Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- South Africa
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Fukomys damarensis
- 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
- Freeze dried specimen Freeze dried specimen,freeze dried specimen
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Frozen samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Freeze dried samples.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Freeze dried samples are samples preservation treatment stored and transported at ambient temperature until DNA extraction.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 2
Source: Figure 4, Table S1
Description: Log-transformed relative abundances of families with > 1% mean relative abundance between Frozen and Freeze-dried sample preservation treatments.
Abundance in Group 1: decreased abundance in Freeze dried samples.
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae | ||
| Lachnospiraceae | ||
| Oscillospiraceae |
Revision editor(s): Tosin
