Gut metagenomes after FMT or MET-2 for recurrent C. diff (Canada)
72 stool samples from Canadian adults with recurrent C. difficile infection, collected before and after treatment with fecal microbiota transplant or microbial consortium therapy (MET-2), in an interventional study. machine-written summary
72 samples · 72 runs · CA · Age unknown · 2023 · 4.22 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 720 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 72 sample values (antibiotic exposure) · PMC10506460 |
| ○ 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
20 people have samples in more than one arm.
Faecal microbiota transplantation Defined bacterial consortium / live biotherapeutic product design non_randomized_controlled · population gi_infection_or_diarrhoea · Microbial consortium (MET-2) vs FMT for recurrent C. difficile infection
“microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT” — abstract:37404011 (study level; per-sample arms are in the intervention column below)
longitudinal
20 of 20 people sampled more than once (72 samples; median 4, up to 4 per person) · follow-up median 4 mo (max 9 mo) · median interval between samples 31 d (time from collection months (month precision)). Schedule stated by the source: “MET-2: baseline, ~2 weeks, 1 month, 4 months post; FMT: baseline, 1, 3, 6 months post” (time origin: intervention_start); stated follow-up 6 mo.
Each row is one person (19 shown of 20); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 61 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 | 72 | 100% | ||||
| country | 72 | 100% | 72 | |||
| health_condition | 72 | 100% | 72 | |||
| subject_id | 72 | 100% | 72 | |||
| antibiotic_exposure | 72 | 100% | 72 | |||
| collection_date | 72 | 100% | 72 | |||
| detailed_location | 72 | 100% | ||||
| health_condition_detail | 72 | 100% | 72 | |||
| intervention | 72 | 100% | 72 | |||
| latitude | 72 | 100% | 72 | |||
| location_locality | 72 | 100% | 72 | |||
| location_region | 72 | 100% | 72 | |||
| longitude | 72 | 100% | 72 |
- A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection. 2023 PMID 37404011 PMC10506460 own_data
Archive description
The goal of the study was to measure Proteobacteria, obligate anaerobes, butyrate-producers, and antimicrobial resistant genes after therapy with a microbial consortia or FMT for recurrent Clostridioides difficile infection.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human feces metagenome”
- body site sample.attr.host_body_product · “stool (n=72/72)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA111499558 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods | both cohorts were on antibiotic therapies prior |
| SAMEA111499558 | collection_date | 2017-10 | R1 | 0.90 | biosample.attribute:collection_date | 2017-10 |
| SAMEA111499558 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA111499558 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:project_name | CDI-MET2_FMT |
| SAMEA111499558 | health_condition_detail | CDI-MET2_FMT | R1 | 0.85 | biosample.attribute:project_name | CDI-MET2_FMT |
| SAMEA111499558 | intervention | fmt | R1 | 0.85 | biosample.attribute:description | Stool sample taken 3 months post-FMT |
| SAMEA111499558 | latitude | 43.6500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.65 -79.37 |
| SAMEA111499558 | location_locality | Toronto | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Toronto |
| SAMEA111499558 | location_region | Ontario | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.65 -79.37 |
| SAMEA111499558 | longitude | -79.3700 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 43.65 -79.37 |
| SAMEA111499558 | subject_id | FMT01 | R1 | 0.70 | sample.name_rule:alias | FMT01090 |
Sequencing
72 runs over 72 samples · mean 4.23 Gbp per run (median 4.22 Gbp, total 304.79 Gbp; 72 runs with a base count) · layout PAIRED 72 · platform ILLUMINA 72 · models Illumina NovaSeq 6000 (72) · 85% of runs with a Sandpiper profile · first public 2023-01-30
Authors (11)
Rooney AM first · Cochrane K · Fedsin S · Yao S · Anwer S · Dehmiwal S · Hota S · Poutanen S · Allen-Vercoe E · Coburn B · MTOP Investigators last
Downloads
PRJEB56674.csv.gz (3.0 KB) · parquet (74.0 KB) — all 72 samples, every field with route and confidence · PRJEB56674_determinations.csv.gz (6.5 KB) — 792 evidence rows