Association of dietary fibre intake and gut microbiota in adults
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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 States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- diet Dietary,Diets,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- high fiber (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
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
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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 height, body weight, race, smoking behavior, body mass index
Signature 1
Source: Figure 2.
Description: Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2
Abundance in Group 1: increased abundance in low fiber (Q1 and Q2)
NCBI | Links |
---|---|
Actinomyces | |
Bacteroides uniformis | |
Odoribacter | |
Amedibacillus dolichus |
Signature 2
Source: Figure 2.
Description: Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2
Abundance in Group 1: decreased abundance in low fiber (Q1 and Q2)
NCBI | Links |
---|---|
Actinomyces | |
Odoribacter | |
Oscillospira |
Experiment 2
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- diet Dietary,Diets,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- high fiber from FRUITS/VEGETABLES (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber from FRUITS/VEGETABLES (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of FRUIT/VEGETABLE fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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 height, body weight, race, smoking behavior, body mass index
Signature 1
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: increased abundance in low fiber from FRUITS/VEGETABLES (Q1 and Q2)
NCBI | Links |
---|---|
Actinomyces | |
Odoribacter | |
Bacteroides uniformis |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- diet Dietary,Diets,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- high fiber from BEANS (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber from BEANS (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of BEAN fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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 height, body weight, race, smoking behavior, body mass index
Signature 1
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: increased abundance in low fiber from BEANS (Q1 and Q2)
NCBI | Links |
---|---|
Odoribacter | |
Amedibacillus dolichus |
Signature 2
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: decreased abundance in low fiber from BEANS (Q1 and Q2)
NCBI | Links |
---|---|
Faecalibacterium | |
Faecalibacterium prausnitzii |
Revision editor(s): WikiWorks