FMT in IBD patients: longitudinal stool metagenomes, Russia
56 stool samples from CD and UC patients in Odintsovo, Russia, studying fecal microbiota transplantation combined with anti-inflammatory therapy, using a longitudinal shotgun metagenomic design. machine-written summary
56 samples · 56 runs · RU · Age unknown · 2021 · 1.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 498 sample values (country, health condition, health condition detail, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 ibd_unspecified · FMT combined with anti-inflammatory therapy in CD/UC patients
“FMT application combined with the anti-inflammatory therapy in CD” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient — not resolved
16 of 20 people sampled more than once (52 samples; median 3, up to 5 per person).
FMT donors (DONOR2, DONOR3, DONOR7) and 17 CD/UC patient ids sequenced over T1–T5; donor–recipient pairing not stated (no accessible paper).
Genera, mean relative abundance over 38 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 | 56 | 100% | 56 | |||
| health_condition | 53 | 95% | 53 | |||
| subject_id | 56 | 100% | 56 | |||
| detailed_location | 56 | 100% | ||||
| latitude | 56 | 100% | 56 | |||
| location_locality | 56 | 100% | 56 | |||
| location_region | 56 | 100% | 56 | |||
| longitude | 56 | 100% | 56 | |||
| timepoint_label | 56 | 100% | 56 | |||
| health_condition_detail | 53 | 95% | 53 |
- Character of Microbial Engraftment Following the Fecal Microbiota Transplantation in Patients with Inflammatory Bowel Diseases 2021 own_data
Archive description
Here we present a pilot longitudinal data for the study of FMT application combined with the anti-inflammatory therapy in CD (n = 8) and UC (n = 6) patients. Data was obtained using the shotgun sequencing of patients stool samples (n = 56).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “patients stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21440173 | country | RU | R1 | 0.90 | sample.attr.geo_loc_name | Russia: Odintsovo |
| SAMN21440173 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:library_names | CD1_T1 |
| SAMN21440173 | health_condition_detail | CD1_T1 | R1 | 0.70 | sample.name_rule:library_names | CD1_T1 |
| SAMN21440173 | latitude | 55.6800 | R1 | 0.90 | biosample.attribute:lat_lon | 55.68 N 37.27 E |
| SAMN21440173 | location_locality | Odintsovo | R1 | 0.85 | biosample.attribute:geo_loc_name | Russia: Odintsovo |
| SAMN21440173 | location_region | Moskovskaya | R1 | 0.60 | biosample.attribute:lat_lon | 55.68 N 37.27 E |
| SAMN21440173 | longitude | 37.2700 | R1 | 0.90 | biosample.attribute:lat_lon | 55.68 N 37.27 E |
| SAMN21440173 | subject_id | CD1 | R1 | 0.70 | sample.name_rule:library_names | CD1_T1 |
| SAMN21440173 | timepoint_label | T1 | R1 | 0.70 | sample.name_rule:library_names | CD1_T1 |
Sequencing
56 runs over 56 samples · mean 2.17 Gbp per run (median 1.39 Gbp, total 121.42 Gbp; 56 runs with a base count) · layout PAIRED 56 · platform ILLUMINA 56 · models Illumina HiSeq 2500 (56) · 68% of runs with a Sandpiper profile · first public 2021-09-17
Authors (17)
Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA763503.csv.gz (2.5 KB) · parquet (72.1 KB) — all 56 samples, every field with route and confidence · PRJNA763503_determinations.csv.gz (4.4 KB) — 498 evidence rows