FMT in Crohn's disease remission, France, longitudinal
115 samples from adult Crohn's disease patients in France, part of a longitudinal study of fecal microbiota transplantation assessing strain engraftment linked to maintenance of remission. machine-written summary
115 samples · 230 runs · FR · Adult · 2020 · 6.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 801 sample values (age, country, intervention, intervention detail, sex, subject id, timepoint) |
| ✓ Abstract / description | 230 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10989911, PMC12180181, PMC13213781, PMC7725862, PMC9610947 |
| ○ 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 resolved
Faecal microbiota transplantation design single_arm_before_after · population crohns_disease · FMT in CD patients in remission, pre/post sampling
“CD patients receiving FMT while in remission” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
18 of 18 people sampled more than once (111 samples; median 7, up to 8 per person).
Genera, mean relative abundance over 100 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 | 115 | 100% | ||||
| country | 115 | 100% | 115 | |||
| health_condition | 115 | 100% | 115 | |||
| subject_id | 111 | 97% | 111 | |||
| age_at_collection_days | 115 | 100% | 115 | |||
| health_condition_detail | 115 | 100% | 115 | |||
| intervention | 115 | 100% | 115 | |||
| intervention_detail | 115 | 100% | 115 | |||
| sex | 115 | 100% | 115 | |||
| timepoint_label | 115 | 100% | 115 |
- Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease. 2020 PMID 32860788 PMC7725862 own_data
- Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa. 2022 PMID 36296186 PMC9610947 unsure
- StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data. 2022 PMID 38868710 PMC10989911 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
- Cohesive modules of engraftment in fecal microbiota transplantation. 2026 PMID 42211136 PMC13213781 unsure
Archive description
Crohn's Disease (CD) is a chronic gastrointestinal disease resulting from the dysfunctional interplay between the immune system and commensal intestinal microbiota. Emerging evidence suggests that concurrent treatment of both suppression of the immune response and replacement of the microbiota through Fecal Microbiota Transplantation (FMT) is a promising approach for the treatment of CD. Here, we analyze metagenomic data from CD patients receiving FMT while in remission, and assess gut microbiome composition before and after FMT at the species and strain levels. These allowed us to identify the gain, loss, and strain replacement of specific species in the context of remission or relapse. We found that FMT had a long-term effect on patient microbial compositions, though this was primarily driven by the engraftment of donor species which remained at low abundance in the patient. Engraftment of some Actinobacteria, and engraftment or loss of Proteobacteria, were related to better disease outcomes in FMT patients, while transmission of Bacteroidetes was found to be deleterious. Our results suggest clades that may be beneficial to transmit/eliminate through FMT, and thus provide criteria that my help identify personalized FMT donors to more effectively maintain remission in CD patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “strain engraftment in fecal microbiota transplantation with”
- body site study.description · “is a chronic gastrointestinal disease resulting from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14680385 | age_at_collection_days | 12053.2 | R1 | 0.70 | sample.attr.age | 33 |
| SAMN14680385 | country | FR | R1 | 0.90 | sample.attr.geo_loc_name | France |
| SAMN14680385 | health_condition | crohns_disease | R4 | 0.50 | paper.abstract | CD patients in remission |
| SAMN14680385 | health_condition_detail | Crohn's disease patients in remission receiving FMT | R4 | 0.50 | paper.abstract | CD patients in remission |
| SAMN14680385 | intervention | fmt | R1 | 0.90 | biosample.attribute:FMT_SHAM | FMT_SHAM: FMT |
| SAMN14680385 | intervention_detail | FMT recipient arm | R1 | 0.90 | biosample.attribute:FMT_SHAM | FMT_SHAM: FMT |
| SAMN14680385 | sex | male | R1 | 0.90 | sample.attr.sexe | male |
| SAMN14680385 | subject_id | 1_1 | R1 | 0.70 | sample.name_rule:Timepoint | 1_1_W-2 |
| SAMN14680385 | timepoint_label | 1_1_W-2 | R1 | 0.85 | sample.attr.timepoint | 1_1_W-2 |
Sequencing
230 runs over 115 samples · mean 3.10 Gbp per run (median 2.76 Gbp, total 712.64 Gbp; 230 runs with a base count) · layout PAIRED 230 · platform ILLUMINA 230 · models Illumina NovaSeq 6000 (230) · 43% of runs with a Sandpiper profile · first public 2020-10-16 – 2021-05-29
Authors (33)
Kong L first · Lloyd-Price J · Vatanen T · Seksik P · Beaugerie L · Simon T · Vlamakis H · Sokol H · Xavier RJ last · Guzzo GL first · Mittinty MN · Llamas B · Andrews JM · Weyrich LS last · Hu H first · Tan Y · Li C · Chen J · Kou Y · Xu ZZ · Liu YY · Dai L last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Rashidi A first · Minot SS · Lee SJ · Hill GR · Podlesny D last
Downloads
PRJNA625520.csv.gz (3.8 KB) · parquet (74.9 KB) — all 115 samples, every field with route and confidence · PRJNA625520_determinations.csv.gz (7.3 KB) — 1,031 evidence rows