Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab/Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/08/24

Curated date: 2022/07/14

Curator: Sharmilac

Revision editor(s): Sharmilac, Fatima, WikiWorks

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
Response to immunochemotherapy Response to immunochemotherapy,response to immunochemotherapy
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Resistance, Non responders, No colitis
Group 1 name Corresponds to the case (exposed) group for case-control studies
Responders, Colitis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
MM patients that developed an immune-mediated colitis following ipilimumab treatment
Group 0 sample size Number of subjects in the control (unexposed) group
19
Group 1 sample size Number of subjects in the case (exposed) group
7

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

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
3.5

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Fatima on 2022/08/24

Curated date: 2022/08/24

Curator: Fatima

Revision editor(s): Fatima

Source: Figure 4

Description: Gut microbiota composition at baseline predicts ipilimumab-induced colitis.

Abundance in Group 1: increased abundance in Responders, Colitis

NCBI Quality ControlLinks
Bacteroides ovatus
Blautia obeum
Clostridiales bacterium
Fusicatenibacter saccharivorans
Gemmiger formicilis
Lachnospiraceae
Oscillospiraceae
Roseburia inulinivorans

Revision editor(s): Fatima

Signature 2

Reviewed Marked as Reviewed by Fatima on 2022/08/24

Curated date: 2022/08/24

Curator: Fatima

Revision editor(s): Fatima

Source: Figure 4

Description: Gut microbiota composition at baseline predicts ipilimumab-induced colitis

Abundance in Group 1: decreased abundance in Responders, Colitis

NCBI Quality ControlLinks
Prevotella sp.
Bacteroides sp.
Bacteroides uniformis
Faecalibacterium prausnitzii
Bacteroides sp.
Parabacteroides distasonis

Revision editor(s): Fatima