Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort/Experiment 2

From BugSigDB


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, WikiWorks

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
day 6 of INULIN spike-in
Group 1 name Corresponds to the case (exposed) group for case-control studies
day 3 of INULIN spike-in
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
before pectin spike-in
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
9
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
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


Signature 1

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

Source: Figure 1b and text

Description: OTUs that showed statistically significant (DESeq. 2, FDR < 0.1) differential abundance on day 6 compared to day 3 in response to particular spike-ins. Mean relative abundances are computed across all participants and then converted to Z-scores across timepoints, to illustrate relative changes through time. - INULIN

Abundance in Group 1: decreased abundance in day 3 of INULIN spike-in

NCBI Quality ControlLinks
Lachnospiraceae
Bacteroides uniformis
Faecalibacterium prausnitzii

Revision editor(s): WikiWorks