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PRJNA737472 SRP324954

FMT for ulcerative colitis, antibiotic pretreatment

Microbiome sequencing of ulcerative colitis patients receiving fecal microbiota transplantation

224 samples from adults with ulcerative colitis in San Francisco, CA, studying fecal microbiota transplant with antibiotic pretreatment and capsule vs. enema maintenance dosing, in a randomized 2×2 factorial pilot design. machine-written summary

224 samples · 233 runs · US · Adult · 2022 · 15.09 Gbp / sample

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Sources
✓Sequence archive 2,744○Abstract / description○Full text✓Supplementary tables 490–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive2,744 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, intervention, intervention detail)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC11316000, PMC12047655, PMC8976058, PMC9580935
✓ Supplementary tables490 sample values (health condition, health condition detail, subject id, timepoint)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

RFaecal microbiota transplantation: 10 people · 81 samplesFMT 10 people · 81 samplesAntibiotic given as the study intervention (incl. eradication therapy + Faecal microbiota transplantation: 10 people · 74 samplesantibiotic + FMT 10 people · 74 samplesControl / pre-intervention baseline (sample level only): 21 people · 69 samplesno intervention 21 people · 69 samples
randomised to parallel arms

18 people have samples in more than one arm.

Antibiotic given as the study intervention (incl. eradication therapy Faecal microbiota transplantation design randomized_controlled_trial · population ulcerative_colitis · FMT with antibiotic pretreatment vs none; capsule vs enema maintenance, 2x2 factorial

“randomized, pilot, open-label, 2 × 2 factorial design” — abstract:35365713 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult224
Condition
ulcerative_colitis182
healthy_control42
Sex
male113
female69
Country
US224
Body site
primary224
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 1 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all 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: 39 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 170 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 4 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 15.09 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolvedFMT donor → recipient

21 of 23 people sampled more than once (222 samples; median 10, up to 31 per person). Schedule stated by the source: “Baseline, post-antibiotic, before each of 6 weekly maintenance doses (D1-D6), before each of 3 follow-up visits (~2,6,14 wks after last dose)” (time origin: intervention_start).

UC FMT trial: 20 recipients linked to 4 donors via host_assigned_donor_subject_id (19 to 3 sampled donors D0044, D0097, D0485; 42 donor stool samples).

donor: D0044, S0041, S0047, S0053, S0055, S0056, S0059, S0060, S0061D0044 donor of S0041D0044 donor of S0047D0044 donor of S0053D0044 donor of S0055D0044 donor of S0056D0044 donor of S0059D0044 donor of S0060D0044 donor of S0061D0044 — donor · 10 samplesDD0044S0041 — recipient · 9 samplesRS0041S0047 — recipient · 8 samplesRS0047S0053 — recipient · 11 samplesRS0053S0055 — recipient · 10 samplesRS0055S0056 — recipient · 9 samplesRS0056S0059 — recipient · 6 samplesRS0059S0060 — recipient · 9 samplesRS0060S0061 — recipient · 9 samplesRS0061
donor: D0097, S0001, S0004, S0013, S0021, S0024, S0027, S0043D0097 donor of S0001D0097 donor of S0004D0097 donor of S0013D0097 donor of S0021D0097 donor of S0024D0097 donor of S0027D0097 donor of S0043D0097 — donor · 31 samplesDD0097S0001 — recipient · 10 samplesRS0001S0004 — recipient · 11 samplesRS0004S0013 — recipient · 10 samplesRS0013S0021 — recipient · 9 samplesRS0021S0024 — recipient · 11 samplesRS0024S0027 — recipient · 10 samplesRS0027S0043 — recipient · 1 sampleRS0043
donor: D0485, S0007, S0008, S0062, S0064D0485 donor of S0007D0485 donor of S0008D0485 donor of S0062D0485 donor of S0064D0485 — donor · 1 sampleDD0485S0007 — recipient · 8 samplesRS0007S0008 — recipient · 9 samplesRS0008S0062 — recipient · 10 samplesRS0062S0064 — recipient · 11 samplesRS0064
donor: D0065, S0063D0065 donor of S0063D0065 — donor · not sequencedDD0065S0063 — recipient · 11 samplesRS0063

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: 4 linked groups from explicit relations. 23 people in the project overall.

How longitudinal and relatedness information is derived

Community composition
Faecalibacterium 13.3%Bacteroides 6.9%Bifidobacterium 5.9%Roseburia 5.7%Phocaeicola 5.5%Blautia_A 4.8%Collinsella 3.2%Streptococcus 3.1%Gemmiger 2.6%Lachnospira 2.3%Escherichia 2.2%Alistipes 2.1%not assigned to a genus 3.9%other genera 38.4%

