Association of dietary fibre intake and gut microbiota in adults/Experiment 1
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 quartile of TOTAL fiber intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher quartile of TOTAL fiber intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who had a higher total fiber intake
- 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
Curated date: 2021/01/10
Curator: Lora Kasselman
Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing
Source: Figure 2, Supplemental Table 1
Description: Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects
Abundance in Group 1: decreased abundance in Higher quartile of TOTAL fiber intake
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Amedibacillus dolichus | ||
| Bacteroides uniformis | ||
| Odoribacter | ||
| Oscillospira |
Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing
Signature 2
Curated date: 2021/01/10
Curator: Lora Kasselman
Revision editor(s): WikiWorks, Claregrieve1, Merit, ChiomaBlessing, Davvve
Source: Figure 2, Supplemental Table 1
Description: Forest plot of the fold change of microbial abundance in both New York University and National Cancer Institute study populations with significant association with higher fibre intake subjects.
Abundance in Group 1: decreased abundance in Higher quartile of TOTAL fiber intake
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Faecalibacterium prausnitzii | ||
| Lachnospira | ||
| Clostridiaceae |
Revision editor(s): WikiWorks, Claregrieve1, Merit, ChiomaBlessing, Davvve
