A taxonomic signature of obesity in a large study of American adults
-
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 (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 211
- Group 1 sample size Number of subjects in the case (exposed) group
- 142
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
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
- 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, sex, polyp
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Supplemental Table 4
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in obese
Revision editor(s): WikiWorks743, Merit
Signature 2
Source: Supplemental Table 4
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in obese
Revision editor(s): WikiWorks743, Merit
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- overweight
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 211
- Group 1 sample size Number of subjects in the case (exposed) group
- 246
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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, sex, polyp
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table 4
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in overweight
Revision editor(s): WikiWorks743
Signature 2
Source: Supplemental Table 4
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in overweight
NCBI | Links |
---|---|
Christensenellaceae | |
Clostridiaceae | |
Dehalobacterium | |
Erysipelotrichaceae | |
Eubacteriales | |
Oscillospira | |
Oscillospiraceae | |
Parabacteroides |
Revision editor(s): WikiWorks743, Merit
Experiment 3
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight men
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obese men
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 80
- Group 1 sample size Number of subjects in the case (exposed) group
- 70
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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, sex, polyp
Signature 1
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in obese men
NCBI | Links |
---|---|
Parabacteroides distasonis | |
Bacilli | |
Lactobacillales | |
Lactobacillaceae | |
Lactobacillus | |
Streptococcus | |
Blautia | |
Oscillospiraceae | |
Veillonellaceae | |
Pseudomonadota | |
Gammaproteobacteria |
Revision editor(s): WikiWorks743
Signature 2
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in obese men
NCBI | Links |
---|---|
Clostridiaceae | |
Corynebacteriaceae | |
Corynebacterium | |
Dehalobacterium | |
Ruminococcus | |
Tissierellaceae |
Revision editor(s): WikiWorks743, Merit
Experiment 4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight men
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- overweight men
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m3
- Group 0 sample size Number of subjects in the control (unexposed) group
- 80
- Group 1 sample size Number of subjects in the case (exposed) group
- 171
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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, sex, polyp
Signature 1
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in overweight men
NCBI | Links |
---|---|
Bacteroides | |
Bacilli | |
Lactobacillales | |
Lactobacillaceae | |
Lactobacillus | |
Streptococcus | |
Blautia | |
Coprococcus | |
Lachnobacterium |
Revision editor(s): WikiWorks743
Signature 2
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in overweight men
Revision editor(s): WikiWorks743, Merit
Experiment 5
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight women
- 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
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m5
- Group 0 sample size Number of subjects in the control (unexposed) group
- 131
- Group 1 sample size Number of subjects in the case (exposed) group
- 72
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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, sex, polyp
Signature 1
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in obese women
Revision editor(s): WikiWorks743
Signature 2
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in obese women
NCBI | Links |
---|---|
Christensenellaceae | |
Clostridiaceae | |
Dehalobacterium | |
Clostridia | |
Clostridiales bacterium |
Revision editor(s): WikiWorks743, Merit
Experiment 6
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight 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
- Healthy-weight was defined as BMI ≥ 18.5 and <25 kg/m2, overweight as BMI ≥ 25 and <30 kg/m2, and obese as BMI ≥ 30 kg/m7
- Group 0 sample size Number of subjects in the control (unexposed) group
- 131
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- long term use in NYU study. NA for CDC study
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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, sex, polyp
Signature 1
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: increased abundance in overweight women
Revision editor(s): WikiWorks743
Signature 2
Source: Supplemental Table 5
Description: Taxonomic sginature of obesity in a large study of American adults
Abundance in Group 1: decreased abundance in overweight women
NCBI | Links |
---|---|
Clostridiaceae | |
Clostridia |
Revision editor(s): WikiWorks743, Merit