RBX2660 FMT for recurrent C. difficile, USA adults
193 longitudinal fecal metagenome samples from adults with recurrent C. difficile infection across 7 US study sites (Mayo Clinic and others), treated with the fecal microbiota transplant product RBX2660 in an open-label intervention trial. machine-written summary
193 samples · 193 runs · US · Adult · 2020 · 0.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,044 sample values (collection date, country, health condition, health condition detail, location site, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 76 sample values (health condition, health condition detail) · PMC7888090 |
| ○ 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 not resolved
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · RBX2660 microbiota-based FMT, 1 or 2 doses, recurrent CDI
“effects of RBX2660, a microbiota-based investigational therapeutic” — abstract:33593430 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient — not resolved
28 of 29 people sampled more than once (154 samples; median 5, up to 18 per person). Schedule stated by the source: “day 0 (pre-treatment, post-vancomycin), then days 7, 30, 60, 90, 180 post-RBX2660 treatment”; stated follow-up 6 mo.
RBX2660 FMT: 29 recurrent-CDI patients and 4 donors (21 donor samples sequenced); per-recipient donor not stated.
Genera, mean relative abundance over 159 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 | 193 | 100% | ||||
| country | 193 | 100% | 193 | |||
| health_condition | 193 | 100% | 155 | 38 | ||
| subject_id | 155 | 80% | 155 | |||
| collection_date | 193 | 100% | 193 | |||
| detailed_location | 193 | 100% | ||||
| health_condition_detail | 193 | 100% | 155 | 38 | ||
| location_site | 193 | 100% | 193 |
- Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. 2021 PMID 33593430 PMC7888090 own_data
Archive description
This sequence repository contains longitudinal fecal metagenomes from 29 human adults with recurrent C. difficile infection after treatment with a microbiome-based transplant product labeled as RBX2660, which was created from the stool of healthy screened donors. The metagenomes were sequenced by 16S rRNA amplification and by whole genome shotgun sequencing. Additionally, 38 antimicrobial drug resistant isolates were selectively cultured from these metagenomes, and their whole genome shotgun sequences along with 16S sequences are provided.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “fecal metagenomes from 29 human adults”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “fecal metagenomes from 29 human adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16678983 | collection_date | 2013-08-15 | R1 | 0.90 | biosample.attribute:collection_date | 2013-08-15 |
| SAMN16678983 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Mayo Clinic and 6 other study sites |
| SAMN16678983 | health_condition | healthy_control | R1 | 0.70 | biosample.name_rule:TITLE | human gut metagenome: healthy donor |
| SAMN16679139 | health_condition | gi_infection_or_diarrhoea | R3 | 0.70 | paper.fulltext.abstract | patients suffering from recurrent CDI |
| SAMN16678983 | health_condition_detail | healthy donor | R1 | 0.70 | biosample.name_rule:TITLE | human gut metagenome: healthy donor |
| SAMN16679139 | health_condition_detail | recurrent Clostridioides difficile infection (CDI) | R3 | 0.70 | paper.fulltext.abstract | patients suffering from recurrent CDI |
| SAMN16678983 | location_site | Mayo Clinic | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Mayo Clinic and 6 other study sites |
| SAMN16678983 | subject_id | 1 | R1 | 0.70 | biosample.name_rule:alias | 1.1.DP_wgs |
Sequencing
193 runs over 193 samples · mean 0.79 Gbp per run (median 0.59 Gbp, total 153.35 Gbp; 193 runs with a base count) · layout PAIRED 193 · platform ILLUMINA 193 · models Illumina HiSeq 2000 (155), NextSeq 500 (38) · 82% of runs with a Sandpiper profile · first public 2020-11-15
Authors (16)
Langdon A first · Schwartz DJ · Bulow C · Sun X · Hink T · Reske KA · Jones C · Burnham CD · Dubberke ER · Dantas G · CDC Prevention Epicenter Program last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads
PRJNA674880.csv.gz (5.1 KB) · parquet (76.5 KB) — all 193 samples, every field with route and confidence · PRJNA674880_determinations.csv.gz (8.4 KB) — 1,120 evidence rows