FMT for ulcerative colitis in Austria, intervention study
160 fecal samples from Austria, from patients with IBD undergoing fecal microbiota transplantation; the intervention design included antibiotic pretreatment and bowel preparation alongside FMT. machine-written summary
160 samples · 160 runs · AT · Age unknown · 2021 · 6.26 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,562 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9418803 |
| ✓ Supplementary tables | 23 sample values (antibiotic exposure) |
| – 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 |
Antibiotic given as the study intervention (incl. eradication therapy Bowel cleansing / colonoscopy preparation Faecal microbiota transplantation · population ulcerative_colitis · FMT for ulcerative colitis; donor stool transplant
“Fecal microbiota transplantation for treatment of ulcerative colitis” — study.title (study level; per-sample arms are in the intervention column below)
health condition: sequence archive and supplementary table disagree for 38 samples (e.g. healthy_control vs ibd_unspecified) — withheld.
The sources disagree on 38 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (38)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA9561602 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561603 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561610 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561611 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561619 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561620 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561621 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561627 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561628 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561629 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561635 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561643 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561644 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561648 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561655 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561656 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561657 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561664 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561665 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561666 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561737 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561738 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561739 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561740 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561741 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561742 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561743 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561744 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561745 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561746 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561747 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561748 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561749 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561750 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561751 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561752 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561753 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
| SAMEA9561754 | health condition | healthy_control (sequence archive) | ibd_unspecified (supplementary table) | withheld: neither value published |
longitudinalFMT donor → recipient
39 of 43 people sampled more than once (156 samples; median 5, up to 7 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 13 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Patients sampled before FMT and repeatedly after FMT; archive tp values = -10,1,3,14,28,56,90 days relative to FMT” (time origin: transplant).
Each row is one person (36 shown of 39); dots are samples at days since that person's first sample.
UC FMT trial with sequenced donors; 5 donor->recipient links assignable from Table S1A, rest pooled donors.
donorrecipient · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 4 linked groups from explicit relations. 43 people in the project overall.
Genera, mean relative abundance over 146 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 | 160 | 100% | 160 | |||
| health_condition | 122 | 76% | 122 | |||
| subject_id | 160 | 100% | 160 | |||
| collection_date | 160 | 100% | 160 | |||
| detailed_location | 160 | 100% | ||||
| health_condition_detail | 160 | 100% | 160 | |||
| intervention | 160 | 100% | 160 | |||
| latitude | 160 | 100% | 160 | |||
| location_region | 160 | 100% | 160 | |||
| longitude | 160 | 100% | 160 | |||
| timepoint_label | 160 | 100% | 160 | |||
| antibiotic_exposure | 23 | 14% | 23 |
- Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics. 2022 PMID 35931074 PMC9418803 own_data
Archive description
A current hypothesis of UC pathogenesis suggests that changes in the composition of the colonic microbiota, called dysbiosis, cause activation of the mucosal immune system resulting in chronic inflammation. Fecal microbiota transplantation (FMT) is a therapeutic procedure aimed at restoring an altered intestinal microbiota by administrating fecal microorganisms from a healthy donor into the intestinal tract of a patient and thereby correcting dysbiosis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA9561596 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.mmc2.xlsx[S1A. FMT Sample Metadata!Case_ABx] | vancomycin, paramomycin, nystatin |
| SAMEA9561595 | collection_date | 2012-06/2014-07 | R1 | 0.90 | biosample.attribute:collection_date | 2012-06/2014-07 |
| SAMEA9561595 | country | AT | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Austria |
| SAMEA9561595 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:description | P |
| SAMEA9561595 | health_condition_detail | P | R1 | 0.85 | biosample.attribute:description | P |
| SAMEA9561595 | intervention | fmt | R1 | 0.85 | biosample.attribute:description | P |
| SAMEA9561595 | latitude | 47.0707 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA9561595 | location_region | Styria | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA9561595 | longitude | 15.4395 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 47.0707 15.4395 |
| SAMEA9561595 | subject_id | PE | R1 | 0.85 | sample.attr.patientid | PE |
| SAMEA9561595 | timepoint_label | -10 | R1 | 0.85 | sample.attr.tp | -10 |
Sequencing
160 runs over 160 samples · mean 6.55 Gbp per run (median 6.26 Gbp, total 1,047.69 Gbp; 160 runs with a base count) · layout PAIRED 160 · platform ILLUMINA 160 · models unspecified (160) · 91% of runs with a Sandpiper profile · first public 2021-09-05
Authors (8)
Podlesny D first · Durdevic M · Paramsothy S · Kaakoush NO · Högenauer C · Gorkiewicz G · Walter J · Fricke WF last
Downloads
PRJEB47061.csv.gz (5.3 KB) · parquet (76.6 KB) — all 160 samples, every field with route and confidence · PRJEB47061_determinations.csv.gz (9.5 KB) — 1,585 evidence rows