SER-401 microbiome trial with nivolumab in melanoma, Houston
101 fecal samples from adult melanoma patients in Houston, Texas, from a randomized placebo-controlled, biomarker-stratified phase 1b trial testing vancomycin preconditioning plus SER-401 (a Firmicutes-enriched spore formulation) with nivolumab versus placebo. machine-written summary
101 samples · 101 runs · US · Adult · 2024 · 21.61 Gbp / sample · cohort Dietary fiber and probiotics influence the gut mic
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 505 sample values (country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 202 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11215408 |
| ○ 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 not resolved
Antibiotic given as the study intervention (incl. eradication therapy Non-antibiotic pharmaceutical given as the study intervention (metformin Defined bacterial consortium / live biotherapeutic product design randomized_controlled_trial · population other_cancer · SER-401 spore formulation + vancomycin preconditioning + nivolumab vs placebo, melanoma
“randomized to SER-401 arm (oral vancomycin pre-conditioning + SER-401” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 84 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 | 101 | 100% | ||||
| country | 101 | 100% | 101 | |||
| health_condition | 101 | 100% | 101 | |||
| subject_id | 0 | 0% | ||||
| detailed_location | 101 | 100% | ||||
| health_condition_detail | 101 | 100% | 101 | |||
| latitude | 101 | 100% | 101 | |||
| location_locality | 101 | 100% | 101 | |||
| location_region | 101 | 100% | 101 | |||
| longitude | 101 | 100% | 101 |
- Randomized Placebo-Controlled, Biomarker-Stratified Phase Ib Microbiome Modulation in Melanoma: Impact of Antibiotic Preconditioning on Microbiome and Immunity. 2024 PMID 38588588 PMC11215408 unsure
Archive description
Gut microbiota modulation shows promise in improving immune checkpoint blockade response (ICB) however, precision biomarker-driven trials using rationally-designed consortia are lacking. To address this, we performed a multi-center, randomized placebo-controlled, biomarker-stratified phase 1 trial in patients with ICB-naive unresectable or metastatic melanoma using SER-401, a Firmicutes-enriched spore formulation. Baseline gut microbiota were characterized (high versus low Ruminococcaceae abundance), and patients were randomized to SER-401 arm (oral vancomycin pre-conditioning + SER-401, followed by nivolumab + SER-401) versus placebo (with placebo-antibiotic pre-conditioning + placebo microbiome-modulation - PMM, followed by nivolumab + PMM) (NCT03817125). Accrual was negatively impacted by the COVID-19 pandemic, with 14 patients enrolled. Treatment with SER-401 and nivolumab was safe, though increased Ruminococcaceae abundance above baseline was not achieved in most patients ORR was 25% (95% confidence interval [CI] 3.2-65.1%, SER-401 arm) versus 67% (95% CI 22.3-95.7%, placebo arm). Important insights were gained via translational analyses, and additional placebo-controlled biomarker-driven microbiome trials are needed in this age of precision medicine.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Baseline gut microbiota were characterized”
- life stage study.title · “unresectable or metastatic melanoma”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35562094 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Houston,Texas |
| SAMN35562094 | health_condition | other_cancer | R4 | 0.50 | study.description | unresectable or metastatic melanoma |
| SAMN35562094 | health_condition_detail | ICB-naive unresectable or metastatic melanoma | R4 | 0.50 | study.description | unresectable or metastatic melanoma |
| SAMN35562094 | latitude | 29.7604 | R1 | 0.90 | biosample.attribute:lat_lon | 29.7604 N 95.3698 W |
| SAMN35562094 | location_locality | Houston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Houston,Texas |
| SAMN35562094 | location_region | Texas | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Houston,Texas |
| SAMN35562094 | longitude | -95.3698 | R1 | 0.90 | biosample.attribute:lat_lon | 29.7604 N 95.3698 W |
Sequencing
101 runs over 101 samples · mean 22.21 Gbp per run (median 21.61 Gbp, total 2,243.36 Gbp; 101 runs with a base count) · layout PAIRED 101 · platform ILLUMINA 101 · models Illumina NovaSeq 6000 (101) · 83% of runs with a Sandpiper profile · first public 2024-08-01
Authors (30)
Glitza IC first · Seo YD · Spencer CN · Wortman JR · Burton EM · Alayli FA · Loo CP · Gautam S · Damania A · Densmore J · Fairchild J · Cabanski CR · Wong MC · Peterson CB · Weiner B · Hicks N · Aunins J · McChalicher C · Walsh E · Tetzlaff MT · Hamid O · Ott PA · Boland GM · Sullivan RJ · Grossmann KF · Ajami NJ · LaVallee T · Henn MR · Tawbi HA · Wargo JA last
Downloads
PRJNA978931.csv.gz (3.4 KB) · parquet (73.7 KB) — all 101 samples, every field with route and confidence · PRJNA978931_determinations.csv.gz (3.9 KB) — 707 evidence rows