Vancomycin pretreatment & gut microbiota, C. diff trial
129 stool metagenome samples from healthy adult participants in a randomized, placebo-controlled trial, collected after short- or extended-course vancomycin pretreatment, prior to non-toxigenic C. difficile or placebo administration. machine-written summary
129 samples · 129 runs · NL · Adult · 2026 · 5.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 774 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 129 sample values (health condition detail) |
| ✓ Full text | 516 sample values (antibiotic exposure, health condition, location locality, location site) · PMC13408661 |
| ✓ Supplementary tables | 146 sample values (intervention, timepoint) |
| – 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 Defined bacterial consortium / live biotherapeutic product design randomized_controlled_trial · population healthy_control · Vancomycin pretreatment then NTCD spore capsules vs placebo
“administering non-toxigenic C. difficile (NTCD) capsules to healthy participants” — abstract:42286003 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Stool collected after vancomycin pretreatment wash-out: baseline (stage2 D-7/stage3 D-11), D-5, D-3, and D0 (pre-NTCD/placebo dosing)” (time origin: intervention start).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 129 | 100% | ||||
| country | 129 | 100% | 129 | |||
| health_condition | 129 | 100% | 129 | |||
| subject_id | 129 | 100% | 129 | |||
| antibiotic_exposure | 129 | 100% | 129 | |||
| collection_date | 129 | 100% | 129 | |||
| detailed_location | 129 | 100% | ||||
| health_condition_detail | 129 | 100% | 129 | |||
| latitude | 129 | 100% | 129 | |||
| location_locality | 129 | 100% | 129 | |||
| location_region | 129 | 100% | 129 | |||
| location_site | 129 | 100% | 129 | |||
| longitude | 129 | 100% | 129 | |||
| timepoint_label | 129 | 100% | 129 | |||
| intervention | 17 | 13% | 17 |
- Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial. 2026 PMID 42286003 PMC13408661 own_data
Archive description
Stool metagenomic sequencing from healthy participants collected after short- or extended-course vancomycin pretreatment in a randomized, placebo-controlled human colonisation trial with non-toxigenic C. difficile (NTCD). These samples represent the microbiome state after antibiotic exposure and prior to administration of NTCD spores or placebo, and were used to assess antibiotic-induced microbiota disruption and susceptibility to colonisation.
How this project entered the registry
Classified as human gut / stool 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 profiles following”
- body site study.description · “Stool metagenomic sequencing from”
- 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 |
|---|---|---|---|---|---|---|
| SAMN53262295 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | did not use antibiotics |
| SAMN53262295 | collection_date | 2024/2025 | R1 | 0.90 | biosample.attribute:collection_date | 2024/2025 |
| SAMN53262295 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN53262295 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 69 healthy participants aged 18-45 years |
| SAMN53262295 | health_condition_detail | healthy volunteers in experimental C. difficile colonisation trial | R4 | 0.50 | paper.abstract | 69 healthy participants |
| SAMN53262297 | intervention | live_biotherapeutic | R2 | 0.85 | paper.supp.Supplementary_data_files/Supplementary_Data_File_2_mapping.csv[Intervention group] | Unknown_CA061-001R0003: Intervention group=5D 10E7 spores |
| SAMN53262295 | latitude | 52.1658 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1658 N 4.4775 E |
| SAMN53262295 | location_locality | Leiden | R3 | 0.70 | paper.fulltext.methods | Leiden University Medical Centre (LUMC), Leiden, The Netherlands |
| SAMN53262295 | location_region | South Holland | R1 | 0.60 | biosample.attribute:lat_lon | 52.1658 N 4.4775 E |
| SAMN53262295 | location_site | Leiden University Medical Centre | R3 | 0.70 | paper.fulltext.methods | conducted at Leiden University Medical Centre (LUMC), Leiden |
| SAMN53262295 | longitude | 4.4775 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1658 N 4.4775 E |
| SAMN53262295 | subject_id | Unknown_CA061-001R0001 | R1 | 0.85 | sample.attr.sid | Unknown_CA061-001R0001 |
| SAMN53262295 | timepoint_label | Baseline | R2 | 0.85 | paper.supp.41467_2026_74327_MOESM6_ESM.xlsx[Fig. 5a-PCoA points!timepoint] | Baseline |
Sequencing
129 runs over 129 samples · mean 5.23 Gbp per run (median 5.10 Gbp, total 674.11 Gbp; 129 runs with a base count) · layout PAIRED 129 · platform DNBSEQ 129 · models DNBSEQ-T7 (129) · 0% of runs with a Sandpiper profile · first public 2026-04-16
Authors (21)
Hensen ADO first · Harmanus C · Verbeek-Menken PH · Koopman JPR · Lamers OAC · Roozen GVT · Janse JJ · Balke-Buijs M · van der Stoep MYEC · Meij P · van Amerongen-Westra IM · Schipper P · Crul C · Pattacini L · Rox K · Farowski F · Tsakmaklis A · Vehreschild MJGT · Kuijper EJ · Smits WK · Roestenberg M last
Downloads
PRJNA1364832.csv.gz (4.6 KB) · parquet (77.5 KB) — all 129 samples, every field with route and confidence · PRJNA1364832_determinations.csv.gz (10.4 KB) — 1,565 evidence rows