Gut microbiome in melanoma on checkpoint inhibitors (Dallas)
44 gut metagenome samples from adult and elderly cancer patients in Dallas, Texas, USA, studying gut microbes associated with response to immune checkpoint inhibitor drug therapy for melanoma. machine-written summary
44 samples · 44 runs · US · Age unknown · 2017 · 9.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 308 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 39 sample values (medication) · PMC10837094, PMC5602478, PMC8049424 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 166 sample values (age, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3), GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population other_cancer · Immune checkpoint inhibitor therapy in melanoma patients
“immune checkpoint therapy efficacy in melanoma patients” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Pretreatment sample for all patients; 5 patients had a repeat sample within 1 month of starting ICT therapy” (time origin: intervention start); stated follow-up 30 d.
Genera, mean relative abundance over 38 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 | 39 | 89% | ||||
| country | 44 | 100% | 44 | |||
| health_condition | 44 | 100% | 44 | |||
| subject_id | 44 | 100% | 44 | |||
| collection_date | 44 | 100% | 44 | |||
| detailed_location | 44 | 100% | ||||
| health_condition_detail | 44 | 100% | 44 | |||
| latitude | 44 | 100% | 44 | |||
| location_locality | 44 | 100% | 44 | |||
| location_region | 44 | 100% | 44 | |||
| longitude | 44 | 100% | 44 | |||
| age_at_collection_days | 39 | 89% | 39 | |||
| medication | 39 | 89% | 39 | |||
| sex | 39 | 89% | 39 |
- Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. 2017 PMID 28923537 PMC5602478 own_data
- MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data. 2021 PMID 33713107 PMC8049424 own_data
- Protocol to identify fungal profile from fecal metagenomes in cancer patients prior to immunotherapy. 2024 PMID 38277270 PMC10837094 own_data
- Technology-enabled integration of single-cell transcriptomics and microbiome data identifies RNA-targetable host-microbiota networks in colorectal adenoma. 2026 PMID 41241214 own_data
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. 2021 PMID 33175106 PMC7664509 unsure
23 more
- Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma. 2020 PMID 33268597 PMC7714408
- A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors. 2021 PMID 33593881 PMC9053858
- geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. 2021 PMID 33952321 PMC8097837
- 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
- Predicting cancer immunotherapy response from gut microbiomes using machine learning models. 2022 PMID 35875611 PMC9295706
- The microbiome-derived metabolite TMAO drives immune activation and boosts responses to immune checkpoint blockade in pancreatic cancer. 2022 PMID 36083892 PMC9925043
- Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy. 2023 PMID 36809182 PMC10134792
- Gut microbial structural variation associates with immune checkpoint inhibitor response. 2023 PMID 37973916 PMC10654443
- Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. 2024 PMID 38365950 PMC10957474
- 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
- 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
- Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses. 2025 PMID 39929976 PMC11879847
- Microbiome data integration via shared dictionary learning. 2025 PMID 40890119 PMC12402269
- 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
- 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
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities. 2026 PMID 42750046 PMC13584529
Archive description
Metagenomic shotgun sequencing identifies specific human gut microbes that are associated with immune checkpoint therapy efficacy in melanoma patients
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “specific human gut microbes”
- body site study.title · “gut microbiomes of melanoma patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07498097 | age_at_collection_days | 23010.75 | R2 | 0.75 | external.cmd source | age: 63; age_unit: Year; age_group: Adult |
| SAMN07498097 | collection_date | 2016-05-28 | R1 | 0.90 | biosample.attribute:collection_date | 2016-05-28 |
| SAMN07498097 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Dallas, Texas |
| SAMN07498097 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | disease: Melanoma;Metastatic Malignant Neoplasm in the Lung |
| SAMN07498098 | health_condition | other_cancer | R2 | 0.75 | external.gmrepo source | phenotype: Melanoma |
| SAMN07498097 | health_condition_detail | Melanoma;Metastatic Malignant Neoplasm in the Lung | R2 | 0.75 | external.cmd source | disease: Melanoma;Metastatic Malignant Neoplasm in the Lung |
| SAMN07498098 | health_condition_detail | Melanoma | R2 | 0.75 | external.gmrepo source | phenotype: Melanoma |
| SAMN07498097 | latitude | 32.8094 | R1 | 0.90 | biosample.attribute:lat_lon | 32.8094 N 96.8365 W |
| SAMN07498097 | location_locality | Dallas | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Dallas, Texas |
| SAMN07498097 | location_region | Texas | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Dallas, Texas |
| SAMN07498097 | longitude | -96.8365 | R1 | 0.90 | biosample.attribute:lat_lon | 32.8094 N 96.8365 W |
| SAMN07498097 | medication | immunosuppressant_or_biologic | R3 | 0.85 | paper.body.Table 2[ICT Therapy] | IN |
| SAMN07498097 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN07498097 | subject_id | P7 | R1 | 0.85 | sample.attr.patient | P7 |
Sequencing
44 runs over 44 samples · mean 8.57 Gbp per run (median 9.06 Gbp, total 377.00 Gbp; 44 runs with a base count) · layout PAIRED 44 · platform ILLUMINA 44 · models Illumina HiSeq 2000 (44) · 86% of runs with a Sandpiper profile · first public 2017-11-09
Authors (49)
Zhang L first · Zhou DD · Feng J · Liao ZJ · Shu XL · Yang RM · Gao YC · Zhou HH · Zhang W · Zou Y · Liu R last · Ma B first · Hu H · Lin Y · Wang Z · Song Q last · Orletskaia VA first · Olekhnovich EI last · Candeliere F first · Busi E · Cerri S · Sola L · Lombardi M · Greco S · Pedroni S · Amaretti A · Raimondi S · Chiavelli C · Vitale MG · Bertolini F · Depenni R · Franchini G · Dominici M · Rossi M 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
PRJNA397906.csv.gz (2.7 KB) · parquet (73.1 KB) — all 44 samples, every field with route and confidence · PRJNA397906_determinations.csv.gz (6.6 KB) — 513 evidence rows