Gut microbiome in melanoma immunotherapy response (UK/NL/Spain)
165 stool samples from advanced melanoma patients in the UK, Netherlands, and Spain, studied for gut microbiome and metabolomic links to immunotherapy response, using a case-control design. machine-written summary
165 samples · 165 runs · GB, NL, ES · Adult · 2021 · 6.20 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,155 sample values (age, bmi, collection date, country, latitude, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 165 sample values (subject id) · PMC10134792, PMC10654443, PMC10917649, PMC10957474, PMC10957475, PMC11629153, PMC11879847, PMC11937697, PMC11959079, PMC12475161, PMC12654497, PMC12807719, PMC13114121, PMC13173278, PMC13274128, PMC13388844, PMC13400165, PMC8938272 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 492 sample values (antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
bmi: sequence archive and curatedMetagenomicData disagree for 1 sample (e.g. 57.74 vs 26.5) — withheld.
The sources disagree on 1 sample. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA8072307 | bmi | 57.74 (sequence archive) | 26.5 (curatedMetagenomicData) | withheld: neither value published |
Genera, mean relative abundance over 155 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 163 | 99% | ||||
| country | 165 | 100% | 165 | |||
| health_condition | 165 | 100% | 165 | |||
| subject_id | 165 | 100% | 165 | |||
| collection_date | 165 | 100% | 165 | |||
| detailed_location | 165 | 100% | ||||
| health_condition_detail | 165 | 100% | 165 | |||
| latitude | 165 | 100% | 165 | |||
| location_region | 165 | 100% | 165 | |||
| longitude | 165 | 100% | 165 | |||
| sex | 165 | 100% | 165 | |||
| antibiotic_exposure | 162 | 98% | 162 | |||
| bmi | 154 | 93% | 154 | |||
| age_at_collection_days | 11 | 7% | 11 |
- Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth. 2026 PMID 42447866 PMC13400165 own_data
- Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. 2022 PMID 35228751 PMC8938272 unsure
- Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy. 2023 PMID 36809182 PMC10134792 unsure
- Gut microbial structural variation associates with immune checkpoint inhibitor response. 2023 PMID 37973916 PMC10654443 unsure
- Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. 2024 PMID 38365950 PMC10957474 unsure
13 more
- A gut microbial signature for combination immune checkpoint blockade across cancer types. 2024 PMID 38429524 PMC10957475
- Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy. 2024 PMID 38448159 PMC10917649
- Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients. 2024 PMID 39481388 PMC11629153
- Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses. 2025 PMID 39929976 PMC11879847
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697
- Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology. 2025 PMID 40170844 PMC11959079
- Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis. 2025 PMID 41006325 PMC12475161
- Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts. 2025 PMID 41304278 PMC12654497
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
- Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types. 2026 PMID 42026803 PMC13114121
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types. 2026 PMID 42146906 PMC13173278
- Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis. 2026 PMID 42189287 PMC13388844
- Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset. 2026 PMID 42298353 PMC13274128
Archive description
The PRIMM studies are two separate observational cohort studies recruiting subjects in parallel in the U.K. (PRIMM-UK) and Netherlands (PRIMM-NL) since 2018. These cohorts of previously ICI-naive advanced melanoma patients were used to study the role of the gut microbiome in ICI response using shotgun metagenomic sequencing of stool samples together with three additional cohorts of ICI-naive patients with advanced cutaneous melanoma (originating from Barcelona, Leeds, and Manchester).
How this project entered the registry
Classified as human gut / stool / skin shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “for Melanoma With Gut Microbiome and Metabolomics”
- body site study.description · “role of the gut microbiome in ICI”
- body site study.description · “patients with advanced cutaneous melanoma (originating from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age_5yr_bin · “60-65 (n=95/165)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8072152 | age_at_collection_days | 16461.8 | R1 | 0.85 | sample.attr.host_age_5yr_bin | 45-50 |
| SAMEA8072152 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA8072152 | bmi | 28.71 | R1 | 0.90 | sample.attr.host_body_mass_index | 28.7132112 |
| SAMEA8072152 | collection_date | 2016-03-02 | R1 | 0.90 | biosample.attribute:collection_date | 2016-03-02 |
| SAMEA8072152 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA8072152 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | disease: Melanoma |
| SAMEA8072152 | health_condition_detail | Melanoma | R2 | 0.75 | external.cmd source | disease: Melanoma |
| SAMEA8072152 | latitude | 41.3902 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39016802 2.152483561 |
| SAMEA8072152 | location_region | Catalonia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39016802 2.152483561 |
| SAMEA8072152 | longitude | 2.1525 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39016802 2.152483561 |
| SAMEA8072152 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA8072152 | subject_id | SAMEA8072152 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Of 190 baseline samples collected across the five observational cohorts, 25 samples failed the metagenomic sequencing and preprocessing pipeline |
Sequencing
165 runs over 165 samples · mean 7.62 Gbp per run (median 6.20 Gbp, total 1,258.02 Gbp; 165 runs with a base count) · layout PAIRED 165 · platform ILLUMINA 165 · models unspecified (165) · 94% of runs with a Sandpiper profile · first public 2021-12-17 – 2022-09-30
Authors (44)
Zhou Y first · Han W · Feng Y · Wang Y · Liu X · Sun T · Xu J last · Zhang L first · Zhou DD · Feng J · Liao ZJ · Shu XL · Yang RM · Gao YC · Zhou HH · Zhang W · Zou Y · Liu R last · Qiao T first · Zhu Z last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last · Strokach A first · Zakharevich N · Aginova V · Grigoryevskaya Z · Petukhova I · Bagirova N · Romanov M · Dyachkova M · Morozov M · Veselovsky V · Kanaeva V · Kalinin D · Larin A · Shitikov E · Klimina K last
Downloads
PRJEB43119.csv.gz (7.0 KB) · parquet (80.7 KB) — all 165 samples, every field with route and confidence · PRJEB43119_determinations.csv.gz (18.1 KB) — 1,812 evidence rows