Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment
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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
- India
- 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
- Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hyperglycemia High blood glucose,High blood sugar,Hyperglycemia,hyperglycemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normoglycemic group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hyperglycemic group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The hyperglycemic group consists of subjects with fasting plasma glucose(FPG) > 100 mg/dl and hemoglobin A1C (HbA1c) ≥ 5.7%.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6–8 weeks
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "sequencing batch effects" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sequencing batch effects
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3C
Description: Histograms showing the differential abundant features in duodenal microbiota obtained using DESeq2 in hyperglycemic and normoglycemic subjects at order, family, and genus-species level.
Abundance in Group 1: increased abundance in Hyperglycemic group
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Acinetobacter haemolyticus | ||
| Turicibacter sanguinis | ||
| Dolosigranulum pigrum | ||
| Neisseria subflava | ||
| Veillonella tobetsuensis | ||
| Streptococcus cristatus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3C
Description: Histograms showing the differential abundant features in duodenal microbiota obtained using DESeq2 in hyperglycemic and normoglycemic subjects at order, family, and genus-species level.
Abundance in Group 1: decreased abundance in Hyperglycemic group
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces , Duodenum 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,Proximal intestine,Upper intestine,Duodenum,duodenum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Stool samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Biopsy samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Duodenal biopsy samples from 54 participants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 54
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Table 1
Description: Table depicting differentially abundant species in biopsy compared to stool, analyzed using DESeq2 package.
Abundance in Group 1: increased abundance in Biopsy samples
Revision editor(s): Aleru Divine
Signature 2
Source: Supplementary Table 2
Description: Table depicting differentially abundant species in stool compared to biopsy analysed using DESeq2 package.
Abundance in Group 1: decreased abundance in Biopsy samples
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Duodenal biopsy samples from participants with hyperglycemia.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 1
Description: Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.
Abundance in Group 1: increased abundance in Biopsy samples
Revision editor(s): Aleru Divine
Signature 2
Source: Supplementary Figure 1
Description: Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.
Abundance in Group 1: decreased abundance in Biopsy samples
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonadales | ||
| Bacillota | ||
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Clostridia | ||
| Erysipelotrichia | ||
| Eubacteriales | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Prevotellaceae | ||
| Succinivibrionaceae |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Duodenal biopsy samples from normoglycemic participants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 1
Description: Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.
Abundance in Group 1: increased abundance in Biopsy samples
Revision editor(s): Aleru Divine
Signature 2
Source: Supplementary Figure 1
Description: Boxplot showing the comparison of top taxa between hyperglycemic and normoglycemic groups in stool and duodenum samples at Phylum, Class, Order and Family levels.
Abundance in Group 1: decreased abundance in Biopsy samples
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Bacillota | ||
| Bacteroidia | ||
| Clostridia | ||
| Erysipelotrichia | ||
| Bacteroidales | ||
| Aeromonadales | ||
| Eubacteriales | ||
| Prevotellaceae | ||
| Succinivibrionaceae | ||
| Lachnospiraceae | ||
| Oscillospiraceae |
Revision editor(s): Aleru Divine
