Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 33
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 0 hour
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unspiked pig feces(P1) at 16 hours (-80°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 -80°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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4
Description: Prevotella (class Bacteroidia), the most abundant genus in pig feces, was more abundant for P1 frozen samples than in samples undergoing immediate DNA isolation, Phascolarctobacterium (class Negativicutes), also had higher abundance in stored samples than for samples processed immediately.
Abundance in Group 1: increased abundance in Unspiked pig feces(P1) at 16 hours (-80°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| 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 16 hours (-80°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema | ||
| Faecalibacterium | ||
| Roseburia |
Revision editor(s): Bolanle
