Gut microbiota and anti-PD-1 response in NSCLC/RCC, France
219 fecal samples from adult and elderly cancer (NSCLC/RCC) patients in France, studying gut microbiota composition relative to clinical response to anti-PD-1 therapy, antibiotics, and Akkermansia muciniphila supplementation; case-control design. machine-written summary
219 samples · 219 runs · FR · Adult · 2017 · 2.99 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,961 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, intervention, intervention detail) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11916936, PMC12439585, PMC7176420, PMC9069064 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
31 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin Faecal microbiota transplantation Probiotic (live microorganisms; single strain or mixture) design observational_with_procedure · population other_cancer · Anti-PD-1 therapy; FMT and A. muciniphila supplementation in mouse models
“Fecal microbiota transplantation (FMT) from cancer patients who responded to ICI” — bioproject.description (study level; per-sample arms are in the intervention column below)
sex differs between samples of the same subject id (19 subjects, 45 samples) — sex withheld; subject ids shared by samples of both sexes (22 ids, 60 samples) — ids withheld.
The sources disagree on 64 samples. 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 (40 of 105)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA104416141 | sex | female (sequence archive) | subject I_018: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416146 | sex | female (sequence archive) | subject I_038: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416147 | sex | female (sequence archive) | subject I_040: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416188 | sex | female (sequence archive) | subject I_045: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA104416189 | sex | female (sequence archive) | subject I_047: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA104416195 | sex | male (sequence archive) | subject I_049: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416196 | sex | male (sequence archive) | subject I_051: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416198 | sex | male (sequence archive) | subject I_054: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416204 | sex | male (sequence archive) | subject I_068: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416206 | sex | male (sequence archive) | subject I_070: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416209 | sex | male (sequence archive) | subject I_076: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416216 | sex | female (sequence archive) | subject I_009: male in 3 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416218 | sex | female (sequence archive) | subject I_015: female in 2 samples, male in 1 sample | withheld: neither value published |
| SAMEA104416219 | sex | female (sequence archive) | subject I_015: female in 2 samples, male in 1 sample | withheld: neither value published |
| SAMEA104416223 | sex | male (sequence archive) | subject I_056: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416224 | sex | male (sequence archive) | subject I_061: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416226 | sex | female (sequence archive) | subject I_006: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA104416228 | sex | female (sequence archive) | subject I_036: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416239 | sex | male (sequence archive) | subject I_005: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416242 | sex | male (sequence archive) | subject I_022: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416250 | sex | female (sequence archive) | subject I_005: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416254 | sex | female (sequence archive) | subject I_022: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416261 | sex | female (sequence archive) | subject I_049: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416262 | sex | female (sequence archive) | subject I_051: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416263 | sex | female (sequence archive) | subject I_054: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416264 | sex | female (sequence archive) | subject I_056: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416265 | sex | female (sequence archive) | subject I_061: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416268 | sex | female (sequence archive) | subject I_068: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416269 | sex | female (sequence archive) | subject I_070: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416272 | sex | female (sequence archive) | subject I_076: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA104416279 | sex | male (sequence archive) | subject I_006: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMEA104416283 | sex | male (sequence archive) | subject I_009: male in 3 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416284 | sex | male (sequence archive) | subject I_009: male in 3 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416285 | sex | male (sequence archive) | subject I_009: male in 3 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416294 | sex | male (sequence archive) | subject I_015: female in 2 samples, male in 1 sample | withheld: neither value published |
| SAMEA104416298 | sex | male (sequence archive) | subject I_018: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416299 | sex | male (sequence archive) | subject I_018: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416320 | sex | male (sequence archive) | subject I_036: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416321 | sex | male (sequence archive) | subject I_036: male in 2 samples, female in 1 sample | withheld: neither value published |
| SAMEA104416322 | sex | male (sequence archive) | subject I_038: male in 2 samples, female in 1 sample | withheld: neither value published |
longitudinal
43 of 84 people sampled more than once (118 samples; median 3, up to 5 per person) · follow-up median 9.0 y (max 27.0 y) · median interval between samples 9.0 y (time from age at collection). Schedule stated by the source: “Samples at T0 (baseline), T1 (after one month), T2 (after two months)” (time origin: treatment start); stated follow-up 2 mo.
