Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 44

From BugSigDB


Needs review

Curated date: 2024/03/26

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 Microbiome,microbiome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (-80°C)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Unspiked pig feces(P1) at 16 hours (5°C)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Unspiked P1 sample stored at a temperature of 5°C for 16 hours
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
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: higher abundance with increasing temperature and time was detected in samples processed immediately.

Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Treponema
Faecalibacterium
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/04/02

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: There was lower abundance of the taxa in frozen samples than what was detected in samples processed immediately.

Abundance in Group 1: decreased abundance in Unspiked pig feces(P1) at 16 hours (5°C)

NCBI Quality ControlLinks
Prevotella
Phascolarctobacterium

Revision editor(s): Bolanle