Gut metagenomics in Crohn's disease and UC, Sweden
206 fecal metagenome samples from a Swedish case-control study comparing individuals with Crohn's disease or ulcerative colitis to age- and gender-matched controls, examining links between gut microbiota, inflammation, and bile acids. machine-written summary
206 samples · 206 runs · SE · Age unknown · 2025 · 13.84 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,648 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 618 sample values (antibiotic exposure, location locality, location site) · PMC12508173 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 206 | 100% | 206 | |||
| health_condition | 206 | 100% | 206 | |||
| subject_id | 206 | 100% | 206 | |||
| antibiotic_exposure | 206 | 100% | 206 | |||
| collection_date | 206 | 100% | 206 | |||
| detailed_location | 206 | 100% | ||||
| health_condition_detail | 206 | 100% | 206 | |||
| latitude | 206 | 100% | 206 | |||
| location_locality | 206 | 100% | 206 | |||
| location_region | 206 | 100% | 206 | |||
| location_site | 206 | 100% | 206 | |||
| longitude | 206 | 100% | 206 |
- Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis. 2025 PMID 41062543 PMC12508173 own_data
Archive description
Our study explores signatures for Crohn’s disease (CD) and Ulcerative Colitis (UC) reflecting the interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD (‘CD’ n=64 and ‘UC’ n= 55), were age- and gender-matched to controls without findings during colonoscopy. Taxonomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG 167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls. In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host study.description · “1,257 individuals scheduled for colonoscopy”
- body site study.description · “Taxonomic profiles of the fecal microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115285640 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | using antibiotics less than three months before colonoscopy were excluded |
| SAMEA115285640 | collection_date | 2016-11-22 | R1 | 0.90 | biosample.attribute:collection_date | 2016-11-22 |
| SAMEA115285640 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA115285640 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:DESCRIPTION | Ulcerative Remission |
| SAMEA115285640 | health_condition_detail | Ulcerative Remission | R1 | 0.85 | biosample.attribute:DESCRIPTION | Ulcerative Remission |
| SAMEA115285640 | latitude | 59.3922 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.392201 18.039314 |
| SAMEA115285640 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | a tertiary center in Stockholm |
| SAMEA115285640 | location_region | Stockholm | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.392201 18.039314 |
| SAMEA115285640 | location_site | Danderyd Hospital | R3 | 0.70 | paper.fulltext.methods | referred for colonoscopy at Danderyd Hospital |
| SAMEA115285640 | longitude | 18.0393 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.392201 18.039314 |
| SAMEA115285640 | subject_id | 10003 | R1 | 0.85 | biosample.attribute:alias | 10003 |
Sequencing
206 runs over 206 samples · mean 15.68 Gbp per run (median 13.84 Gbp, total 3,230.10 Gbp; 206 runs with a base count) · layout PAIRED 206 · platform DNBSEQ 206 · models DNBSEQ-T7 (206) · 0% of runs with a Sandpiper profile · first public 2025-05-16
Authors (12)
Prast-Nielsen S first · Granström AL · Kiasat A · Ahlström G · Edfeldt G · Rautiainen S · Boulund F · Andersson FO · Lindberg J · Schuppe-Koistinen I · Gustafsson UO · Engstrand L last
Downloads
PRJEB72371.csv.gz (7.4 KB) · parquet (80.5 KB) — all 206 samples, every field with route and confidence · PRJEB72371_determinations.csv.gz (17.1 KB) — 2,266 evidence rows