High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome/Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2021/02/11

Curator: Lorakasselman

Revision editor(s): Lorakasselman, Claregrieve1, WikiWorks, Peace Sandy

Subjects

Location of subjects

Italy

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

vegetarians

Group 1 name Corresponds to the case (exposed) group for case-control studies

omnivores

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

individuals who eat animal products in addition to other foods (plants, grains, etc)

Group 0 sample size Number of subjects in the control (unexposed) group

51

Group 1 sample size Number of subjects in the case (exposed) group

51

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

3 months

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

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

Alpha Diversity

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/02/11

Curator: Lorakasselman

Revision editor(s): Lorakasselman, Claregrieve1

Source: Table S2

Description: Differential microbial abundance between omnivores and vegetarians

Abundance in Group 1: decreased abundance in omnivores

NCBI	Quality Control	Links
Lachnospira

Revision editor(s): Lorakasselman, Claregrieve1

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/01/01

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table S2

Description: Differential microbial abundance between omnivores and vegetarians

Abundance in Group 1: increased abundance in omnivores

NCBI	Quality Control	Links
Ruminococcus
Veillonellaceae

Revision editor(s): Claregrieve1