Roseburia hominis improves host metabolism in diet-induced obesity
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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
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- High fat diet HF - High fat diet,High fat diet (finding),High fat diet,high fat diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Fat Diet-Phosphate-buffered saline (HFD-PBS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Fat Diet- Roseburia hominis (HFD-RH)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice were fed high-fat diet (40% fat), and orally challenged with 10⁹ colony forming units of Roseburia hominis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
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).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4c and Figure 4d
Description: LDA effect size at the genus and species level between HFD-RH and HFD-PBS group by LEfSe
Abundance in Group 1: increased abundance in High Fat Diet- Roseburia hominis (HFD-RH)
Signature 2
Source: Figure 4c and Figure 4d
Description: LDA effect size at the genus and species level between HFD-RH and HFD-PBS group by LEfSe
Abundance in Group 1: decreased abundance in High Fat Diet- Roseburia hominis (HFD-RH)
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body weight gain Body weight gain,body weight gain
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Body Weight gain
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Body Weight gain
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Mice were characterized based on body weight gain.
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure 4E
Description: Body weight gain correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High Body Weight gain
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis | ||
| Staphylococcus xylosus |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Body weight gain correlation of differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High Body Weight gain
| NCBI | Quality Control | Links |
|---|---|---|
| Herbinix luporum | ||
| Turicimonas muris | ||
| Butyrivibrio fibrisolvens |
Revision editor(s): Z.uk.a
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body mass index BMI,Quetelet's Index,Body mass index,body mass index
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Body Mass Index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Body Mass Index
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Mice were differentiated based on changes in Body Mass Index.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Body Mass Index correlation of differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High Body Mass Index
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis | ||
| Staphylococcus xylosus | ||
| Faecalibaculum rodentium |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Body Mass Index correlation of differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High Body Mass Index
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body fat percentage Body fat percentage,body fat percentage
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Body Fat Percentage [Lee Index}
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Body Fat Percentage [Lee Index]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 consists of mice who were characterized by their Body fat percentage (Lee Index)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Body Fat Percentage correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High Body Fat Percentage [Lee Index]
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis | ||
| Staphylococcus xylosus |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Body Fat Percentage correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High Body Fat Percentage [Lee Index]
Revision editor(s): Z.uk.a
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Insulin resistance Drug resistance to insulin (disorder),Insulin resistance,insulin resistance
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low insulin resistance
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High insulin resistance
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The mice in Group 1 were selected as those with high insulin resistance
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Insulin Receptors correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High insulin resistance
| NCBI | Quality Control | Links |
|---|---|---|
| Romboutsia ilealis | ||
| Staphylococcus xylosus |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Insulin receptors correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High insulin resistance
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium sp. YL32 | ||
| Lactobacillus johnsonii | ||
| Parabacteroides goldsteinii | ||
| Turicimonas muris |
Revision editor(s): Z.uk.a
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Total cholesterol measurement cholesterol, total,total cholesterol levels,Total cholesterol measurement,total cholesterol measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low total cholesterol
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High total cholesterol
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 consists of mice with High Cholesterol levels.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Total Cholesterol correlation of differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High total cholesterol
| NCBI | Quality Control | Links |
|---|---|---|
| Berryella intestinalis | ||
| Faecalibaculum rodentium | ||
| Romboutsia ilealis | ||
| Staphylococcus xylosus | ||
| Eggerthella guodeyinii |
Signature 2
Source: Figure 4E
Description: Total Cholesterol correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High total cholesterol
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triglyceride change measurement Triglyceride change measurement,triglyceride change measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low triglycerides
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High triglycerides
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1 Mice were distinguished by High Triglyceride levels
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Triglyceride correlation differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High triglycerides
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibaculum rodentium | ||
| Staphylococcus xylosus |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Triglyceride correlation of differential species in mice between HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High triglycerides
Revision editor(s): Z.uk.a
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Aspartate aminotransferase measurement Aspartate transaminase measurement,Aspartate aminotransferase measurement,aspartate aminotransferase measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low in aspartate aminotransferase
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High in aspartate aminotransferase
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice were characterized by having high levels of aspartate aminotransferase enzymes
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Aspartate aminotransferase levels show differential correlation between species in mice from the HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High in aspartate aminotransferase
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibaculum rodentium | ||
| Romboutsia ilealis | ||
| Staphylococcus xylosus |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Aspartate aminotransferase levels show differential correlation between species in mice from the HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High in aspartate aminotransferase
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium sp. YL32 | ||
| Lactobacillus johnsonii | ||
| Parabacteroides goldsteinii |
Revision editor(s): Z.uk.a
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alanine measurement Alanine measurement,alanine measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low in alanine transaminase
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High in alanine transaminase
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice in this group are characterized by high levels of alanine transaminase enzymes
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Alanine transaminase correlation of differential species in mice between the HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High in alanine transaminase
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibaculum rodentium |
Revision editor(s): Z.uk.a
Signature 2
Source: Figure 4E
Description: Alanine transaminase correlation of differential species in mice between the HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High in alanine transaminase
| NCBI | Quality Control | Links |
|---|---|---|
| Herbinix luporum | ||
| Lachnoclostridium sp. YL32 | ||
| Butyrivibrio fibrisolvens | ||
| [Clostridium] innocuum | ||
| Lactobacillus johnsonii |
Revision editor(s): Z.uk.a
Experiment 10
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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
- Lean control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obese patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects with BMI greater than or equal to 28 Kg/m2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
Signature 1
Source: Figure 1A,B & D
Description: The prevalence and relative abundance of bacteria in obese and lean subjects detected by metagenomics sequencing .
Abundance in Group 1: decreased abundance in Obese patients
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia hominis |
Experiment 11
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Triglyceride C6H5O6R3,Triacylglycerol,triacylglycerols,Triglycerid,Triglyceride,triglycerides,Triglyzerid,triglyceride
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Hepatic triglycerides
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Hepatic triglycerides
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The mice in group 1 consists of mice with High levels of hepatic triglycerides
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Signature 1
Source: Figure 4E
Description: Hepatic triglyceride correlation of differential species in mice between the HFD-PBS and HFD-RH groups
Abundance in Group 1: increased abundance in High Hepatic triglycerides
| NCBI | Quality Control | Links |
|---|---|---|
| Berryella intestinalis | ||
| Faecalibaculum rodentium | ||
| Romboutsia ilealis | ||
| Staphylococcus xylosus | ||
| Eggerthella guodeyinii |
Signature 2
Source: Figure 4E
Description: Hepatic triglyceride levels exhibit differential correlations with species in mice between the HFD-PBS and HFD-RH groups
Abundance in Group 1: decreased abundance in High Hepatic triglycerides
Revision editor(s): Z.uk.a
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to high fat food intake Response to high fat food intake,response to high fat food intake
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Fat Diet- Roseburia hominis (HFD-RH) mice at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Fat Diet- Roseburia hominis (HFD-RH) mice at endpoint
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice were characterized after the intervention of Roseburia hominis for 11 weeks
Signature 1
Source: Figure S2B
Description: The change of relative abundance of Roseburia hominis in HFD-fed mice before and after the intervention for 11 weeks.
Abundance in Group 1: increased abundance in High Fat Diet- Roseburia hominis (HFD-RH) mice at endpoint
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia hominis |
Revision editor(s): Ese
