Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project
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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
- Russian Federation
- 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
- high vegetable, fruit, grain
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low vegetable, fruit, grains,
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- low fiber
- Group 0 sample size Number of subjects in the control (unexposed) group
- 215
- Group 1 sample size Number of subjects in the case (exposed) group
- 215
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
- 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
Signature 1
Source: Figure 1 and Figure 2
Description: Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary recommendations. Red branches of the cladogram denote the taxa that were increased in abundance, while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of the effect size >2 in LEfSe method (n = 430 paired samples).
Abundance in Group 1: increased abundance in Low vegetable, fruit, grains,
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Porphyromonadaceae | ||
| Prevotellaceae | ||
| Rikenellaceae | ||
| Oscillospiraceae | ||
| Acidaminococcaceae | ||
| Veillonellaceae | ||
| Sutterellaceae | ||
| Desulfovibrionaceae | ||
| Lactobacillaceae |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 1 and Figure 2
Description: Figure 1. Associations of the microbial taxa with long-term dietary habits and other factors from the questionnaire (n = 207 subjects). Analysis was performed for the baseline samples at taxonomic levels from species to phyla. Rows are sorted in alphabetic order. Cell color denotes the value of the linear model coefficient from the MaAsLin analysis. All significant associations (FDR adjusted p < 0.1) are marked with one of the symbols (&, #, @): “&”. Figure 2. Major changes in the gut community structure of the volunteers after following the dietary recommendations. Red branches of the cladogram denote the taxa that were increased in abundance, while the blue ones—decreased. Significance criterion: p < 0.05 in metagenomeSeq model and log10 of the effect size >2 in LEfSe method (n = 430 paired samples).
Abundance in Group 1: decreased abundance in Low vegetable, fruit, grains,
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- before dietary intervention
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- two weeks after a dietry intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S8
Description: Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.
Abundance in Group 1: increased abundance in two weeks after a dietry intervention
Revision editor(s): WikiWorks
Signature 2
Source: Figure S8
Description: Сhanges in relative abundance of microbial taxa after dietary intervention. The analysis was performed using metagenomeSeq. For each taxon, the columns “Beta” and “Eff. size” contain the values of linear model coefficient and effect size calculated using LEfSe.
Abundance in Group 1: decreased abundance in two weeks after a dietry intervention