Each row is one person (24 shown of 43); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 219 | 100% | ||||
| country | 219 | 100% | 219 | |||
| health_condition | 219 | 100% | 219 | |||
| subject_id | 159 | 73% | 159 | |||
| age_at_collection_days | 219 | 100% | 219 | |||
| antibiotic_exposure | 219 | 100% | 219 | |||
| collection_date | 219 | 100% | 219 | |||
| detailed_location | 219 | 100% | ||||
| health_condition_detail | 219 | 100% | 219 | |||
| intervention | 219 | 100% | 219 | |||
| intervention_detail | 219 | 100% | 219 | |||
| latitude | 219 | 100% | 219 | |||
| location_region | 219 | 100% | 219 | |||
| longitude | 219 | 100% | 219 | |||
| timepoint_label | 219 | 100% | 219 | |||
| sex | 174 | 79% | 174 |
- Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. 2018 PMID 29097494 own_data
- Distinct Functional Metagenomic Markers Predict the Responsiveness to Anti-PD-1 Therapy in Chinese Non-Small Cell Lung Cancer Patients. 2022 PMID 35530307 PMC9069064 own_data
- Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis. 2025 PMID 40098172 PMC11916936 own_data
- Metagenomic growth rate inferences of strains in situ. 2020 PMID 32494636 PMC7176420 unsure
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers. 2021 PMID 33175106 PMC7664509 unsure
13 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
- Gut microbial structural variation associates with immune checkpoint inhibitor response. 2023 PMID 37973916 PMC10654443
- Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis? 2024 PMID 39204125 PMC11357004
- 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
- Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types. 2025 PMID 40151642 PMC11937697
- Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches. 2025 PMID 40792105 PMC12336193
- Live biotherapeutic <i>enterococcus lactis</i> MNC-168 promotes the efficacy of immune checkpoint blockade in cancer therapy by activating STING pathway via bacterial membrane vesicles. 2025 PMID 40937720 PMC12439585
- 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
- Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis. 2026 PMID 42189287 PMC13388844
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities. 2026 PMID 42750046 PMC13584529
Archive description
Immune checkpoint inhibitors (ICI) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizeable minority of cancer patients. Here, we show that primary resistance to ICI can be due to an abnormal gut microbiota. Antibiotics (ATB) inhibited the clinical benefit of ICI in advanced cancer patients. Fecal microbiota transplantation (FMT) from cancer patients who responded to ICI (but not from non-responding patients) into germ-free or ATB-treated mice ameliorated the antitumor effects of PD-1 blockade. Metagenomics of patient stools at diagnosis revealed correlations between clinical responses to ICI and the relative abundance of Akkermansia muciniphila. Oral supplementation with A. muciniphila post-FMT with non-responder feces restored the efficacy of PD-1 blockade in an IL-12-dependent manner, by increasing the recruitment of CCR9+CXCR3+CD4+ T lymphocytes into tumor beds.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Gut mictobiota composition correlation”
- life stage study.title · “NSCLC and RCC patients”
- life stage sample.attr.host_age · “68 (n=85/219)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104416127 | age_at_collection_days | 28124.2 | R1 | 0.70 | sample.attr.host_age | 77 |
| SAMEA104416127 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | no |
| SAMEA104416127 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA104416127 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA104416127 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | NSCLC |
| SAMEA104416127 | health_condition_detail | NSCLC | R1 | 0.90 | sample.attr.host_disease_status | NSCLC |
| SAMEA104416127 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:Timepoint | Timepoint: T0 |
| SAMEA104416127 | intervention_detail | baseline before anti-PD-1 therapy | R1 | 0.80 | biosample.attribute:Timepoint | Timepoint: T0 |
| SAMEA104416127 | latitude | 48.7955 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.795496 2.347477 |
| SAMEA104416127 | location_region | Ile-de-France | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.795496 2.347477 |
| SAMEA104416127 | longitude | 2.3475 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.795496 2.347477 |
| SAMEA104416127 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMEA104416127 | subject_id | C_008 | R1 | 0.85 | sample.attr.patient_id | C_008 |
| SAMEA104416127 | timepoint_label | T0 | R1 | 0.85 | sample.attr.timepoint | T0 |
Sequencing
219 runs over 219 samples · mean 2.97 Gbp per run (median 2.99 Gbp, total 651.18 Gbp; 219 runs with a base count) · layout SINGLE 219 · platform ION_TORRENT 219 · models Ion Torrent Proton (219) · 0% of runs with a Sandpiper profile · first public 2017-12-05 – 2018-01-07
Authors (80)
Routy B first · Le Chatelier E · Derosa L · Duong CPM · Alou MT · Daillère R · Fluckiger A · Messaoudene M · Rauber C · Roberti MP · Fidelle M · Flament C · Poirier-Colame V · Opolon P · Klein C · Iribarren K · Mondragón L · Jacquelot N · Qu B · Ferrere G · Clémenson C · Mezquita L · Masip JR · Naltet C · Brosseau S · Kaderbhai C · Richard C · Rizvi H · Levenez F · Galleron N · Quinquis B · Pons N · Ryffel B · Minard-Colin V · Gonin P · Soria JC · Deutsch E · Loriot Y · Ghiringhelli F · Zalcman G · Goldwasser F · Escudier B · Hellmann MD · Eggermont A · Raoult D · Albiges L · Kroemer G · Zitvogel L last · Koh H first · Kim J · Jang H 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 · 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
Downloads
PRJEB22863.csv.gz (7.6 KB) · parquet (80.6 KB) — all 219 samples, every field with route and confidence · PRJEB22863_determinations.csv.gz (17.5 KB) — 2,961 evidence rows