Gut microbiota in RCDI patients treated by FMT
92 fecal samples from recurrent C. difficile infection patients undergoing fecal microbial transplantation, delivered by colonoscopy or capsules, in an intervention study of treatment route and microbiome changes. machine-written summary
92 samples · 92 runs · Age unknown · 2017 · 0.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 44 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 184 sample values (health condition, health condition detail) · PMC10143790, PMC10821315, PMC9163076 |
| ✓ Supplementary tables | 28 sample values (intervention, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Faecal microbiota transplantation design randomized_controlled_trial · population gi_infection_or_diarrhoea · FMT via capsules or colonoscopy for recurrent C. difficile infection
“FMT was delivered into CDI patients either by colonoscopy or by capsules” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
7 of 13 people sampled more than once (20 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “Stool collected pre-FMT and at weeks 1, 4, and 12 post-FMT”; stated follow-up 3 mo.
Each row is one person (2 shown of 7); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 70 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 | 0 | 0% | ||||
| health_condition | 92 | 100% | 92 | |||
| subject_id | 26 | 28% | 26 | |||
| health_condition_detail | 92 | 100% | 92 | |||
| timepoint_label | 26 | 28% | 18 | 8 | ||
| intervention | 20 | 22% | 20 |
- In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection. 2023 PMID 37110500 PMC10143790 own_data
- Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. 2022 PMID 35654877 PMC9163076 unsure
- Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. 2023 PMID 37910603 PMC10821315 unsure
Archive description
Fecal microbial transplantation (FMT) is an effective treatment against Clostridium difficile (CDI) infections, but it is not known whether the route of delivery of FMT affects efficacy of treatment. In this study, FMT was delivered into CDI patients either by colonoscopy or by capsules. The same percentage of patients (96.2%) were cured in each of the treatments.
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 metagenome”
- body site study.title · “Microbiota of RCDI patients”
- body site study.description · “Fecal microbial transplantation (FMT)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07634964 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.abstract | recurrent Clostridioides difficile infection (RCDI) |
| SAMN07634964 | health_condition_detail | recurrent Clostridioides difficile infection (RCDI) treated with FMT | R3 | 0.70 | paper.fulltext.abstract | recurrent Clostridioides difficile infection (RCDI) |
| SAMN07635030 | intervention | fmt | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip[!Type] | Colonoscopy |
| SAMN07635030 | subject_id | CAL016 | R1 | 0.70 | sample.name_rule:alias+library_name | CAL016-W1 |
| SAMN07635030 | timepoint_label | week 1 | R1 | 0.70 | sample.name_rule:alias | CAL016-W1 |
| SAMN07635032 | timepoint_label | BFMT | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip[!Time] | BFMT |
Sequencing
92 runs over 92 samples · mean 0.14 Gbp per run (median 0.14 Gbp, total 12.77 Gbp; 92 runs with a base count) · layout PAIRED 92 · platform ILLUMINA 92 · models Illumina MiSeq (92) · 77% of runs with a Sandpiper profile · first public 2017-11-09
Authors (50)
Stockdale SR first · Harrington RS · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O'Reagan O · Nolan JA · Sheehan D · Lavelle A · Draper LA · Shanahan F · Ross RP · Hill C last · Dahiya M first · Jovel J · Monaghan T · Wong K · Elhenawy W · Chui L · McAlister F · Kao D last · Woodworth MH first · Conrad RE · Haldopoulos M · Pouch SM · Babiker A · Mehta AK · Sitchenko KL · Wang CH · Strudwick A · Ingersoll JM · Philippe C · Lohsen S · Kocaman K · Lindner BG · Hatt JK · Jones RM · Miller C · Neish AS · Friedman-Moraco R · Karadkhele G · Liu KH · Jones DP · Mehta CC · Ziegler TR · Weiss DS · Larsen CP · Konstantinidis KT · Kraft CS last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, subject_id. Share metadata
Downloads
PRJNA406958.csv.gz (3.0 KB) · parquet (73.5 KB) — all 92 samples, every field with route and confidence · PRJNA406958_determinations.csv.gz (2.5 KB) — 256 evidence rows