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PRJEB47909 ERP132229

FMT triads in rCDI, IBD, and MDRB colonization patients

FMT datasets of patients with recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), and colonization from multi-drug resistant bacteria (MDRB)

115 stool samples from adults undergoing fecal microbiota transplantation (FMT), spanning donor/pre-FMT/post-FMT triads, across recurrent C. difficile infection, IBD, and multi-drug resistant bacteria colonization. machine-written summary

115 samples · 115 runs · IT · Adult · 2022 · 6.70 Gbp / sample

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Sources
✓Sequence archive 55○Abstract / description✓Full text 119✓Supplementary tables 33✓External resources 426–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive55 sample values (subject id)
○ Abstract / descriptionread; no usable statement
✓ Full text119 sample values (country, location locality) · PMC11869744, PMC13236588, PMC9499858
✓ Supplementary tables33 sample values (subject id)
✓ External resources426 sample values (antibiotic exposure, country, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Faecal microbiota transplantation design observational_with_procedure · population ibd_or_gi_disease · Fecal microbiota transplantation in rCDI, IBD, MDRB colonization patients

“n=115 samples corresponding to 23 FMT triads” — bioproject.description (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 country
Age
adult115
Condition
other_infection95
ibd_unspecified6
healthy_control1
Country
IT115
Body site
primary115
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 3 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 2 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 2 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 8 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 75 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 25 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 6.70 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalFMT donor → recipient

10 of 63 people sampled more than once (35 samples; median 4, up to 5 per person) · follow-up median 30 d (max 6 mo) · median interval between samples 15 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Pre-FMT (t0) and post-FMT follow-up samples at t7, t15, t30, t90, t180 days per recipient; donor sampled once” (time origin: transplant); stated follow-up 6 mo.

R13R13: day 0R13: day 15R2R2: day 0R2: day 8R2: day 23R2: day 173R5R5: day 0R5: day 7R5: day 300 d43 d3 mo4 mo6 mo

Each row is one person (3 shown of 10); dots are samples at days since that person's first sample.

23 FMT triads (rCDI, IBD, MDRB); 48 recipient samples linked to donors via paper Supplementary Table 2 (14 to a donor sample; 4 links where the donor is the recipient's father).

