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PRJNA1249606 SRP589404

Pediatric Crohn's microbiome case-control, Cincinnati

Microbiome in pediatric inflammatory bowel disease (Part 2)

136 gut microbiome samples from pediatric Crohn's disease patients in Cincinnati, Ohio, USA, examining microbial shifts and C. difficile association with bowel resection surgery timing; case-control design. machine-written summary

136 samples · 136 runs · US · Child · 2025 · 5.03 Gbp / sample

One study deposited as 2 BioProjects (284 catalog samples together): PRJNA1249606 · PRJNA1249971 · show together

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 816✓Abstract / description 272–Full text–Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive816 sample values (collection date, country, latitude, location locality, location region, longitude)
✓ Abstract / description272 sample values (health condition, health condition detail)
– Full textno open-access full text linked · PMC7365806
– Supplementary tablesno supplementary tables available (or none open access)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
child136
Condition
crohns_disease136
Country
US136
Body site
primary136
Collected 2016–2018
2016: 23 samples2017: 108 samples2018: 5 samples20162018
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 2 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 7 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 124 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 3 samplesall 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 5.03 Gbp per sample0130Gbp
Community composition
Bacteroides 18.8%Phocaeicola 11.9%Roseburia 4.8%Alistipes 3.5%Faecalibacterium 3.0%Blautia_A 3.0%Prevotella 2.8%Salinibacter 2.6%Escherichia 2.5%Bifidobacterium 2.5%Parabacteroides 1.9%Lachnospira 1.6%not assigned to a genus 7.3%other genera 33.9%

Genera, mean relative abundance over 134 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category136 100%
country136 100%136
health_condition136 100%136
subject_id0 0%
collection_date136 100%136
detailed_location136 100%
health_condition_detail136 100%136
latitude136 100%136
location_locality136 100%136
location_region136 100%136
longitude136 100%136
Papers (1)
  • Microbial Shifts and Shorter Time to Bowel Resection Surgery Associated with C. difficile in Pediatric Crohn's Disease. 2020 PMID 31725875 PMC7365806 own_data
Details
Archive description

Microbial Shifts and Shorter Time to Bowel Resection Surgery Associated with C. difficile in Pediatric Crohn's Disease</p><p>PMID 31725875

How this project entered the registry

Classified as human gut / stool 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 external_curation.infant_catalog · “body_site_call stool”
  • life stage study.title · “Microbiome in pediatric inflammatory bowel disease”
  • life stage study.description · “C. difficile in Pediatric Crohn's Disease</p><p>PMID 31725875”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN47909135collection_date2017-09-27R10.90biosample.attribute:collection_date2017-09-27
SAMN47909135countryUSR10.90sample.attr.geo_loc_nameUSA: Ohio, Cincinnati
SAMN47909135health_conditioncrohns_diseaseR40.50paper.abstractA prospective single-center study of 70 CD patients utilized C. difficile testing and shotgun metagenomic sequencing of fecal samples
SAMN47909135health_condition_detailCD (Crohn's disease)R40.50paper.abstractA prospective single-center study of 70 CD patients utilized C. difficile testing and shotgun metagenomic sequencing of fecal samples
SAMN47909135latitude39.1000R10.90biosample.attribute:lat_lon39.10 N 84.51 W
SAMN47909135location_localityCincinnatiR10.85biosample.attribute:geo_loc_nameUSA: Ohio, Cincinnati
SAMN47909135location_regionOhioR10.85biosample.attribute:geo_loc_nameUSA: Ohio, Cincinnati
SAMN47909135longitude-84.5100R10.90biosample.attribute:lat_lon39.10 N 84.51 W
Sequencing

136 runs over 136 samples · mean 5.27 Gbp per run (median 5.03 Gbp, total 717.28 Gbp; 136 runs with a base count) · layout PAIRED 136 · platform ILLUMINA 136 · models NextSeq 500 (136) · 99% of runs with a Sandpiper profile · first public 2025-06-09

Authors (0)

No author record.

Downloads

PRJNA1249606.csv.gz (4.5 KB) · parquet (75.8 KB) — all 136 samples, every field with route and confidence · PRJNA1249606_determinations.csv.gz (7.4 KB) — 1,088 evidence rows

Samples (136 · every field this project has values for · hover a cell for its source)
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