Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial
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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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo group (End of study)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prebiotic group (End of study)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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).
- centered log-ratio
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "twin pairs" 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.twin pairs
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, diet, sex, Confounders controlled for: "appetite score" 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.appetite score, Confounders controlled for: "zygosity" 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.zygosity
Signature 1
Curated date: 2024/10/07
Curator: Rukaya-lab
Revision editor(s): Chloe, Rahila, Chrisawoke, Rukaya-lab
Source: Figure 2
Description: Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study
Abundance in Group 1: increased abundance in Prebiotic group (End of study)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetes | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Bifidobacterium | ||
| Actinomycetota |
Revision editor(s): Chloe, Rahila, Chrisawoke, Rukaya-lab
Signature 2
Curated date: 2024/10/11
Curator: Rukaya-lab
Revision editor(s): Chloe, MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Source: Figure 2
Description: Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.
Abundance in Group 1: decreased abundance in Prebiotic group (End of study)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Clostridia | ||
| Eubacteriales | ||
| Merdimmobilis | ||
| Merdimmobilis hominis | ||
| Bacteroidota |
Revision editor(s): Chloe, MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo (change between baseline and study end)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prebiotic(change between baseline and study end)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who received prebiotic supplements (inulin and fructo-oligosaccharides) along with BCAA (branched-chain amino acid) supplementation and resistance exercise and follow up was done after 12 weeks. Study end was adjusted for baseline in this experiment.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "time point" 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.time point, Confounders controlled for: "twin pair" 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.twin pair
Signature 1
Curated date: 2024/10/08
Curator: Rukaya-lab
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Source: Figure 2
Description: Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.
Abundance in Group 1: increased abundance in Prebiotic(change between baseline and study end)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Actinomycetes |
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Signature 2
Curated date: 2024/10/11
Curator: Rukaya-lab
Revision editor(s): Chloe, MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Source: Figure 2
Description: Twin-paired group comparisons between prebiotic and placebo supplements, including data from the end of the study or the difference between baseline and end of study.
Abundance in Group 1: decreased abundance in Prebiotic(change between baseline and study end)
Revision editor(s): Chloe, MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline Placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- End of Study Placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 12 (End of study) participants who received protein (BCAA) supplement powder combined with a placebo supplement (maltodextrin).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "baseline microbiota" 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.baseline microbiota, Confounders controlled for: "zygosity" 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.zygosity
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S6
Description: Significant Microbiota Features between Baseline and Study End
Abundance in Group 1: increased abundance in End of Study Placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii |
Revision editor(s): Rukaya-lab, Rahila, Chrisawoke
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline Prebiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- End of study Prebiotic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 12 (End of study) participants who received daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months.
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "zygosity" 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.zygosity, Confounders controlled for: "baseline microbiota" 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.baseline microbiota
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Curated date: 2024/10/11
Curator: Rukaya-lab
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Source: Supplementary Figure S6
Description: Significant Microbiota Features identified between Baseline Prebiotic and Study End Prebiotic using Linear models.
Abundance in Group 1: increased abundance in End of study Prebiotic
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Signature 2
Curated date: 2024/10/11
Curator: Rukaya-lab
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Source: Supplementary Figure S6
Description: Significant Microbiota Features identified between Baseline Prebiotic and Study End Prebiotic using Linear models.
Abundance in Group 1: decreased abundance in End of study Prebiotic
Revision editor(s): MyleeeA, Rahila, Chrisawoke, Rukaya-lab
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline prebiotics and placebo
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- End of study prebiotics and placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 12 (End of study) participants who received protein (BCAA) supplement powder combined with a placebo supplement (maltodextrin) and daily prebiotic supplementation (inulin and fructo-oligosaccharides) along with branched-chain amino acids (BCAA) and resistance exercise.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 70
- Group 1 sample size Number of subjects in the case (exposed) group
- 68
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 Months
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S6
Description: Significant Microbiota Features Between Baseline and Study End
Abundance in Group 1: increased abundance in End of study prebiotics and placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces graevenitzii | ||
| Anaerostipes | ||
| Anaerostipes hadrus | ||
| Parvimonas micra | ||
| Eubacterium ventriosum |
Revision editor(s): Chrisawoke, Chloe
Signature 2
Source: Figure S6
Description: 2.6 Supplementary Figure S6: Significant Microbiota Features between Baseline and Study End Paired group comparison of relative abundance (a) and prevalence (p) of bacterial taxa between baseline and end of study, including data from both study arms.
Abundance in Group 1: decreased abundance in End of study prebiotics and placebo
Revision editor(s): Chloe
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo (Correlated with Cognition Factor)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prebiotic (Correlated with Cognition Factor)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 12 (End of study) participants in prebiotic group positively correlated with Cognition Factor.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 Months.
Signature 1
Source: Supplementary Figure 9 and 10
Description: Microbiota features that positively correlated with Cognition Factor.
Abundance in Group 1: increased abundance in Prebiotic (Correlated with Cognition Factor)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Veillonellales | ||
| Coriobacteriales | ||
| Actinomycetota |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 9 and 10
Description: Microbiota features that Negatively correlated with Cognition Factor.
Abundance in Group 1: decreased abundance in Prebiotic (Correlated with Cognition Factor)
| NCBI | Quality Control | Links |
|---|---|---|
| Lacrimispora |
Revision editor(s): MyleeeA
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo (Correlated with Chair Rise time)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prebiotic (Correlated with Chair Rise time)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 12 (End of study) participants in prebiotic group positively correlated with Chair Rise time (CST).
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 Months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Supplementary Figure 8
Description: Microbiota features that Positively correlated with Physical Activity (Chair Rise Time).
Abundance in Group 1: increased abundance in Prebiotic (Correlated with Chair Rise time)
Revision editor(s): MyleeeA, Chrisawoke
Signature 2
Source: Supplementary Figure 8
Description: Microbiota features that Negatively correlated with Physical Activity (Chair Rise Time).
Abundance in Group 1: decreased abundance in Prebiotic (Correlated with Chair Rise time)
Revision editor(s): MyleeeA
