Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women
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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
- Ghana
- 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
- 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
- Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean Ghanaians (GL)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the Lean Ghanaians (GL) group were women from Ghana with body mass index (BMI) < 25 kg/m2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 71
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Linear Regression
- 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
Signature 1
Source: Figure 3F and Table S4
Description: Fold change difference of the average abundance of all phenotypic differences (i.e., African American women and obese Ghanaians) versus lean Ghanaians.
Abundance in Group 1: increased abundance in Lean Ghanaians (GL)
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3F and Table S4
Description: Fold change difference of the average abundance of all phenotypic differences (i.e., African American women and obese Ghanaians) versus lean Ghanaians.
Abundance in Group 1: decreased abundance in Lean Ghanaians (GL)
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Location of subjects
- Ghana
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Ghanaians (GL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese Ghanaians(GO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the Obese Ghanaians (GO) group were women from Ghana with body mass index (BMI) > 25 kg/m2.
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)
Abundance in Group 1: increased abundance in Obese Ghanaians(GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)
Abundance in Group 1: decreased abundance in Obese Ghanaians(GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Bacillota | ||
| Bacteria | ||
| Bacteroides | ||
| Bacteroides ovatus | ||
| Bacteroides uniformis | ||
| Odoribacter | ||
| Oscillospiraceae | ||
| Phascolarctobacterium | ||
| Rikenellaceae |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Location of subjects
- Ghana
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Obese Ghanaians(GO)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese Americans (UO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the Obese Americans (UO) group were women from America with body mass index (BMI) > 25 kg/m2.
- 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
- 37
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)
Abundance in Group 1: increased abundance in Obese Americans (UO)
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)
Abundance in Group 1: decreased abundance in Obese Americans (UO)
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Location of subjects
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Americans (UL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese Americans(UO)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese)
Abundance in Group 1: increased abundance in Obese Americans(UO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Collinsella aerofaciens | ||
| Eubacteriales | ||
| Oscillospiraceae | ||
| Segatella copri |
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in Obese Americans(UO)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| Oscillospiraceae |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Location of subjects
- Ghana
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Ghanaians(GL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean Americans (UL)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the Lean Americans (UL) group were women from America with body mass index (BMI) < 25 kg/m2.
- 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
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in Lean Americans (UL)
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in Lean Americans (UL)
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ghana Women (GL + GO)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- American Women (UL + UO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the American Women (UL + UO) group were women from America who were both lean and obese.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in American Women (UL + UO)
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in American Women (UL + UO)
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- All Lean Women (UL + GL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- All Obese Women (UO + GO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in the All Obese Women (UO + GO) group were women from both America and Ghana with body mass index (BMI) > 25 kg/m2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in All Obese Women (UO + GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella aerofaciens | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Segatella copri | ||
| [Ruminococcus] torques |
Revision editor(s): Aleru Divine
Signature 2
Source: Table S4
Description: Sequences with significantly different levels across the groups: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in All Obese Women (UO + GO)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Bacteroides | ||
| Bacteroides uniformis | ||
| Oscillospira | ||
| Oscillospiraceae |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Location of subjects
- Ghana
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Ghanaians (GL) humanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese Ghanaians(GO) humanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice humanized by fecal samples from participants in the Obese Ghanaians (GO) group, defined as women from Ghana with a body mass index (BMI) > 25 kg/m².
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.001
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S15
Description: Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in Obese Ghanaians(GO) humanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Parabacteroides distasonis |
Revision editor(s): Aleru Divine
Experiment 9
Experiment 10
Experiment 11
Subjects
- Location of subjects
- Ghana
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Ghanaians(GL) humanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean Americans (UL) humanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice humanized by fecal samples from participants in the Lean Americans (UL) group, defined as women from America with a body mass index (BMI) < 25 kg/m².
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S15
Description: Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in Lean Americans (UL) humanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Ligilactobacillus ruminis | ||
| Parabacteroides distasonis | ||
| Sutterella |
Revision editor(s): Aleru Divine
Experiment 12
Subjects
- Location of subjects
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lean Ghana (GL) humanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese Americans(UO) humanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice humanized by fecal samples from participants in the Obese Americans (GO) group, defined as women from America with a body mass index (BMI) < 25 kg/m².
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S15
Description: Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: increased abundance in Obese Americans(UO) humanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Sutterella |
Revision editor(s): Aleru Divine
Experiment 13
Subjects
- Location of subjects
- Ghana
- United States of America
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ghana Women (GL + GO) humanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- American Women (UL + UO) humanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice humanized by fecal samples from the African American women groups (UL + UO).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Table S15
Description: Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in American Women (UL + UO) humanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Parabacteroides distasonis |
Revision editor(s): Aleru Divine
Experiment 14
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- (Obese Ghanaians(GO) + Obese Americans(UO) + Lean Americans(UL)) humanized mice
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lean Ghanaians (GL) humanized mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice humanized by fecal samples from participants in the Lean Ghanaians (GL) group, defined as women from Ghana with a body mass index (BMI) < 25 kg/m².
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Table S15
Description: Sequences with significantly different levels across the groups in the Murine samples: GL (Ghana Lean), GO (Ghana Obese), UL (USA Lean), and UO (USA Obese).
Abundance in Group 1: decreased abundance in Lean Ghanaians (GL) humanized mice
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Parabacteroides distasonis | ||
| Sutterella |
Revision editor(s): Aleru Divine
