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PRJNA759642 SRP335413

Pediatric ulcerative colitis vs healthy children, US

16s and shotgun sequencing from human faecal

57 faecal samples from the USA (16S rRNA and shotgun sequencing), comparing ulcerative colitis cases to healthy controls, spanning child, adolescent, and adult age categories, in a case-control design. machine-written summary

57 samples · 57 runs · US · Adult · 2021 · 1.00 Gbp / sample

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Sources
✓Sequence archive 114✓Abstract / description 49✓Full text 22○Supplementary tables✓External resources 148–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive114 sample values (collection date, country)
✓ Abstract / description49 sample values (health condition detail)
✓ Full text22 sample values (antibiotic exposure) · PMC11650326, PMC12866134, PMC9018687
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources148 sample values (age, antibiotic exposure, health condition, health condition detail, sex) · from Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
adult32
adolescent18
child7
Condition
healthy_control27
ulcerative_colitis8
Sex
male18
female17
Country
US57
Body site
primary57
Collected 2018–2019
2018: 44 samples2019: 13 samples20182019
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 11 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 15 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 29 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)all projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 1.00 Gbp per sample0130Gbp
Community composition
Bacteroides 10.6%Roseburia 8.0%Faecalibacterium 6.2%Blautia_A 5.5%Phocaeicola 5.3%Bifidobacterium 4.1%Ruminococcoides 2.7%Gemmiger 2.5%Alistipes 2.5%Veillonella 2.3%Escherichia 2.2%Mediterraneibacter 2.0%not assigned to a genus 13.1%other genera 33.0%

Genera, mean relative abundance over 51 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category57 100%
country57 100%57
health_condition35 61%35
subject_id0 0%
antibiotic_exposure57 100%3522
collection_date57 100%57
health_condition_detail57 100%849
age_at_collection_days35 61%35
sex35 61%35
Papers (3)
  • 16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis. 2022 PMID 35440670 PMC9018687 own_data
  • Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326 unsure
  • Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder. 2026 PMID 41421350 PMC12866134 unsure
Details
Archive description

16s and shotgun reads of ulcerative colitis patients and controls.

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 · “sequencing from human faecal”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN21175538age_at_collection_days6574.5R20.70external.meta2db sourcehost_age: 18
SAMN21175538antibiotic_exposurenoR20.70external.meta2db sourceantibiotics: FALSE
SAMN21175539antibiotic_exposurenoR30.70paper.fulltext.methodsnone of the subjects used antibiotics
SAMN21175538collection_date2018R10.90biosample.attribute:collection_date2018
SAMN21175538countryUSR10.90sample.attr.geo_loc_nameUSA
SAMN21175538health_conditionhealthy_controlR20.70external.meta2db sourcehealth_disease_stat: control
SAMN21175540health_condition_detailulcerative colitisR20.70external.meta2db sourceulcerative colitis
SAMN21175538health_condition_detailmixed_case_control: pediatric ulcerative colitis patients vs healthy childrenR40.40paper.abstract19 pediatric UC and 23 healthy children
SAMN21175538sexmaleR20.70external.meta2db sourcehost_sex: male
Sequencing

57 runs over 57 samples · mean 0.86 Gbp per run (median 1.00 Gbp, total 49.29 Gbp; 57 runs with a base count) · layout PAIRED 57 · platform ILLUMINA 57 · models NextSeq 500 (57) · 89% of runs with a Sandpiper profile · first public 2021-09-03

Authors (34)

Zuo W first · Wang B · Bai X · Luan Y · Fan Y · Michail S · Sun F last · Ha SM first · Lee K · Kim GH · Hurych J · Cinek O · Shim JO last · Chen W first · Wang X · Zhu R · Gao W · Tao L · Yang R · Wei Q · Zhang Y · Gong Y · Zhong H · Huang L · Zhu X · Yang Y · Zhang L · Wan L · Yang G · Li Y · Jiao N · Wang J · Qin H · Zhu L last

Downloads

PRJNA759642.csv.gz (2.5 KB) · parquet (72.0 KB) — all 57 samples, every field with route and confidence · PRJNA759642_determinations.csv.gz (4.1 KB) — 333 evidence rows

Samples (57 · every field this project has values for · hover a cell for its source)
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