Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition/Experiment 42
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 measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FastDNA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- QIAStool+BB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from pig fecal samples using QIAamp® DNA Stool Mini Kit, Qiagen +Bead Beating (QIAStool+BB).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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)
- 0.1
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Needs review
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Erysipelotrichaceae |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2E
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in QIAStool+BB
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Oscillospiraceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae |
Revision editor(s): Aleru Divine
