Pediatric ulcerative colitis gut microbiome, USA
241 stool and rectal biopsy samples from pediatric patients with new-onset ulcerative colitis in the USA, collected longitudinally to study gut microbiome factors in treatment response to two conventional drug therapies. machine-written summary
241 samples · 241 runs · US · Child · 2024 · 1.12 Gbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 482 sample values (country, subject id) |
| ✓ Abstract / description | 241 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC10859715, PMC10923022, PMC11441152, PMC11650326, PMC12259524, PMC13079761, PMC13081238, PMC6277984, PMC6318335, PMC8895431, PMC9728153 |
| ○ 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
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population ulcerative_colitis · Conventional UC treatments (e.g. 5-ASA, corticosteroids) compared pre/post
“efficacy of two conventional treatments” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
81 of 95 people sampled more than once (227 samples; median 3, up to 4 per person). Schedule stated by the source: “Up to 4 samples per patient at weeks 0, 4, 12, and 52”; stated follow-up 12 mo.
Genera, mean relative abundance over 219 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 | 241 | 100% | ||||
| country | 241 | 100% | 241 | |||
| health_condition | 241 | 100% | 241 | |||
| subject_id | 241 | 100% | 241 |
- Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. 2018 PMID 30308161 PMC6277984 own_data
- Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. 2019 PMID 30604764 PMC6318335 own_data
- Inflammation-associated nitrate facilitates ectopic colonization of oral bacterium Veillonella parvula in the intestine. 2022 PMID 36138166 PMC9728153 own_data
- Gut microbiota signatures in inflammatory bowel disease. 2024 PMID 38041519 PMC10859715 own_data
- Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. 2024 PMID 38215740 PMC10923022 own_data
6 more
- Stratification of human gut microbiomes by succinotype is associated with inflammatory bowel disease status. 2024 PMID 39350289 PMC11441152
- An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data. 2026 PMID 41796297 PMC13081238
- Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease. 2022 PMID 35251123 PMC8895431
- Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326
- Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation. 2025 PMID 40658318 PMC12259524
- SpiR is a gut microbial enzyme that drives cholesterol conversion. 2026 PMID 41980965 PMC13079761
Archive description
This project collected and profiled stool samples and rectal biopsies from pediatric patients with new-onset ulcerative colitis (UC) to evaluate the role of the gut microbiome in the efficacy of two conventional treatments.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “Gut microbial factors implicated”
- body site study.description · “collected and profiled stool samples and rectal”
- body site study.description · “samples and rectal biopsies from pediatric patients”
- life stage study.title · “treatment response in pediatric ulcerative colitis”
- life stage study.description · “rectal biopsies from pediatric patients with new-onset”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38849470 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN38849470 | health_condition | ulcerative_colitis | R4 | 0.50 | study.description | pediatric patients with new-onset ulcerative colitis |
| SAMN38849470 | subject_id | Subject11516 | R1 | 0.85 | biosample.attribute:subject_information | STL50520_Subject11516 |
Sequencing
241 runs over 241 samples · mean 1.38 Gbp per run (median 1.12 Gbp, total 332.84 Gbp; 241 runs with a base count) · layout PAIRED 241 · platform ILLUMINA 241 · models Illumina HiSeq 2500 (241) · 91% of runs with a Sandpiper profile · first public 2024-03-24
Authors (45)
Kubinski R first · Djamen-Kepaou JY · Zhanabaev T · Hernandez-Garcia A · Bauer S · Hildebrand F · Korcsmaros T · Karam S · Jantchou P · Kafi K · Martin RD last · Vestergaard MV first · Allin KH · Eriksen C · Zakerska-Banaszak O · Arasaradnam RP · Alam MT · Kristiansen K · Brix S · Jess T last · Yu S first · Li J · Ye Z · Zhang M · Guo X · Wang X · Liu L · Wang Y · Zhou X · Fu W · Zhang MQ · Chen YG last · Shi K first · He Q · Wang S · Guo J last · Arp G first · Levy S · Jiang AK · Dufault-Thompson K · Zhong A · Grant M · Li Y · Jiang X · Hall B last
Downloads
PRJNA436359.csv.gz (6.6 KB) · parquet (77.8 KB) — all 241 samples, every field with route and confidence · PRJNA436359_determinations.csv.gz (6.8 KB) — 723 evidence rows