Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 100

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Curated date: 2024/03/26

Curator: Bolanle

Revision editor(s): Bolanle

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

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

Spiked pig feces(P2) at 16 hours (-20°C)

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

Spiked pig feces(P2) at 64 hours (5°C)

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

P2 sample spiked with a mock community and stored at a temperature of 64 hours (5°C)

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

1

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

1

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)

0.01

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

No

Alpha Diversity

Pielou Quantifies how equal the community is numerically

increased

Chao1 Abundance-based estimator of species richness

decreased

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

increased