FMT from Crohn's disease patients into germ-free mice, USA
6 samples from a case-control study (Tucson, USA) of fecal microbiota transplantation from healthy and Crohn's ileocolitis (CD_L3) donors into germ-free mice, assessing effects on mucosal homeostasis. machine-written summary
6 samples · 6 runs · US · Age unknown · 2023 · 11.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 42 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 12 sample values (antibiotic exposure, location site) · PMC10978031 |
| ○ 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 |
intervention — arms not resolved
Faecal microbiota transplantation design single_arm_before_after · population crohns_disease · FMT from Crohn's disease patients into germ-free mice
“transferred fecal microbiota from healthy patients and patients with defined Crohn's” — abstract:38532703 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 6 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 | 6 | 100% | 6 | |||
| health_condition | 4 | 67% | 4 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 6 | 100% | 6 | |||
| collection_date | 6 | 100% | 6 | |||
| detailed_location | 6 | 100% | ||||
| latitude | 6 | 100% | 6 | |||
| location_locality | 6 | 100% | 6 | |||
| location_site | 6 | 100% | 6 | |||
| longitude | 6 | 100% | 6 | |||
| health_condition_detail | 4 | 67% | 4 | |||
| sex | 4 | 67% | 4 |
- Transplant of microbiota from Crohn's disease patients to germ-free mice results in colitis. 2024 PMID 38532703 PMC10978031 own_data
Archive description
Inoculation of fecal microbiota
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.47. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Inoculation of fecal microbiota”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN35668369 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not treated with any antibiotics for at least 5 months |
| SAMN35668369 | collection_date | 2019-02-02 | R1 | 0.90 | biosample.attribute:collection_date | 2019-02-02 |
| SAMN35668369 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Tucson |
| SAMN35668369 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | Mctrl |
| SAMN35668369 | health_condition_detail | ctrl | R1 | 0.70 | sample.name_rule:alias | Mctrl |
| SAMN35668369 | latitude | 32.2540 | R1 | 0.90 | biosample.attribute:lat_lon | 32.2540 N 110.9742 W |
| SAMN35668369 | location_locality | Tucson | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Tucson |
| SAMN35668369 | location_site | Center for Comprehensive Treatment of Inflammatory Bowel Disease Regional Hospital No. 2 | R3 | 0.70 | paper.fulltext.methods | Center for Comprehensive Treatment of Inflammatory Bowel Disease Regional Hospital No. 2 |
| SAMN35668369 | longitude | -110.9742 | R1 | 0.90 | biosample.attribute:lat_lon | 32.2540 N 110.9742 W |
| SAMN35668369 | sex | male | R1 | 0.70 | sample.name_rule:alias | Mctrl |
Sequencing
6 runs over 6 samples · mean 15.86 Gbp per run (median 11.04 Gbp, total 95.17 Gbp; 6 runs with a base count) · layout PAIRED 6 · platform ILLUMINA 6 · models NextSeq 550 (6) · 100% of runs with a Sandpiper profile · first public 2023-06-21 – 2023-06-25
Authors (12)
Sheikh IA first · Bianchi-Smak J · Laubitz D · Schiro G · Midura-Kiela MT · Besselsen DG · Vedantam G · Jarmakiewicz S · Filip R · Ghishan FK · Gao N · Kiela PR last
Downloads
PRJNA981221.csv.gz (1.2 KB) · parquet (71.1 KB) — all 6 samples, every field with route and confidence · PRJNA981221_determinations.csv.gz (1.2 KB) — 54 evidence rows