donor: SAMEA14367104, SAMEA14367106, SAMEA14367109, SAMEA14367110, SAMEA14367112, SAMEA14367115, SAMEA14367116, SAMEA14367119, SAMEA14367120, SAMEA14367123, SAMEA14367127, SAMEA14367136, SAMEA14367139, SAMEA14367140, SAMEA14367143, SAMEA14367154, SAMEA14367156, SAMEA14367163, SAMEA14367165, SAMEA143donor:D2 donor of SAMEA14367104donor:D2 donor of SAMEA14367106donor:D2 donor of SAMEA14367109donor:D2 donor of SAMEA14367110donor:D2 donor of SAMEA14367112donor:D2 donor of SAMEA14367115donor:D2 donor of SAMEA14367116donor:D2 donor of SAMEA14367119donor:D2 donor of SAMEA14367120donor:D2 donor of SAMEA14367123donor:D2 donor of SAMEA14367127donor:D2 donor of SAMEA14367136donor:D2 donor of SAMEA14367139donor:D2 donor of SAMEA14367140donor:D2 donor of SAMEA14367143donor:D2 donor of SAMEA14367154donor:D2 donor of SAMEA14367156donor:D2 donor of SAMEA14367163donor:D2 donor of SAMEA14367165donor:D2 donor of SAMEA14367166donor:D2 donor of SAMEA14367167donor:D2 donor of SAMEA14367168SAMEA14367104 — recipient · 1 sampleRSAMEA14367106 — recipient · 1 sampleRSAMEA14367109 — recipient · 1 sampleRSAMEA14367110 — recipient · 1 sampleRSAMEA14367112 — recipient · 1 sampleRSAMEA14367115 — recipient · 1 sampleRSAMEA14367116 — recipient · 1 sampleRSAMEA14367119 — recipient · 1 sampleRSAMEA14367120 — recipient · 1 sampleRSAMEA14367123 — recipient · 1 sampleRSAMEA14367127 — recipient · 1 sampleRSAMEA14367136 — recipient · 1 sampleRSAMEA14367139 — recipient · 1 sampleRSAMEA14367140 — recipient · 1 sampleRSAMEA14367143 — recipient · 1 sampleRSAMEA14367154 — recipient · 1 sampleRSAMEA14367156 — recipient · 1 sampleRSAMEA14367163 — recipient · 1 sampleRSAMEA14367165 — recipient · 1 sampleRSAMEA14367166 — recipient · 1 sampleRSAMEA14367167 — recipient · 1 sampleRSAMEA14367168 — recipient · 1 sampleRdonor:D2 — donor · not sequencedD
donor: SAMEA14367099, SAMEA14367100, SAMEA14367103, SAMEA14367157, SAMEA14367159, SAMEA14367160, SAMEA14367164, SAMEA14367169, SAMEA14367182SAMEA14367182 donor of SAMEA14367099SAMEA14367182 donor of SAMEA14367100SAMEA14367182 donor of SAMEA14367103SAMEA14367182 donor of SAMEA14367157SAMEA14367182 donor of SAMEA14367159SAMEA14367182 donor of SAMEA14367160SAMEA14367182 donor of SAMEA14367164SAMEA14367182 donor of SAMEA14367169SAMEA14367099 — recipient · 1 sampleR099SAMEA14367100 — recipient · 1 sampleR100SAMEA14367103 — recipient · 1 sampleR103SAMEA14367157 — recipient · 1 sampleR157SAMEA14367159 — recipient · 1 sampleR159SAMEA14367160 — recipient · 1 sampleR160SAMEA14367164 — recipient · 1 sampleR164SAMEA14367169 — recipient · 1 sampleR169SAMEA14367182 — donor · 1 sampleD182SAMEA14367…
donor: SAMEA14367090, SAMEA14367185, SAMEA14367186, SAMEA14367187, SAMEA14367192, SAMEA14367193SAMEA14367090 donor of SAMEA14367185SAMEA14367090 donor of SAMEA14367186SAMEA14367090 donor of SAMEA14367187SAMEA14367090 donor of SAMEA14367192SAMEA14367090 donor of SAMEA14367193SAMEA14367090 — donor · 1 sampleD090SAMEA14367185 — recipient · 1 sampleR185SAMEA14367186 — recipient · 1 sampleR186SAMEA14367187 — recipient · 1 sampleR187SAMEA14367192 — recipient · 1 sampleR192SAMEA14367193 — recipient · 1 sampleR193SAMEA14367…
donor: SAMEA14367091, SAMEA14367190, SAMEA14367191, SAMEA14367198, SAMEA14367199SAMEA14367091 donor of SAMEA14367190SAMEA14367091 donor of SAMEA14367191SAMEA14367091 donor of SAMEA14367198SAMEA14367091 donor of SAMEA14367199SAMEA14367091 — donor · 1 sampleD091SAMEA14367190 — recipient · 1 sampleR190SAMEA14367191 — recipient · 1 sampleR191SAMEA14367198 — recipient · 1 sampleR198SAMEA14367199 — recipient · 1 sampleR199SAMEA14367…
donor: SAMEA14367161, SAMEA14367177, SAMEA14367178, donor:D1donor:D1 donor of SAMEA14367161donor:D1 donor of SAMEA14367177donor:D1 donor of SAMEA14367178SAMEA14367161 — recipient · 1 sampleRSAMEA14367177 — recipient · 1 sampleRSAMEA14367178 — recipient · 1 sampleRdonor:D1 — donor · not sequencedD
donor / father: SAMEA14367086, SAMEA14367194, SAMEA14367195SAMEA14367086 donor of SAMEA14367194SAMEA14367086 father of SAMEA14367194SAMEA14367086 donor of SAMEA14367195SAMEA14367086 father of SAMEA14367195SAMEA14367086 — father · 1 sampleF086SAMEA14367194 — recipient · 1 sampleR194SAMEA14367195 — recipient · 1 sampleR195SAMEA14367…
donor / father: SAMEA14367088, SAMEA14367188, SAMEA14367189SAMEA14367088 donor of SAMEA14367188SAMEA14367088 father of SAMEA14367188SAMEA14367088 donor of SAMEA14367189SAMEA14367088 father of SAMEA14367189SAMEA14367088 — father · 1 sampleF088SAMEA14367188 — recipient · 1 sampleR188SAMEA14367189 — recipient · 1 sampleR189SAMEA14367…
donor: SAMEA14367089, SAMEA14367183, SAMEA14367184SAMEA14367089 donor of SAMEA14367183SAMEA14367089 donor of SAMEA14367184SAMEA14367089 — donor · 1 sampleD089SAMEA14367183 — recipient · 1 sampleR183SAMEA14367184 — recipient · 1 sampleR184SAMEA14367…

