Donor and recipient gut metagenomes in FMT for CDI, Calgary
109 stool metagenome samples from FMT donors and recipients in Calgary, Canada, including individuals with gastrointestinal infection/diarrhoea or ulcerative colitis; case-control design studying fecal microbiota transplantation. machine-written summary
109 samples · 109 runs · CA · Age unknown · 2021 · 9.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,271 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, intervention detail, latitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10108530, PMC11081829, PMC11211831, PMC12180181, PMC13213781, PMC9621045 |
| ✓ Supplementary tables | 39 sample values (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 resolved
Faecal microbiota transplantation design observational_with_procedure · population gi_infection_or_diarrhoea · FMT for recurrent C. difficile infection from healthy donors
“ten FMT recipients (five recipients per donor)” — bioproject.description (study level; per-sample arms are in the intervention column below)
health condition: sample names and supplementary table disagree for 10 samples (e.g. healthy_control vs ibd_or_gi_disease) — withheld.
The sources disagree on 10 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 (10)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN17918343 | health condition | healthy_control (sample names) | ibd_or_gi_disease (supplementary table) | withheld: neither value published |
| SAMN17918344 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918345 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918349 | health condition | healthy_control (sample names) | ibd_or_gi_disease (supplementary table) | withheld: neither value published |
| SAMN17918350 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918366 | health condition | healthy_control (sample names) | ibd_or_gi_disease (supplementary table) | withheld: neither value published |
| SAMN17918367 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918370 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918372 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
| SAMN17918373 | health condition | healthy_control (sample names) | gi_infection_or_diarrhoea (supplementary table) | withheld: neither value published |
longitudinalFMT donor → recipient
12 of 12 people sampled more than once (109 samples; median 8, up to 24 per person) · follow-up median 11 mo (max 21 mo) · median interval between samples 22 d (time from collection dates). Schedule stated by the source: “Recipients: baseline pre-FMT sample, then 5-9 post-FMT samples over up to 336 days; Donors: 24 (A) and 15 (B) samples over 636/532 days” (time origin: transplant); stated follow-up 11 mo.
Each row is one person (12 shown); dots are samples at days since that person's first sample.
FMT: 2 donors (DA, DB) sampled longitudinally, each linked to 5 recipients (10 donor->recipient pairs).
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: 2 linked groups from explicit relations. 12 people in the project overall.
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 | 0 | 0% | ||||
| country | 109 | 100% | 109 | |||
| health_condition | 99 | 91% | 99 | |||
| subject_id | 109 | 100% | 109 | |||
| collection_date | 109 | 100% | 109 | |||
| detailed_location | 109 | 100% | ||||
| health_condition_detail | 109 | 100% | 109 | |||
| intervention | 109 | 100% | 109 | |||
| latitude | 109 | 100% | 109 | |||
| location_locality | 109 | 100% | 109 | |||
| location_region | 109 | 100% | 109 | |||
| longitude | 109 | 100% | 109 | |||
| timepoint_label | 109 | 100% | 70 | 39 | ||
| intervention_detail | 70 | 64% | 70 | |||
| antibiotic_exposure | 51 | 47% | 51 |
- Metabolic independence drives gut microbial colonization and resilience in health and disease. 2023 PMID 37069665 PMC10108530 own_data
- Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut 2021 own_data
- Functional profile of host microbiome indicates Clostridioides difficile infection. 2022 PMID 36289064 PMC9621045 unsure
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. 2024 PMID 38565143 PMC11081829 unsure
- Floria: fast and accurate strain haplotyping in metagenomes. 2024 PMID 38940183 PMC11211831 unsure
2 more
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181
- Cohesive modules of engraftment in fecal microbiota transplantation. 2026 PMID 42211136 PMC13213781
Archive description
Stool sample metagenomes from two healthy FMT donors and ten FMT recipients (five recipients per donor). All recipients had chronic, recurrent Clostridium difficile infection (CDI) and received vancomycin for a minimum of ten days prior to FMT. Recipients did not take any antibiotics on the day of transplant, or for the remaining duration of the sampling period.
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.title · “stool metagenomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17918377 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:sample_alias | DA_R01_CDI_P_02_POST |
| SAMN17918336 | collection_date | 2014-12-12 | R1 | 0.90 | biosample.attribute:collection_date | 2014-12-12 |
| SAMN17918336 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Calgary |
| SAMN17918336 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_alias | DA_D_01 |
| SAMN17918375 | health_condition | gi_infection_or_diarrhoea | R1 | 0.90 | biosample_attr | Clostridium difficile infection |
| SAMN17918336 | health_condition_detail | D | R1 | 0.70 | sample.name_rule:sample_alias | DA_D_01 |
| SAMN17918375 | health_condition_detail | Clostridium difficile infection | R1 | 0.90 | sample.attr.host_disease | Clostridium difficile infection |
| SAMN17918336 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:sample_alias | DA_D_01 |
| SAMN17918375 | intervention | fmt | R1 | 0.90 | biosample.attribute:FMT_method | FMT_method: pill |
| SAMN17918375 | intervention_detail | FMT administered via pill | R1 | 0.90 | biosample.attribute:FMT_method | FMT_method: pill |
| SAMN17918336 | latitude | 51.0447 | R1 | 0.90 | biosample.attribute:lat_lon | 51.0447 N 114.0719 W |
| SAMN17918336 | location_locality | Calgary | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Calgary |
| SAMN17918336 | location_region | Alberta | R1 | 0.60 | biosample.attribute:lat_lon | 51.0447 N 114.0719 W |
| SAMN17918336 | longitude | -114.0719 | R1 | 0.90 | biosample.attribute:lat_lon | 51.0447 N 114.0719 W |
| SAMN17918336 | subject_id | DA | R1 | 0.70 | sample.name_rule:sample_alias | DA_D_01 |
| SAMN17918375 | timepoint_label | pre-FMT | R1 | 0.70 | sample.name_rule:sample_alias | DA_R01_CDI_P_08_PRE |
| SAMN17918336 | timepoint_label | day 0 | R2 | 0.85 | paper.supp.13059_2023_2924_MOESM1_ESM.xlsx[a) Donor samples!DaysRelative to First Sampling Date] | DA_D_01: 0 |
Sequencing
109 runs over 109 samples · mean 10.50 Gbp per run (median 9.51 Gbp, total 1,143.99 Gbp; 109 runs with a base count) · layout PAIRED 109 · platform ILLUMINA 109 · models NextSeq 500 (109) · 92% of runs with a Sandpiper profile · first public 2021-03-05
Authors (38)
Watson AR first · Füssel J · Veseli I · DeLongchamp JZ · Silva M · Trigodet F · Lolans K · Shaiber A · Fogarty E · Runde JM · Quince C · Yu MK · Söylev A · Morrison HG · Lee STM · Kao D · Rubin DT · Jabri B · Louie T · Eren AM last · Shaw J first · Gounot JS · Chen H · Nagarajan N · Yu YW last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last · Rashidi A first · Minot SS · Lee SJ · Hill GR · Podlesny D last · Lee ST
Downloads
PRJNA701961.csv.gz (4.6 KB) · parquet (76.7 KB) — all 109 samples, every field with route and confidence · PRJNA701961_determinations.csv.gz (11.3 KB) — 1,310 evidence rows