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SRP057027 SRP057027

Gut microbiome in pediatric Crohn's disease study

Inflammation, Antibiotics, and Diet as Concurrent Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

369 stool samples examined for gut microbiome changes related to inflammation, antibiotics, and diet in pediatric Crohn's disease; no further sample demographics or design details provided. machine-written summary

369 samples · 369 runs · Child · 2015 · 2.08 Gbp / sample

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Sources
✓Sequence archive 1,642✓Abstract / description 203○Full text✓Supplementary tables 332–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,642 sample values (intervention, intervention detail, medication, medication detail, subject id, timepoint)
✓ Abstract / description203 sample values (health condition)
○ Full textread; no usable statement or table · PMC10191612, PMC10246480, PMC10756304, PMC10827402, PMC10842462, PMC10939037, PMC11293350, PMC12259524, PMC12268991, PMC13059687, PMC13271634, PMC5808452, PMC6068170, PMC6289653, PMC6670193, PMC6717631, PMC6759048, PMC7216530, PMC7498351, PMC8269207, PMC8564485, PMC8612635, PMC8667605, PMC9040671, PMC9880954
✓ Supplementary tables332 sample values (health condition, health condition detail)
– 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
Age
child369
Condition
crohns_disease351
healthy_control18
Body site
primary369
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 21 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 6 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 9 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 44 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 185 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 103 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 1 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 2.08 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

87 of 87 people sampled more than once (343 samples; median 4, up to 4 per person). Schedule stated by the source: “archive time labels: visit 03, visit 01, visit 02, visit 04”.

How longitudinal and relatedness information is derived

Community composition

No Sandpiper profile for this project's samples yet.

Field coverage
fieldsamplescoverageR1R2R3R4
age_category369 100%
country0 0%
health_condition369 100%166203
subject_id343 93%343
intervention343 93%343
intervention_detail343 93%343
timepoint_label343 93%343
health_condition_detail166 45%166
medication135 37%135
medication_detail135 37%135
Papers (25)
  • A role for bacterial urease in gut dysbiosis and Crohn's disease. 2017 PMID 29141885 PMC5808452 cites_accession
  • From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease. 2018 PMID 30083388 PMC6068170 cites_accession
  • Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. 2018 PMID 30420687 PMC6289653 cites_accession
  • Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048 cites_accession
  • Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. 2019 PMID 31370880 PMC6670193 cites_accession
20 more
  • Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. 2019 PMID 31472697 PMC6717631
  • Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment. 2020 PMID 32393180 PMC7216530
  • Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju. 2020 PMID 32633756 PMC7498351
  • Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models. 2021 PMID 33947803 PMC8269207
  • Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. 2021 PMID 34678170 PMC8667605
  • The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome. 2021 PMID 34745023 PMC8564485
  • Optimal Permutation Recovery in Permuted Monotone Matrix Model. 2021 PMID 34840367 PMC8612635
  • More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. 2022 PMID 35493727 PMC9040671
  • Successful Dietary Therapy in Paediatric Crohn's Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls. 2023 PMID 36106847 PMC9880954
  • Deciphering associations between gut microbiota and clinical factors using microbial modules. 2023 PMID 37084255 PMC10191612
  • Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
  • Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont. 2023 PMID 37967555 PMC10842462
  • Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation. 2023 PMID 38127978 PMC10756304
  • Enteral nutrition promotes the remission of colitis by gut bacteria-mediated histidine biosynthesis. 2024 PMID 38215690 PMC10827402
  • Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
  • Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. 2024 PMID 38942021 PMC11293350
  • A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
  • Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation. 2025 PMID 40658318 PMC12259524
  • Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway. 2025 PMID 41118772 PMC13059687
  • Gut Lactate Boosts Ruminococcus via Histone Lactylation to Mediate Time-Restricted Feeding Protection in Crohn's Disease. 2026 PMID 41945859 PMC13271634
Details
How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of child and adolescent by sonnet_x2 with confidence 0.70. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.title · “Gut Microbiome in Pediatric Crohn's Disease”
  • life stage study.title · “Pediatric Crohn's Disease”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN03469224health_conditionhealthy_controlR20.85paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Subject Health Status]healthy
SAMN03469222health_conditioncrohns_diseaseR40.50study.titlePediatric Crohn's Disease
SAMN03469224health_condition_detailhealthyR20.85paper.supp.DataSheet_1.zip/additional_datasheets/table_s4_sample_info_update.xlsx[sample_info!Subject Health Status]healthy
SAMN03469248interventiondrug_therapyR10.80biosample.attribute:Treatment.SpecificTreatment.Specific: antiTNF
SAMN03469248intervention_detailanti-TNF biologic therapyR10.80biosample.attribute:Treatment.SpecificTreatment.Specific: antiTNF
SAMN03469252medicationcorticosteroidR10.85biosample.attribute:steroidssteroids: Use
SAMN03469252medication_detailsteroids: UseR10.85biosample.attribute:steroidssteroids: Use
SAMN03469248subject_id5001R10.70sample.name_rule:alias5001-01
SAMN03469248timepoint_labelvisit 01R10.70sample.name_rule:alias5001-01
Sequencing

369 runs over 369 samples · mean 2.33 Gbp per run (median 2.08 Gbp, total 859.24 Gbp; 369 runs with a base count) · layout PAIRED 369 · platform ILLUMINA 369 · models Illumina HiSeq 2000 (369) · 0% of runs with a Sandpiper profile · first public 2015-08-07 – 2015-08-09

Authors (0)

No author record.

Downloads

SRP057027.csv.gz (9.8 KB) · parquet (83.5 KB) — all 369 samples, every field with route and confidence · SRP057027_determinations.csv.gz (16.4 KB) — 2,177 evidence rows

Samples (369 · every field this project has values for · hover a cell for its source)
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