Faecal microbial transfer and complex carbohydrates mediate protection against COPD/Experiment 3
From BugSigDB
Needs review
Subjects
- Location of subjects
- Australia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Fecal samples baseline(Week 0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fecal samples at the end of the experiment(Week 12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal samples at the end of the experiment(Week 12) refers to fecal samples collected at the completion of the experiment.
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)
- 0.05
- 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
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Needs review
Source: Supplementary Table 5
Description: Differentially abundant taxa between fecal samples at baseline(Week 0) and at completion of the experiment(Week 12)
Abundance in Group 1: increased abundance in Fecal samples at the end of the experiment(Week 12)
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Table 5
Description: Differentially abundant taxa between fecal samples at baseline(Week 0) and at completion of the experiment(Week 12)
Abundance in Group 1: decreased abundance in Fecal samples at the end of the experiment(Week 12)
Revision editor(s): KateRasheed
