Pediatric IBD vs healthy siblings gut metagenomes, Germany
24 fecal metagenome samples from German children: 12 healthy controls, 7 with Crohn's disease, and 5 with ulcerative colitis, in a case-control (sibling) design. machine-written summary
24 samples · 48 runs · DE · Child · 2024 · 5.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 168 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 24 sample values (subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
siblings — not resolved
6 CD + 6 UC children with 12 healthy siblings; pairing per sample not committed (replicates disagreed).
Genera, mean relative abundance over 22 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 | 24 | 100% | ||||
| country | 24 | 100% | 24 | |||
| health_condition | 24 | 100% | 24 | |||
| subject_id | 24 | 100% | 24 | |||
| collection_date | 24 | 100% | 24 | |||
| detailed_location | 24 | 100% | ||||
| health_condition_detail | 24 | 100% | 24 | |||
| latitude | 24 | 100% | 24 | |||
| location_region | 24 | 100% | 24 | |||
| longitude | 24 | 100% | 24 |
- Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis. 2017 PMID 28039159 own_data
Archive description
Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn’s disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. Publication: https://doi.org/10.1152/ajpgi.00293.2016
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 study.title · “Gut microbiota differs between”
- body site study.description · “effects. Manipulating the gut microbiota via fecal”
- life stage study.title · “microbiota differs between children with Inflammatory Bowel”
- life stage study.description · “Current treatment for pediatric inflammatory bowel disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115753918 | collection_date | 2013/2014 | R1 | 0.90 | biosample.attribute:collection_date | 2013/2014 |
| SAMEA115753918 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA115753918 | health_condition | ulcerative_colitis | R1 | 0.70 | sample.name_rule:title | IBD_58_UC |
| SAMEA115753918 | health_condition_detail | UC | R1 | 0.70 | sample.name_rule:title | IBD_58_UC |
| SAMEA115753918 | latitude | 50.2400 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.24 9.29 |
| SAMEA115753918 | location_region | Hesse | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.24 9.29 |
| SAMEA115753918 | longitude | 9.2900 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.24 9.29 |
| SAMEA115753918 | subject_id | SAMEA115753918 | R4 | 0.60 | design.one_sample_per_subject:abstract | six children with Crohn's disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings |
Sequencing
48 runs over 24 samples · mean 2.67 Gbp per run (median 0.53 Gbp, total 128.28 Gbp; 48 runs with a base count) · layout PAIRED 24, SINGLE 24 · platform ILLUMINA 48 · models Illumina HiSeq 2000 (48) · 46% of runs with a Sandpiper profile · first public 2024-06-18
Authors (8)
Knoll RL first · Forslund K · Kultima JR · Meyer CU · Kullmer U · Sunagawa S · Bork P · Gehring S last
Downloads
PRJEB76677.csv.gz (1.6 KB) · parquet (70.8 KB) — all 24 samples, every field with route and confidence · PRJEB76677_determinations.csv.gz (2.1 KB) — 192 evidence rows