Gut microbiome in ICI-treated cancer patients, Canada
194 fecal samples from melanoma/NSCLC patients in Quebec and Ontario, Canada, plus antibiotic-pretreated, FMT-recipient mice; case-control design examining gut microbiome links to immune-related adverse events during checkpoint inhibitor therapy. machine-written summary
194 samples · 194 runs · CA · Age unknown · 2025 · 3.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,164 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 194 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC13288583 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy Faecal microbiota transplantation design single_arm_before_after · population other_cancer · FMT from ir-colitis patient into antibiotic-pretreated tumor-bearing mice
“received fecal microbiota transfer (FMT) from a lung cancer patient” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
30 of 156 people sampled more than once (68 samples; median 2, up to 4 per person) · follow-up median 4 mo (max 22 mo) · median interval between samples 4 mo (time from collection dates). Schedule stated by the source: “Paired stool samples per patient: baseline before ICI initiation and at onset of acute ir-colitis (n=9 patients with both timepoints)”.
Each row is one person (28 shown of 30); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 190 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 | 0 | 0% | ||||
| country | 194 | 100% | 194 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 194 | 100% | 194 | |||
| collection_date | 194 | 100% | 194 | |||
| detailed_location | 194 | 100% | ||||
| health_condition_detail | 194 | 100% | 194 | |||
| latitude | 194 | 100% | 194 | |||
| location_region | 194 | 100% | 194 | |||
| longitude | 194 | 100% | 194 |
- Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer. 2026 PMID 42083059 PMC13288583 own_data
Archive description
This project includes human and mouse gut microbiome sequencing datasets investigating the role of the microbiome in the development of immune-related adverse events (irAE) and immune checkpoint inhibitors (ICI) efficacy.</p><p>The human dataset consists of shotgun metagenomic sequencing data from fecal samples of patients with non-small cell lung cancer and melanoma treated with ICI. Samples were collected at baseline, prior to ICI initiation and before the onset of irAEs. These data support analyses of baseline microbiome taxonomic composition of cancer patient to assess predictive potential for irAE development and associations with treatment efficacy.</p><p>The mouse dataset contains 16S rRNA gene (V3-V4 region) sequencing data from fecal samples of tumor-bearing mice that received fecal microbiota transfer (FMT) from a lung cancer patient who developed immune-related colitis. All mice, including water-treated controls, were pretreated with antibiotics. Fecal samples were collected four weeks after FMT, corresponding to the time after the second ICI administration. These data provide complementary insights into the contribution of the gut microbiome to irAE pathogenesis in the context of cancer immunotherapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “fecal samples of patients with non-small cell lung cancer”
- body site study.description · “fecal samples of patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN50925194 | collection_date | 2019-05-17 | R1 | 0.90 | biosample.attribute:collection_date | 2019-05-17 |
| SAMN50925194 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Ontario |
| SAMN50925194 | health_condition_detail | mixed_case_control: melanoma and NSCLC patients with grade ≥2 irAE vs without grade ≥2 irAE | R4 | 0.50 | paper.abstract | melanoma and non-small cell lung cancer |
| SAMN50925194 | latitude | 43.7228 | R1 | 0.90 | biosample.attribute:lat_lon | 43.7228 N 79.3729 W |
| SAMN50925194 | location_region | Ontario | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Ontario |
| SAMN50925194 | longitude | -79.3729 | R1 | 0.90 | biosample.attribute:lat_lon | 43.7228 N 79.3729 W |
| SAMN50925194 | subject_id | 002_PreC1 | R1 | 0.85 | biosample.attribute:source_material_id | 002_PreC1 |
Sequencing
194 runs over 194 samples · mean 4.74 Gbp per run (median 3.05 Gbp, total 919.27 Gbp; 194 runs with a base count) · layout SINGLE 149, PAIRED 45 · platform ILLUMINA 194 · models Illumina NovaSeq 6000 (194) · 98% of runs with a Sandpiper profile · first public 2025-09-17 – 2025-09-21
Authors (20)
Diop K first · Benlaïfaoui M · Hunter S · Méndez-Salazar EO · Hakozaki T · Richard C · Prifti DK · Kourtian S · Proulx-Rocray F · Naimi S · Ponce M · Messaoudene M · Cauchois F · Belkaid W · Bataille V · Lee K · Mihalcioiu C · Watson IR · Elkrief A · Routy B last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1314234.csv.gz (6.9 KB) · parquet (79.6 KB) — all 194 samples, every field with route and confidence · PRJNA1314234_determinations.csv.gz (11.2 KB) — 1,358 evidence rows