Habitual dietary fibre intake influences gut microbiota response to an inulin-type fructan prebiotic: a randomised, double-blind, placebo-controlled, cross-over, human intervention study
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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
- New Zealand
- 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
- Prebiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Placebo
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- placebo (control for prebiotic intake - representing lower fiber group)
- 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
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Text, Table 4, Figure 5, and Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.
Abundance in Group 1: increased abundance in Placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Coprococcus | ||
| Dorea | ||
| Oscillospira | ||
| Lachnospiraceae |
Revision editor(s): WikiWorks
Signature 2
Source: Text, Table 4, Figure 5, and Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.
Abundance in Group 1: decreased abundance in Placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacterium |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- prebiotic (inulin-type fructan) - in participants with low dietary fiber
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- placebo
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
Signature 1
Source: Text, Table 4, Figure 5, and Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.
Abundance in Group 1: decreased abundance in placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- prebiotic (inulin-type fructan) - in participants with high dietary fiber
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
Signature 1
Source: Text, Table 4, Figure 5, and Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.
Abundance in Group 1: increased abundance in placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Coprococcus | ||
| Dorea | ||
| Lachnospiraceae |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Text, Table 4, Figure 5, and Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low and high dietary fibre groups.
Abundance in Group 1: decreased abundance in placebo
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low dietary fiber
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High dietary fiber
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Placebo (control for prebiotic intake - representing lower fiber group)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
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
Signature 1
Source: Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as analysed by a two-way repeated-measures ANOVA (blocked by participant) and least significant difference test.
Abundance in Group 1: increased abundance in High dietary fiber
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Oscillospiraceae |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Figure 7
Description: Mean genus level changes after the prebiotic intervention between the low ( ) and high dietary fibre ( ) groups. * Significant change (P <0·05) as analysed by a two-way repeated-measures ANOVA (blocked by participant) and least significant difference test.
Abundance in Group 1: decreased abundance in High dietary fiber
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Peace Sandy
