Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition/Experiment 46

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Curated date: 2024/04/22

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Subjects

Location of subjects

Denmark

Host species Species from which microbiome was sampled. Contact us to have more species added.

Sus scrofa domesticus

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

Microbiome measurement Microbiome measurement,microbiome measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies

MagNAPure

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

Easy-DNA

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

DNA isolation from pig fecal samples using Easy-DNATM gDNA Purification Kit, Invitrogen (Easy-DNA).

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

3

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

3

Lab analysis

Sequencing type

WMS

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

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

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)

0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Chao1 Abundance-based estimator of species richness

decreased