Gut Metagenomes in IBD Patients and Controls, Germany
79 fecal metagenome samples from Germany in a case-control study comparing IBD patients (Crohn's disease, ulcerative colitis) and healthy controls, examining microbial bile acid metabolism and its link to TGR5 receptor activity. machine-written summary
79 samples · 79 runs · DE · Adult · 2025 · 12.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 432 sample values (country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 79 sample values (location site) · PMC13388663 |
| ○ 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 |
Genera, mean relative abundance over 77 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 | 79 | 100% | ||||
| country | 79 | 100% | 79 | |||
| health_condition | 58 | 73% | 58 | |||
| subject_id | 0 | 0% | ||||
| detailed_location | 79 | 100% | ||||
| latitude | 79 | 100% | 79 | |||
| location_region | 79 | 100% | 79 | |||
| location_site | 79 | 100% | 79 | |||
| longitude | 79 | 100% | 79 | |||
| health_condition_detail | 58 | 73% | 58 |
- Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease. 2026 PMID 42481656 PMC13388663 own_data
Archive description
The gut microbiota composition is closely linked to the pathogenesis of inflammatory bowel disease (IBD) and therapy response. Bile acids (BAs) are crucial for modulating intestinal immune responses, and dysbiosis can alter the intestinal BA profile. This study investigates whether dysbiosis in IBD affects metabolic pathways for microbial conversion of BAs, host BA composition and BA-induced Takeda G protein-coupled receptor 5 (TGR5) bioactivity. Here, metagenomic sequencing was performed on fecal samples from 61 IBD patients (33 CD, 28 UC) and 21 healthy controls (HC). Microbial BA pathways were analyzed within the metabolic networks. BA profiles in stool and plasma were measured by mass spectrometry, and TGR5 bioactivity was assessed.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “fecal samples from 61 IBD patients”
- body site run.scientific_name · “feces metagenome”
- life stage study.description · “61 IBD patients (33 CD, 28 UC)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120449123 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA120449123 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:host_disease_status | DOID:8778 |
| SAMEA120449123 | health_condition_detail | DOID:8778 | R1 | 0.90 | sample.attr.host_disease_status | DOID:8778 |
| SAMEA120449123 | latitude | 50.9282 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.9281717 11.5879359 |
| SAMEA120449123 | location_region | Thuringia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.9281717 11.5879359 |
| SAMEA120449123 | location_site | Jena University Hospital, Department of Internal Medicine | R3 | 0.70 | paper.fulltext.methods | Jena University Hospital's Department of Internal Medicine |
| SAMEA120449123 | longitude | 11.5879 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.9281717 11.5879359 |
Sequencing
79 runs over 79 samples · mean 10.45 Gbp per run (median 12.10 Gbp, total 825.89 Gbp; 79 runs with a base count) · layout PAIRED 79 · platform ILLUMINA 79 · models Illumina NovaSeq 6000 (79) · 97% of runs with a Sandpiper profile · first public 2025-10-29
Authors (12)
Stallhofer J first · Leonhardt J · Semmler J · Neugebauer S · Kiehntopf M · Löhden W · Homeister L · Ungelenk M · Hübner CA · Steube A · Waschina S · Stallmach A last
Downloads
PRJEB101774.csv.gz (3.0 KB) · parquet (73.5 KB) — all 79 samples, every field with route and confidence · PRJEB101774_determinations.csv.gz (3.5 KB) — 511 evidence rows