Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome
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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 Kingdom
- 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
- Beverage consumption measurement Beverage consumption measurement,beverage consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non yoghurt eaters
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Yoghurt eaters
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individual who have consumed yoghurt for at least once in a week.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 400
- Group 1 sample size Number of subjects in the case (exposed) group
- 1057
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mixed-Effects 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, sex, body mass index, Confounders controlled for: "healthy eating index" 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.healthy eating index, Confounders controlled for: "family structure" 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.family structure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 4: Supplementary Table 3
Description: Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using 16S rRNA sequencing
Abundance in Group 1: increased abundance in Yoghurt eaters
Revision editor(s): Agatha, KateRasheed
Signature 2
Source: Additional file 4: Supplementary Table 3
Description: Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using 16S rRNA sequencing
Abundance in Group 1: decreased abundance in Yoghurt eaters
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Flavonifractor | ||
| Lachnoclostridium | ||
| Thomasclavelia |
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 144
- Group 1 sample size Number of subjects in the case (exposed) group
- 400
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "healthy eating index" 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.healthy eating index, Confounders controlled for: "family structure" 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.family structure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Additional file 5: Supplementary Table 4
Description: Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using shotgun metabolomic sequencing
Abundance in Group 1: increased abundance in Yoghurt eaters
Revision editor(s): KateRasheed
Signature 2
Source: Additional file 5: Supplementary Table 4
Description: Differential abundance of taxa between yoghurt eaters and non-yoghurt eaters using shotgun metabolomic sequencing
Abundance in Group 1: decreased abundance in Yoghurt eaters
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Yoghurt consumers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Yoghurt consumers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low Yoghurt consumers refers to those that consumed yoghurt 1-5 times in a week
- Group 1 sample size Number of subjects in the case (exposed) group
- 183
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 1C-D
Description: Differential abundance of taxa between low yoghurt consumers and non-yoghurt consumers using linear regression
Abundance in Group 1: increased abundance in Low Yoghurt consumers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus | ||
| Bifidobacterium animalis |
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Yoghurt consumers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers refers to individuals that consume yoghurt more than 5times in a week.
- Group 1 sample size Number of subjects in the case (exposed) group
- 217
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 1C-D
Description: Differential abundance of taxa between high yoghurt eaters and non-yoghurt eaters using linear regression.
Abundance in Group 1: increased abundance in High Yoghurt consumers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus | ||
| Bifidobacterium animalis |
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Yoghurt consumers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 183
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 1C-D
Description: Differential abundance of taxa between high yoghurt eaters and low yoghurt eaters using linear regression.
Abundance in Group 1: increased abundance in High Yoghurt consumers
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus | ||
| Bifidobacterium animalis |
Revision editor(s): KateRasheed
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Yoghurt consumers(consumed yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers(consumed yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "healthy eating index" 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.healthy eating index
Signature 1
Source: Fig. 2A-B
Description: Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(consumed yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis subsp. lactis | ||
| Streptococcus thermophilus |
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Yoghurt consumers(consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers refers to those who ate yoghurt a day before sampling (24hours before sampling)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2A-B
Description: Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(consume yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus | ||
| Bifidobacterium animalis subsp. lactis |
Revision editor(s): KateRasheed
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Yoghurt consumers (consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2A
Description: Differential abundant taxa between low-yoghurt consumers (consumed yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(consume yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis subsp. lactis |
Revision editor(s): KateRasheed
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Yoghurt Consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
Lab analysis
Statistical Analysis
Signature 2
Source: Fig. 2A
Description: Differential abundant taxa between high-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(consume yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium animalis subsp. lactis |
Revision editor(s): KateRasheed
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling) refers to high intake yoghurt consumers who did not consume yoghurt 24hrs before fecal sampling
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2B
Description: Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(didn't consume yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus |
Revision editor(s): KateRasheed
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling) refers to those who did not take yoghurt a day before sampling (24hours before sampling).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2B
Description: Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and high yoghurt eaters(didn't consume yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in High Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus |
Revision editor(s): KateRasheed
Experiment 12
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Yoghurt consumers(consumed yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low Yoghurt consumers(consume yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2B
Description: Differential abundant taxa between low-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and low yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in Low Yoghurt consumers(consumed yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus |
Revision editor(s): KateRasheed
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Yoghurt consumers(didn't consume yoghurt 24hrs before sampling)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low Yoghurt consumers(consumed yoghurt 24hrs before sampling) refers to those who ate yoghurt a day before sampling (24hours before sampling).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2B
Description: Differential abundant taxa between non-yoghurt consumers (didn't consume yoghurt 24hrs before sampling) and low yoghurt eaters(consumed yoghurt 24hrs before sampling).
Abundance in Group 1: increased abundance in Low Yoghurt consumers(consumed yoghurt 24hrs before sampling)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus thermophilus |
Revision editor(s): KateRasheed
