Fecal Transplant for UC & C. difficile Infection, Australia
26 samples from Australia, part of an FMT intervention study of patients with recurrent C. difficile infection or ulcerative colitis. machine-written summary
26 samples · 52 runs · AU · Age unknown · 2022 · 3.43 Gbp / sample · cohort Drivers and determinants of strain dynamics follow
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 184 sample values (collection date, country, health condition, health condition detail, intervention, latitude, 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 resolved
Faecal microbiota transplantation design single_arm_before_after · population ulcerative_colitis · Fecal microbiota transplantation for recurrent C. difficile infection or ulcerative colitis
“Fecal Microbiota Transplantation in patients suffering from recurrent” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
6 of 6 people sampled more than once (26 samples; median 5, up to 5 per person) · follow-up median 30 d (max 8 mo) · median interval between samples 7 d (time from collection dates).
Each row is one person (6 shown); dots are samples at days since that person's first sample.
FMT for rCDI/UC: 5 recipients plus one donor (DON) sampled; recipient-specific donor links not stated.
Genera, mean relative abundance over 26 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 | 26 | 100% | 26 | |||
| health_condition | 2 | 8% | 2 | |||
| subject_id | 26 | 100% | 26 | |||
| collection_date | 26 | 100% | 26 | |||
| latitude | 26 | 100% | 26 | |||
| longitude | 26 | 100% | 26 | |||
| timepoint_label | 26 | 100% | 26 | |||
| intervention | 24 | 92% | 24 | |||
| health_condition_detail | 2 | 8% | 2 |
- Drivers and determinants of strain dynamics following fecal microbiota transplantation. 2022 PMID 36109636 PMC9499871 unsure
Archive description
Longitudinal metagenomic sequencing data for a proof-of-principle study of Fecal Microbiota Transplantation in patients suffering from recurrent Clostridiodes difficile infection or ulcerative colitis.
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.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site study.title · “Fecal Microbiota Transplantation”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA9457803 | collection_date | 2015-02-28 | R1 | 0.90 | biosample.attribute:collection_date | 2015-02-28 |
| SAMEA9457803 | country | AU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Australia |
| SAMEA9457806 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | alias: FMT_AU_DON-11-0-0 |
| SAMEA9457806 | health_condition_detail | FMT_AU_DON-11-0-0 | R1 | 0.70 | sample.name_rule:alias | alias: FMT_AU_DON-11-0-0 |
| SAMEA9457803 | intervention | fmt | R1 | 0.70 | sample.name_rule:alias | alias: FMT_AU_3-11-17-0 |
| SAMEA9457803 | latitude | -34.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | -34 151 |
| SAMEA9457803 | longitude | 151.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | -34 151 |
| SAMEA9457803 | subject_id | 3 | R1 | 0.70 | sample.name_rule:alias | alias: FMT_AU_3-11-17-0 |
| SAMEA9457803 | timepoint_label | 17 | R1 | 0.70 | sample.name_rule:alias | alias: FMT_AU_3-11-17-0 |
Sequencing
52 runs over 26 samples · mean 1.72 Gbp per run (median 1.53 Gbp, total 89.51 Gbp; 52 runs with a base count) · layout PAIRED 26, SINGLE 26 · platform ILLUMINA 52 · models Illumina HiSeq 4000 (52) · 96% of runs with a Sandpiper profile · first public 2022-04-28
Authors (22)
Schmidt TSB first · Li SS · Maistrenko OM · Akanni W · Coelho LP · Dolai S · Fullam A · Glazek AM · Hercog R · Herrema H · Jung F · Kandels S · Orakov A · Thielemann R · von Stetten M · Van Rossum T · Benes V · Borody TJ · de Vos WM · Ponsioen CY · Nieuwdorp M · Bork P last
Downloads
PRJEB46780.csv.gz (1.7 KB) · parquet (71.1 KB) — all 26 samples, every field with route and confidence · PRJEB46780_determinations.csv.gz (2.1 KB) — 184 evidence rows