Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes
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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
- United States of America
- 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
- Blood , Feces Portion of blood,Vertebrate blood,Whole blood,Blood,blood,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
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-T2D(prediabetes)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- type 2 diabetes (T2D)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Spearman Correlation
- 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, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- 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
- decreased
Signature 1
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraph 2, line 3-6, figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.
Abundance in Group 1: increased abundance in type 2 diabetes (T2D)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lactobacillus | ||
| Veillonella |
Signature 2
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraph 2, line 3-6, figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with age.
Abundance in Group 1: decreased abundance in type 2 diabetes (T2D)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Faecalibacterium | ||
| Faecalibacterium prausnitzii |
Revision editor(s): Folakunmi
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces , Blood 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,Portion of blood,Vertebrate blood,Whole blood,Blood,blood
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cytokine Cytokine,cytokine
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Type 2 Diabetes (Prediabetes)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Type 2 Diabetes
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with chronic metabolic condition characterized by high levels of blood sugar (glucose), insulin resistance, and relative insulin deficiency, after adjusting for age (used as a covariate).
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- 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
- decreased
Signature 1
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraph 3, Figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a
Abundance in Group 1: increased abundance in Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Parabacteroides |
Signature 2
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraph 3, Figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with the inflammatory cytokine TNF-a
Abundance in Group 1: decreased abundance in Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Collinsella aerofaciens |
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- 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
- decreased
Signature 1
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraph 4, Figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with dietary fiber.
Abundance in Group 1: increased abundance in Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Lactobacillus |
Revision editor(s): Folakunmi
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HbA1c measurement A1C measurement,A1c measurement,glycated hemoglobin levels,glycosylated Haemoglobin A level,Glycosylated Hemoglobin,glycosylated Hemoglobin A level,Glycosylated Hemoglobin Measurement,HBA1C,HbA1c levels,Hemoglobin A1C,HbA1c measurement,hbA1c measurement
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- 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
- decreased
Signature 1
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraphs 3 and 4, Figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c
Abundance in Group 1: increased abundance in Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium |
Revision editor(s): Folakunmi
Signature 2
Source: Within result text under "Association between gut microbiota composition and glycemic status", paragraphs 3 and 4, Figure 3
Description: Spearman correlation matrix heatmap of inflammatory associated taxonomic groups with clinical biomarkers and dietary data, showing fecal pro-inflammatory bacteria and anti-inflammatory/SCFA-producing bacteria correlated with HbA1c
Abundance in Group 1: decreased abundance in Type 2 Diabetes
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): Folakunmi
