Fecal microbiome of FMT donors and RCDI patients, Baltimore
87 fecal samples from adults in Baltimore, MD, comparing healthy FMT donors and recurrent C. difficile infection patients before and after fecal microbiota transplant, in an intervention study design. machine-written summary
87 samples · 87 runs · US · Adult · 2021 · 8.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 811 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 1 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11795084, PMC12180181, PMC12247820, PMC13213781, PMC8274925 |
| ✓ Supplementary tables | 37 sample values (health condition, 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 not resolved
Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · FMT from healthy donors to RCDI patients
“donors and RCDI patients before and after FMT” — study.title (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient
25 of 42 people sampled more than once (69 samples; median 2, up to 5 per person) · follow-up median 3 mo (max 2.1 y) · median interval between samples 42 d (time from collection dates). Schedule stated by the source: “Stool before FMT; post-FMT follow-up visits 1 week to 24 months after FMT (median 4 months, IQR 1-5)” (time origin: transplant); stated follow-up 2.0 y.
Each row is one person (25 shown); dots are samples at days since that person's first sample.
22 RCDI recipients each linked to their sequenced FMT donor (21 donor letters; Donor T/U served 2 patients).
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: 21 linked groups from explicit relations. 42 people in the project overall.
Genera, mean relative abundance over 76 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 | 87 | 100% | ||||
| country | 87 | 100% | 87 | |||
| health_condition | 87 | 100% | 86 | 1 | ||
| subject_id | 86 | 99% | 86 | |||
| collection_date | 87 | 100% | 87 | |||
| detailed_location | 87 | 100% | ||||
| health_condition_detail | 87 | 100% | 86 | 1 | ||
| latitude | 87 | 100% | 87 | |||
| location_locality | 87 | 100% | 87 | |||
| location_region | 87 | 100% | 87 | |||
| longitude | 87 | 100% | 87 | |||
| timepoint_label | 67 | 77% | 31 | 36 |
- Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects. 2021 PMID 34252073 PMC8274925 own_data
- Detection of Human Y Chromosome and the SRY Gene in Fecal Samples of Female Patients Following Fecal Microbiota Transplantation. 2025 PMID 39911724 PMC11795084 own_data
- Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. 2025 PMID 39316685 PMC12247820 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
- Cohesive modules of engraftment in fecal microbiota transplantation. 2026 PMID 42211136 PMC13213781 unsure
Archive description
The goal of this study is to characterize the fecal microbiome of healthy donors and recurrent C. difficile infection patients before and after receiving fecal microbiota transplant therapy. A central aim is to identify organisms at the strain level for better understanding of engraftment and for design of synthetic microbiota therapies that may one day replace FMT.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Fecal microbiota of donors”
- body site study.description · “to characterize the fecal microbiome of healthy”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18106008 | collection_date | 2012-01-17 | R1 | 0.90 | biosample.attribute:collection_date | 2012-01-17 |
| SAMN18106008 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Baltimore, MD |
| SAMN18106008 | health_condition | gi_infection_or_diarrhoea | R1 | 0.70 | sample.name_rule:library_names | PreFMT.A |
| SAMN18106078 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:title | Donor R |
| SAMN18106087 | health_condition | healthy_control | R2 | 0.75 | paper.supp.40168_2025_2046_MOESM8_ESM.xlsx[S2!Condition] | healthy_donor |
| SAMN18106008 | health_condition_detail | PreFMT.A | R1 | 0.70 | sample.name_rule:library_names | PreFMT.A |
| SAMN18106078 | health_condition_detail | Donor R | R1 | 0.70 | sample.name_rule:title | Donor R |
| SAMN18106087 | health_condition_detail | mixed_case_control: RCDI patients vs healthy donors | R4 | 0.50 | study.description | healthy donors and recurrent C. difficile infection patients |
| SAMN18106008 | latitude | 39.2900 | R1 | 0.90 | biosample.attribute:lat_lon | 39.29 N 76.61 W |
| SAMN18106008 | location_locality | Baltimore | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Baltimore, MD |
| SAMN18106008 | location_region | Maryland | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Baltimore, MD |
| SAMN18106008 | longitude | -76.6100 | R1 | 0.90 | biosample.attribute:lat_lon | 39.29 N 76.61 W |
| SAMN18106008 | subject_id | Patient_A | R1 | 0.70 | sample.name_rule:library_names | PreFMT.A |
| SAMN18106078 | subject_id | Donor_R | R1 | 0.70 | sample.name_rule:title | Donor R |
| SAMN18106008 | timepoint_label | pre-FMT | R1 | 0.70 | sample.name_rule:library_names | PreFMT.A |
| SAMN18106009 | timepoint_label | 84 | R2 | 0.75 | paper.supp.40168_2025_2046_MOESM8_ESM.xlsx[S2!FMT_time_point] | 84 |
Sequencing
87 runs over 87 samples · mean 8.58 Gbp per run (median 8.13 Gbp, total 746.62 Gbp; 87 runs with a base count) · layout PAIRED 87 · platform ILLUMINA 87 · models Illumina NovaSeq 6000 (87) · 87% of runs with a Sandpiper profile · first public 2021-05-30
Authors (48)
Verma S first · Dutta SK · Firnberg E · Phillips L · Vinayek R · Nair PP last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Ke S first · Villafuerte Gálvez JA · Sun Z · Cao Y · Pollock NR · Chen X · Kelly CP · Liu YY last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last · Rashidi A first · Minot SS · Lee SJ · Hill GR · Podlesny D last
Downloads
PRJNA705895.csv.gz (4.3 KB) · parquet (75.9 KB) — all 87 samples, every field with route and confidence · PRJNA705895_determinations.csv.gz (8.9 KB) — 849 evidence rows