Association of dietary fibre intake and gut microbiota in adults/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-22
Subjects
- Location of subjects
- United States of America
- 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
- low fiber intake from BEANS
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher fiber intake from BEANS
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who had a higher fiber intake from BEANS
- 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
- Illumina, Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- 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, body mass index, sex, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-22
Source: Supplemental Table 4, Figure 3
Description: Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from BEANS in the NCI and NYU study population
Abundance in Group 1: increased abundance in Higher fiber intake from BEANS
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus | ||
| Faecalibacterium | ||
| Faecalibacterium prausnitzii |
Revision editor(s): ChiomaBlessing, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-22
Source: Figure 3, supplementary table 4
Description: Heatmap analysis representing fold changes of taxa in higher fiber intake from BEANS in the meta-analysis of NCI and NYU study populations
Abundance in Group 1: decreased abundance in Higher fiber intake from BEANS
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Amedibacillus dolichus | ||
| Bacteroides | ||
| Deltaproteobacteria | ||
| Desulfovibrionales | ||
| Odoribacter | ||
| Odoribacteraceae | ||
| Ruminococcus | ||
| Desulfovibrionaceae |
Revision editor(s): ChiomaBlessing, Folakunmi
