Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns/Experiment 162
From BugSigDB
Needs review
Subjects
- Location of subjects
- Denmark
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Not specified
- 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 sewage samples (S1) at 64 hours (-80°C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Unspiked sewage samples (S1) at 16 hours (5°C)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Unspiked S1 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
- 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: : Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1
Abundance in Group 1: increased abundance in Unspiked sewage samples (S1) at 16 hours (5°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Arcobacter | ||
| Acinetobacter | ||
| Parabacteroides | ||
| Prevotella |
Revision editor(s): Bolanle
Signature 2
Source: Figure 4
Description: Differential abundance of selected highly abundant bacteria between the storage conditions in unspiked sewage sample S1
Abundance in Group 1: decreased abundance in Unspiked sewage samples (S1) at 16 hours (5°C)
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonas |
Revision editor(s): Bolanle
