Gut microbiome in IBD patients before/after treatment, Norway
90 faecal samples from IBD patients in Norway, studied longitudinally before and after drug therapy. machine-written summary
90 samples · 90 runs · NO · Age unknown · 2025 · 4.54 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 660 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 90 sample values (antibiotic exposure) · PMC13255511 |
| ✓ Supplementary tables | 150 sample values (health condition, timepoint) |
| – 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 |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population ibd_unspecified · IBD treatment, faecal samples before and after
“IBD patients, before and after treatment” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
45 of 45 people sampled more than once (90 samples; median 2, up to 2 per person). Schedule stated by the source: “Stool samples collected at inclusion (before IBD medication) and at one-year follow-up after treatment” (time origin: enrolment); stated follow-up 12 mo.
Genera, mean relative abundance over 87 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 | 0 | 0% | ||||
| country | 90 | 100% | 90 | |||
| health_condition | 90 | 100% | 30 | 60 | ||
| subject_id | 90 | 100% | 90 | |||
| antibiotic_exposure | 90 | 100% | 90 | |||
| collection_date | 90 | 100% | 90 | |||
| detailed_location | 90 | 100% | ||||
| health_condition_detail | 90 | 100% | 90 | |||
| latitude | 90 | 100% | 90 | |||
| location_region | 90 | 100% | 90 | |||
| longitude | 90 | 100% | 90 | |||
| timepoint_label | 90 | 100% | 90 |
- Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients. 2026 PMID 42045813 PMC13255511 own_data
Archive description
See Lindstrøm et al, 2025, BMC Microbiology
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “faecal contents from IBD patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117984980 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | no use of antimicrobial therapy the last 12 weeks prior to inclusion or during the follow-up period |
| SAMEA117984980 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMEA117984980 | country | NO | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Norway |
| SAMEA117984982 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:host_disease_status | DOID:8778 |
| SAMEA117984980 | health_condition | ulcerative_colitis | R2 | 0.85 | paper.supp.2025-04-28_ENA_METADATA.tsv[DIAGNOSIS] | UC |
| SAMEA117984980 | health_condition_detail | DOID:8577 | R1 | 0.90 | sample.attr.host_disease_status | DOID:8577 |
| SAMEA117984980 | latitude | 59.9318 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.9318 10.9937 |
| SAMEA117984980 | location_region | Akershus | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.9318 10.9937 |
| SAMEA117984980 | longitude | 10.9937 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 59.9318 10.9937 |
| SAMEA117984980 | subject_id | 23 | R1 | 0.85 | sample.attr.host_subject_id | 23 |
| SAMEA117984980 | timepoint_label | 0 | R2 | 0.85 | paper.supp.2025-04-28_ENA_METADATA.tsv[SAMPLETIME] | 0 |
Sequencing
90 runs over 90 samples · mean 4.70 Gbp per run (median 4.54 Gbp, total 422.68 Gbp; 90 runs with a base count) · layout PAIRED 90 · platform ILLUMINA 90 · models Illumina NovaSeq 6000 (90) · 97% of runs with a Sandpiper profile · first public 2025-04-30
Authors (0)
No author record.
Downloads
PRJEB88212.csv.gz (3.2 KB) · parquet (73.9 KB) — all 90 samples, every field with route and confidence · PRJEB88212_determinations.csv.gz (6.4 KB) — 900 evidence rows