Pediatric severe UC, antibiotics vs steroids RCT
186 gut microbiome samples from pediatric/adolescent acute severe ulcerative colitis patients, mainly in Israel, with smaller numbers from Italy, Canada, and Finland, in a randomized controlled trial comparing IV corticosteroids alone versus corticosteroids plus a four-drug oral antibiotic regimen. machine-written summary
186 samples · 186 runs · IL, IT, CA · Child · 2019 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,426 sample values (age, country, health condition, health condition detail, intervention, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11650326, PMC12268991 |
| ○ 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 |
age: two sequence archives disagree for 13 samples (e.g. 168.0 vs 1674.1) — withheld.
The sources disagree on 13 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 (13)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11408420 | age | 168.0 (sequence archive) | 1674.1 (sequence archive) | withheld: neither value published |
| SAMN11408448 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408465 | age | 168.0 (sequence archive) | 1674.1 (sequence archive) | withheld: neither value published |
| SAMN11408489 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408506 | age | 168.0 (sequence archive) | 1674.1 (sequence archive) | withheld: neither value published |
| SAMN11408523 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408526 | age | 168.0 (sequence archive) | 1674.1 (sequence archive) | withheld: neither value published |
| SAMN11408550 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408563 | age | 168.0 (sequence archive) | 1674.1 (sequence archive) | withheld: neither value published |
| SAMN11408573 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408592 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408604 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
| SAMN11408605 | age | 3.1 (sequence archive) | 3135.1 (sequence archive) | withheld: neither value published |
longitudinal
36 of 43 people sampled more than once (179 samples; median 5, up to 10 per person) · follow-up median 3 mo (max 12 mo) · median interval between samples 30 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Repeated stool sampling per subject at stated days since treatment start (e.g. 0,2,3,5,30,60,90,180,360) and at discharge” (time origin: treatment start); stated follow-up 12 mo.
Each row is one person (22 shown of 36); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 120 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 | 186 | 100% | ||||
| country | 140 | 75% | 140 | |||
| health_condition | 186 | 100% | 186 | |||
| subject_id | 186 | 100% | 186 | |||
| health_condition_detail | 186 | 100% | 186 | |||
| intervention | 186 | 100% | 186 | |||
| sex | 186 | 100% | 186 | |||
| timepoint_label | 186 | 100% | 186 | |||
| age_at_collection_days | 170 | 91% | 170 |
- Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
Archive description
A subset of acute severe ulcerative colitis (ASC) patients receiving antimicrobials experience accelerated remission and given the link between IBD and the gut microbiome, we investigated potential mechanisms of action of antimicrobial-induced remission in relation to alterations in the gut microbiome. To this end, we conducted a randomized control trial, in which one group received standard of care intravenous corticosteroids (IVCS) and another received IVCS supplemented with a multidrug regimen of four oral antibiotics (amoxycillin, doxycyclin/ciprofloxacin, metronidazole, vancomycin).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “PRASCO gut microbiome profile of”
- body site study.description · “IBD and the gut microbiome, we investigated”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “microbiome profile of Pediatric Severe Acute Ulcerative”
- life stage sample.attr.host_age · “15.91666667 (n=71/186)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11408407 | age_at_collection_days | 4677.0 | R1 | 0.85 | sample.attr.host_age | 12.83333333 |
| SAMN11408410 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel |
| SAMN11408407 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | Severe chronic ulcerative colitis |
| SAMN11408407 | health_condition_detail | severe acute ulcerative colitis | R1 | 0.90 | sample.attr.gastrointest_disord | severe acute ulcerative colitis |
| SAMN11408407 | intervention | drug_therapy | R1 | 0.85 | biosample.attribute:chem_administration | Corticosteroids |
| SAMN11408407 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN11408407 | subject_id | SCH-009OL | R1 | 0.85 | sample.attr.host_subject_id | SCH-009OL |
| SAMN11408407 | timepoint_label | 0 | R1 | 0.85 | sample.attr.days_since_treatment_start | 0 |
Sequencing
186 runs over 186 samples · mean 0.72 Gbp per run (median 0.47 Gbp, total 134.44 Gbp; 186 runs with a base count) · layout PAIRED 186 · platform ILLUMINA 186 · models Illumina HiSeq 2500 (186) · 65% of runs with a Sandpiper profile · first public 2019-11-26
Authors (17)
Ha SM first · Lee K · Kim GH · Hurych J · Cinek O · Shim JO last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last
Downloads
PRJNA532645.csv.gz (6.1 KB) · parquet (78.1 KB) — all 186 samples, every field with route and confidence · PRJNA532645_determinations.csv.gz (10.2 KB) — 1,426 evidence rows