Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-1-29
Subjects
- Location of subjects
- Italy
- 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
- Melanoma malignant melanoma,melanoma,melanoma (disease),melanoma, malignant,Naevocarcinoma,Melanoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-complete responders (nCR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- complete responders (CR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group represents the Complete Responders (CR) to anti-PD-1 therapy in melanoma patients for 2-6 months (early therapy) .
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
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).
- log transformation
- Statistical test
- MaAsLin2
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-29
Source: Figure S2D
Description: Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.
Abundance in Group 1: increased abundance in complete responders (CR)
Revision editor(s): Joiejoie, Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-29
Source: Figure S2D
Description: Differential abundance of CR (blue) and ncR (red) stable taxa on log-transformed relative abundance, based on Maaslin2 linear model (LM) coefficient.
Abundance in Group 1: decreased abundance in complete responders (CR)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes sp. An66 |
Revision editor(s): Aleru Divine
