Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition/Experiment 49
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
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Space surrounding organism External to organism,Outside of body,Space surrounding organism,space surrounding organism
- 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
- InnuPURE
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MagNAPure
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- DNA isolation from sewage samples using MagNA Pure LC DNA isolation Kit III, Roche (MagNAPure).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: increased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Neisseriaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2F
Description: The differentially abundant bacteria taxa between the DNA isolation procedures identified using DESeq2.
Abundance in Group 1: decreased abundance in MagNAPure
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacteraceae | ||
| Oscillospiraceae | ||
| Bacteroidaceae | ||
| Lachnospiraceae | ||
| Opitutaceae |
Revision editor(s): Aleru Divine