Genera, mean relative abundance over 197 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category224 100%
country224 100%224
health_condition224 100%18242
subject_id224 100%42182
collection_date224 100%224
detailed_location224 100%
health_condition_detail224 100%18242
intervention224 100%224
intervention_detail224 100%224
latitude224 100%224
location_locality224 100%224
location_region224 100%224
longitude224 100%224
timepoint_label224 100%224
age_at_collection_days182 81%182
antibiotic_exposure182 81%182
sex182 81%182
Papers (7)
  • Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. 2022 PMID 35365713 PMC8976058 own_data
  • Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. 2022 PMID 36304283 PMC9580935 own_data
  • Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients. 2024 PMID 39122767 PMC11316000 own_data
  • Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC. 2025 PMID 40210439 PMC12047655 own_data
  • 36 ANTIBIOTIC PRETREATMENT PRIOR TO FECAL MICROBIOTA TRANSPLANTATION INCREASES RATES OF REMISSION IN PATIENTS WITH MILD TO MODERATE ULCERATIVE COLITIS: RESULTS FROM A PILOT RANDOMIZED CLINICAL TRIAL 2020 own_data
2 more
  • Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC 2024
  • Constructing inflammatory bowel disease diagnostic models based on k-mer and machine learning. 2025 PMID 40636504 PMC12239758
Details
Archive description

Fecal microbiota transplant is a promising therapy for a variety of conditions, including ulcerative colitis where a third of recipients achieve clinical remission after treatment. Parameters maximizing the effectiveness of the therapy are not yet clear, and it is not known how important the transmission of donor microbes to recipients is. Here we have tested the effects of both antibiotic pretreatment and two modes of maintenance dose delivery, capsules versus enema, in a factorial design with 22 patients.

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 · “colitis patients receiving fecal microbiota transplantation”
  • body site study.description · “Fecal microbiota transplant is”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN19715387age_at_collection_days13149.0R10.85sample.attr.host_age36
SAMN19715387antibiotic_exposureyesR10.90biosample_attrABX+
SAMN19715324collection_date2017/2020R10.90biosample.attribute:collection_date2017/2020
SAMN19715324countryUSR10.90sample.attr.geo_loc_nameUSA: San Francisco, CA
SAMN19715387health_conditionulcerative_colitisR10.90biosample_attrulcerative colitis
SAMN19715324health_conditionhealthy_controlR20.85paper.supp.sample.tsv[sample_type]sample_type: donor
SAMN19715387health_condition_detailulcerative colitisR10.90sample.attr.gastrointest_disordulcerative colitis
SAMN19715324health_condition_detaildonorR20.85paper.supp.sample.tsv[sample_type]sample_type: donor
SAMN19715324interventionno_interventionR10.90biosample.attribute:host_is_fmt_recipienthost_is_fmt_recipient: False
SAMN19715387interventionno_interventionR10.80biosample.attribute:collection_days_post_initial_fmtcollection_days_post_initial_fmt: -11
SAMN19715324intervention_detailsample taken before subject received FMTR10.90biosample.attribute:host_is_fmt_recipienthost_is_fmt_recipient: False
SAMN19715387intervention_detailcollection_days_post_initial_fmt = -11 (before intervention start); assigned arm: sample taken after FMT administrationR10.80biosample.attribute:collection_days_post_initial_fmtcollection_days_post_initial_fmt: -11
SAMN19715324latitude42.3900R10.90biosample.attribute:lat_lon42.39 N 71.12 W
SAMN19715324location_localitySan FranciscoR10.85biosample.attribute:geo_loc_nameUSA: San Francisco, CA
SAMN19715324location_regionCaliforniaR10.75biosample.attribute:geo_loc_nameUSA: San Francisco, CA
SAMN19715324longitude-71.1200R10.90biosample.attribute:lat_lon42.39 N 71.12 W
SAMN19715387sexmaleR10.90sample.attr.host_sexmale
SAMN19715324subject_idD0044R10.85sample.attr.host_subject_idD0044
SAMN19715387subject_idS0004R20.80archive
SAMN19715324timepoint_labelS041V01R20.85paper.supp.visit.tsv[!visit_id]S041V01
Sequencing

233 runs over 224 samples · mean 14.10 Gbp per run (median 14.90 Gbp, total 3,286.20 Gbp; 233 runs with a base count) · layout PAIRED 233 · platform ILLUMINA 233 · models Illumina NovaSeq 6000 (233) · 87% of runs with a Sandpiper profile · first public 2022-04-01 – 2024-04-28

Authors (34)

Smith BJ first · Piceno Y · Zydek M · Zhang B · Syriani LA · Terdiman JP · Kassam Z · Ma A · Lynch SV · Pollard KS · El-Nachef N last · Magnaye KM · Stryker E · Porsche CE · Hertz S · McCauley KE · Zhao C · Dubinkina V · Jin X · Zahavi L · Shoer S · Moltzau-Anderson J · Segal E · Li L first · Liu Z · Qin J · Xiong G · Yang C · Cai F · Huang J last · Smith B · Syriani L · Pollard K · Lynch S last

Downloads

PRJNA737472.csv.gz (7.5 KB) · parquet (80.9 KB) — all 224 samples, every field with route and confidence · PRJNA737472_determinations.csv.gz (23.8 KB) — 3,234 evidence rows

Samples (224 · every field this project has values for · hover a cell for its source)
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