between Overweight and Lean pre-pregnancy body mass index
Abundance in Group 1: decreased abundance in Overweight women
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter |
Revision editor(s): Rahila
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese women
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Operational taxonomic units differentially abundant in women with Obesity during third trimester of pregnancy
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S10
Description: Operational taxonomic units differentially abundant in pregnant women between Obese and Lean pre-pregnancy body mass index
Abundance in Group 1: increased abundance in Obese women
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Blautia | ||
| Erysipelotrichaceae incertae sedis | ||
| Roseburia | ||
| Ruminococcus2Ruminococcus2 | ||
| Faecalibacterium |
Revision editor(s): Rahila
Signature 2
Source: Table S10
Description: Operational taxonomic units differentially abundant in pregnant women between Obese and Lean pre-pregnancy body mass index
Abundance in Group 1: decreased abundance in Obese women
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Streptococcus | ||
| Blautia | ||
| Eisenbergiella | ||
| Butyricicoccus | ||
| Oscillibacter | ||
| Papillibacter | ||
| Sporobacter | ||
| Asteroleplasma |
Revision editor(s): Rahila
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycaemic adjusting for pre-pregnancy BMI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM adjusting for pre-pregnancy BMI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Operational taxonomic units differentially abundant in pregnant women with GDM adjusted for pre-pregnancy BMI
- Group 0 sample size Number of subjects in the control (unexposed) group
- 143
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S11.
Description: Operational taxonomic units differentially abundant in pregnant women with GDM and normal glucose regulation adjusted for pre-pregnancy BMI
Abundance in Group 1: increased abundance in GDM adjusting for pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Faecalibacterium |
Revision editor(s): Rahila
Signature 2
Source: Table S11.
Description: Operational taxonomic units differentially abundant in pregnant women with GDM and normal glucose regulation adjusted for pre-pregnancy BMI
Abundance in Group 1: decreased abundance in GDM adjusting for pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella | ||
| Clostridium sensu strictoClostridium sensu stricto |
Revision editor(s): Rahila
Signature 3
Source: Table S12
Description: Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age
Abundance in Group 1: increased abundance in GDM adjusting for pre-pregnancy BMI
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Eisenbergiella | ||
| Faecalibacterium | ||
| Tardiphaga |
Revision editor(s): Rahila
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycaemic weight gain during pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GDM weight gain during pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S12
Description: Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age
Abundance in Group 1: increased abundance in GDM weight gain during pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Eisenbergiella | ||
| Faecalibacterium | ||
| Tardiphaga |
Revision editor(s): Rahila
Signature 2
Source: Table S12
Description: Operational taxonomic units associated with weight gain during pregnancy adjusted for pre-pregnancy BMI and gestational age
Abundance in Group 1: decreased abundance in GDM weight gain during pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Blautia | ||
| Christensenella | ||
| Oscillibacter | ||
| Sporobacter | ||
| Veillonella | ||
| Clostridium IVClostridium IV |
Revision editor(s): Rahila
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Preceding normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Preceding gestational diabetes mellitus (GDM) pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) pregnancy (third trimester)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 79
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: FIG 2 (B)
Description: Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: increased abundance in Preceding gestational diabetes mellitus (GDM) pregnancy
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (B)
Description: Taxonomic biomarkers of gestational diabetes during 3rd trimester of pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: decreased abundance in Preceding gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerosporobacter | ||
| Acetivibrio | ||
| Marvinbryantia |
Revision editor(s): Rahila
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Previous normoglycaemic pregnancy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Previous gestational diabetes mellitus (GDM) pregnancy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with gestational diabetes mellitus (GDM) pregnancy (8.8 months postpartum)
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: FIG 2 (D)
Description: Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: increased abundance in Previous gestational diabetes mellitus (GDM) pregnancy
Revision editor(s): Rahila
Signature 2
Source: FIG 2 (D)
Description: Taxonomic biomarkers of gestational diabetes during postpartum pregnancy identified by linear discriminant analysis (LDA) using LEfSe .
Abundance in Group 1: decreased abundance in Previous gestational diabetes mellitus (GDM) pregnancy
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Pseudomonadales | ||
| Ruminococcus2Ruminococcus2 |
Revision editor(s): Rahila
