Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2022/09/5
Subjects
- Location of subjects
- United States of America
- 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
- Response to immunochemotherapy Response to immunochemotherapy,response to immunochemotherapy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-responders
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Responders
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients were classified as R if they achieved an objective response (complete or partial response or stable disease lasting at least 6 months)
- 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
- 54
Lab analysis
- Sequencing type
- 16S
- 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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- 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
Reviewed Marked as Reviewed by Fatima on 2022/09/5
Source: Figure 2D
Description: (D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R (blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the Kruskal-Wallis test; LDA score > 3.
Abundance in Group 1: increased abundance in Responders
Revision editor(s): Sharmilac
Signature 2
Reviewed Marked as Reviewed by Fatima on 2022/09/5
Source: Figure 2D
Description: (D) LDA scores computed for differentially-abundant taxa in the fecal microbiomes of R (blue) and NR (red). Length indicates effect size associated with a taxon. p=0.05 for the Kruskal-Wallis test; LDA score > 3.
Abundance in Group 1: decreased abundance in Responders
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella stercoris | ||
| Oleidesulfovibrio alaskensis | ||
| Bacteroides mediterraneensis | ||
| Prevotella histicola | ||
| Gardnerella vaginalis | ||
| Gardnerella | ||
| Bacteroidota | ||
| Bacteroidales | ||
| Bacteroidia |
Revision editor(s): Sharmilac
