Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing
Subjects
- Location of subjects
- France
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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
- Graft versus host disease disease, graft-versus-host,disease, graft-VS-host,disease, homologous wasting,disease, runt,diseases, graft-versus-host,diseases, graft-VS-host,graft versus host disease,graft VS host disease,graft VS. host disease,graft-versus-host disease,graft-versus-host disease, resistance to,graft-versus-host disease, susceptibility to,graft-versus-host diseases,graft-versus-host-disease,graft-VS-host disease,graft-VS-host diseases,GVH,GVHD,GVHDS,homologous wasting disease,runt disease,Graft versus host disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe acute graft-versus-host-disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients who are diagnosed with severe gut acute graft- versus-host disease (between standard stage greater or equal to 2 and less than or equal to 3)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
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
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2C
Description: Differential relative abundance between controls and severe acute graft-versus-host disease patients.
Abundance in Group 1: increased abundance in Severe acute graft-versus-host-disease
| NCBI | Quality Control | Links |
|---|---|---|
| Stenotrophomonas | ||
| Prevotella |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2C
Description: Differential relative abundance between controls and severe acute graft-versus- host disease patients.
Abundance in Group 1: decreased abundance in Severe acute graft-versus-host-disease
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Thomasclavelia ramosa | ||
| Faecalibacterium sp. UBA1819 | ||
| Flavonifractor | ||
| Lachnoclostridium | ||
| Lachnospiraceae | ||
| Sellimonas | ||
| Oscillospiraceae |
Revision editor(s): Claregrieve1, WikiWorks
