Reviewed Marked as Reviewed by Svetlana up on 2025-1-29

Curated date: 2024/11/22

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine, WikiWorks

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 7-13 months (late 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
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).
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

Curated date: 2024/11/27

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine, WikiWorks

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)

NCBI Quality ControlLinks
Clostridia unclassified SGB14951Clostridia unclassified SGB14951
Candidatus Metaruminococcus gallistercoris
Clostridia unclassified SGB14016Clostridia unclassified SGB14016
Candidatus Metalachnospira gallinarum
Veillonellaceae SGB5809 groupVeillonellaceae SGB5809 group
Bacteroides nordii
Evtepia gabavorous
Clostridium SGB6179Clostridium SGB6179
Bifidobacterium pullorum

Revision editor(s): Joiejoie, Aleru Divine, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-29

Curated date: 2025/01/29

Curator: Aleru Divine

Revision editor(s): Aleru Divine, WikiWorks

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 ControlLinks
Alistipes sp. An66
Bacteroides sp. Marseille-P3684

Revision editor(s): Aleru Divine, WikiWorks