Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 43
From BugSigDB
Needs review
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 64 hours (-20°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 -20°C for 64 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
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 64 hours (-20°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium |
Revision editor(s): Bolanle
Signature 2
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 64 hours (-20°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Treponema | ||
| Faecalibacterium | ||
| Roseburia |
Revision editor(s): Bolanle
