Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
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
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
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
Reviewed Marked as Reviewed by Svetlana up on 2025-3-3
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
