Association of dietary fibre intake and gut microbiota in adults/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-1-22

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

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

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi

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 ControlLinks
Coprococcus
Faecalibacterium
Faecalibacterium prausnitzii

Revision editor(s): ChiomaBlessing, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-22

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi

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 ControlLinks
Actinomycetales
Amedibacillus dolichus
Bacteroides
Deltaproteobacteria
Desulfovibrionales
Odoribacter
Odoribacteraceae
Ruminococcus
Desulfovibrionaceae

Revision editor(s): ChiomaBlessing, Folakunmi