Association of dietary fibre intake and gut microbiota in adults

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/4

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 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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/4

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): Claregrieve1, WikiWorks, 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

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Actinomyces
Amedibacillus dolichus
Bacteroides uniformis
Odoribacter
Oscillospira

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/4

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

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: low fiber intake from FRUITS/ VEGETABLES

Group 1 name Corresponds to the case (exposed) group for case-control studies: Higher fiber intake from FRUITS/ VEGETABLES

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 FRUITS/ VEGETABLES

Lab analysis

Statistical Analysis

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

Source: Supplemental Table 2, Figure 3

Description: Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE in the NCI and NYU study population

Abundance in Group 1: decreased abundance in Higher fiber intake from FRUITS/ VEGETABLES

NCBI	Quality Control	Links
Actinomyces
Bacteroides uniformis
Coriobacteriales
Lactobacillales
Odoribacter
Ruminococcus bromii

Revision editor(s): ChiomaBlessing

Signature 2

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

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Supplemental Table 2

Description: Taxonomy-based Meta-analysis to evaluate taxa abundance by higher fibre intake from FRUIT/ VEGETABLE in the NCI and NYU study population

Abundance in Group 1: increased abundance in Higher fiber intake from FRUITS/ VEGETABLES

NCBI	Quality Control	Links
Peptostreptococcaceae

Revision editor(s): ChiomaBlessing

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2023/10/28

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

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 Control	Links
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 Control	Links
Actinomycetales
Amedibacillus dolichus
Bacteroides
Deltaproteobacteria
Desulfovibrionales
Odoribacter
Odoribacteraceae
Ruminococcus
Desulfovibrionaceae

Revision editor(s): ChiomaBlessing, Folakunmi

Experiment 4