fatherdonorrecipient · 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: 8 linked groups from explicit relations. 63 people in the project overall.

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 11.2%Bacteroides 6.4%Blautia_A 5.0%Enterococcus_B 4.3%Streptococcus 4.0%Escherichia 3.7%Alistipes 3.5%Faecalibacterium 3.4%Akkermansia 3.1%Klebsiella 3.0%Veillonella 2.6%Phocaeicola 2.6%not assigned to a genus 3.5%other genera 43.7%

Genera, mean relative abundance over 102 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category115 100%
country115 100%1114
health_condition102 89%102
subject_id88 77%5533
detailed_location115 100%
location_locality115 100%115
antibiotic_exposure111 97%111
health_condition_detail102 89%102
Papers (4)
  • Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. 2022 PMID 36109637 PMC9499858 own_data
  • Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission. 2025 PMID 40022204 PMC11869744 own_data
  • Strain-level transmission inference across multi-kingdom metagenomic data using TRACS. 2026 PMID 42032281 PMC13236588 own_data
  • Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Details
Archive description

FMT datasets of patients with recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), and colonization from multi-drug resistant bacteria (MDRB). n=115 samples corresponding to 23 FMT triads.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.

  • host run.scientific_name · “human gut metagenome”
  • body site run.scientific_name · “human gut metagenome”
  • life stage study.description · “patients with recurrent Clostridioides difficile infection”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA14367086antibiotic_exposurenoR20.75external.cmd sourceantibiotics_current_use: No
SAMEA14367086countryITR20.75external.cmd sourcecountry: Italy
SAMEA14356573countryITR30.70paper.fulltext.methodsliving in Rome, Italy
SAMEA14367092health_conditionother_infectionR20.75external.cmd sourcedisease: Clostridium difficile Infection
SAMEA14367092health_condition_detailClostridium difficile InfectionR20.75external.cmd sourcedisease: Clostridium difficile Infection
SAMEA14356573location_localityRomeR30.70paper.fulltext.methodsliving in Rome, Italy
SAMEA14356573subject_idFMT_46R10.70sample.name_rule:titleFMT_46_t15
SAMEA14367099subject_idR2R20.80archive
Sequencing

115 runs over 115 samples · mean 7.51 Gbp per run (median 6.70 Gbp, total 864.07 Gbp; 115 runs with a base count) · layout PAIRED 115 · platform ILLUMINA 115 · models unspecified (115) · 89% of runs with a Sandpiper profile · first public 2022-05-11

Authors (46)

Ianiro G first · Punčochář M · Karcher N · Porcari S · Armanini F · Asnicar F · Beghini F · Blanco-Míguez A · Cumbo F · Manghi P · Pinto F · Masucci L · Quaranta G · De Giorgi S · Sciumè GD · Bibbò S · Del Chierico F · Putignani L · Sanguinetti M · Gasbarrini A · Valles-Colomer M · Cammarota G · Segata N last · Debray R first · Dickson CC · Webb SE · Archie EA · Tung J last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last · Tonkin-Hill G first · Shao Y · Zarebski AE · Mallawaarachchi S · Xie O · Mäklin T · Thorpe HA · Davies MR · Bentley SD · Lawley TD · Corander J last

Downloads

PRJEB47909.csv.gz (4.0 KB) · parquet (74.5 KB) — all 115 samples, every field with route and confidence · PRJEB47909_determinations.csv.gz (7.5 KB) — 633 evidence rows

Samples (115 · every field this project has values for · hover a cell for its source)
Loading the sample table…