Gut microbiome and PD-1 response in melanoma (USA)
25 fecal metagenome samples from adult melanoma patients in the USA undergoing anti-PD-1 immunotherapy, comparing responders versus non-responders in a case-control design. machine-written summary
25 samples · 25 runs · US · Adult · 2017 · 3.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 50 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 25 sample values (location locality) · PMC13274128, PMC5827966, PMC8097837 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 50 sample values (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 |
Genera, mean relative abundance over 22 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 | 25 | 100% | ||||
| country | 25 | 100% | 25 | |||
| health_condition | 25 | 100% | 25 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 25 | 100% | 25 | |||
| detailed_location | 25 | 100% | ||||
| health_condition_detail | 25 | 100% | 25 | |||
| location_locality | 25 | 100% | 25 |
- Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. 2018 PMID 29097493 PMC5827966 own_data
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. 2021 PMID 33175106 PMC7664509 unsure
- Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma. 2020 PMID 33268597 PMC7714408 unsure
- A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors. 2021 PMID 33593881 PMC9053858 unsure
- geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. 2021 PMID 33952321 PMC8097837 unsure
15 more
- Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. 2022 PMID 35228751 PMC8938272
- Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1. 2022 PMID 35228752 PMC10246505
- The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer. 2022 PMID 36083892 PMC9925043
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy. 2023 PMID 36809182 PMC10134792
- Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. 2024 PMID 38365950 PMC10957474
- Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy. 2024 PMID 38448159 PMC10917649
- Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial. 2024 PMID 39486411 PMC11560503
- MiCML: a causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles. 2025 PMID 39885552 PMC11783787
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697
- Microbiome data integration via shared dictionary learning. 2025 PMID 40890119 PMC12402269
- Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts. 2025 PMID 41304278 PMC12654497
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types. 2026 PMID 42146906 PMC13173278
- Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset. 2026 PMID 42298353 PMC13274128
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities. 2026 PMID 42750046 PMC13584529
Archive description
Pre-clinical mouse models have suggested that the gut microbiome modulates tumor response to checkpoint blockade immunotherapy, however this has not been well-characterized in human cancer patients. Here we examined the oral and gut microbiome of melanoma patients undergoing PD-1 blockade immunotherapy (n=112). Significant differences were observed in the diversity and composition of the patient gut microbiome of responders (R) versus non-responders (NR). Analysis of patient fecal microbiome samples (n=43, 30R, 13NR) showed significantly higher alpha diversity (p<0.01) and relative abundance of Ruminococcaceae bacteria (p<0.01) in R. Metagenomic studies revealed functional differences in gut bacteria in R including enrichment of anabolic pathways. Immune profiling found enhanced systemic and anti-tumor immunity in responding patients with a favorable gut microbiome, as well as in germ-free mice receiving fecal transplants from responding patients. Together, these data have important implications for treatment with immune checkpoint blockade in melanoma.
How this project entered the registry
Classified as human gut / stool / oral cavity / blood / tissue / internal fluids shotgun DNA metagenome of adult 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 · “Gut microbiome impacts response”
- body site study.description · “suggested that the gut microbiome modulates tumor”
- body site study.description · “we examined the oral and gut microbiome”
- body site study.description · “gut microbiome modulates tumor response to checkpoint”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104335941 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA104335941 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA104335941 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | disease: Melanoma;Metastatic Malignant Neoplasm |
| SAMEA104335941 | health_condition_detail | Melanoma;Metastatic Malignant Neoplasm | R2 | 0.75 | external.cmd source | disease: Melanoma;Metastatic Malignant Neoplasm |
| SAMEA104335941 | location_locality | Moscow | R3 | 0.60 | paper.fulltext.results | Russia: Moscow |
Sequencing
25 runs over 25 samples · mean 3.21 Gbp per run (median 3.29 Gbp, total 80.28 Gbp; 25 runs with a base count) · layout PAIRED 25 · platform ILLUMINA 25 · models Illumina HiSeq 2000 (25) · 88% of runs with a Sandpiper profile · first public 2017-11-06
Authors (59)
Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Karcher N · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Koh H first · Kim J · Jang H last · Cai X first · Cho JY · Chen L · Liu Y · Ji F · Salgado K · Ge S · Yang D · Yu H · Shao J · Futreal PA · Sepesi B · Gibbons D · Chen Y · Wang G · Cheng C · Wu M · Zhang J · Hsiao A · Xia T last · Qiao T first · Zhu Z last · Orletskaia VA first · Olekhnovich EI 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
PRJEB22893.csv.gz (1.5 KB) · parquet (70.0 KB) — all 25 samples, every field with route and confidence · PRJEB22893_determinations.csv.gz (1.7 KB) — 125 evidence rows