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PRJNA728680 SRP324763

FMT trial for MDRO decolonization, Atlanta, USA

PREMIX

95 samples from adult and elderly participants in Atlanta, GA, USA, from a randomized clinical trial of fecal microbiota transplant (FMT) for eradication of intestinal multi-drug resistant organism colonization after infection. machine-written summary

95 samples · 155 runs · US · Adult · 2022 · 4.07 Gbp / sample

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Sources
✓Sequence archive 1,229○Abstract / description–Full text–Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,229 sample values (age, country, health condition, health condition detail, intervention, intervention detail, latitude, location locality)
○ Abstract / descriptionread; no usable statement
– Full textno open-access full text linked
– Supplementary tablesno supplementary tables available (or none open access)
– 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 · 51 samplesFMT 10 people · 51 samplesControl / pre-intervention baseline (sample level only): 12 people · 44 samplesno intervention 12 people · 44 samples
randomised to parallel arms

10 people have samples in more than one arm.

Faecal microbiota transplantation design randomized_controlled_trial · population transplant_or_immunocompromised · FMT vs delayed FMT for MDRO decolonization in transplant recipients

“randomized 1:1 to FMT or an observation period” — abstract:37910603 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult51
elderly44
Condition
type2_diabetes52
transplant_or_immunocompromised23
other_infection14
Sex
female52
male43
Country
US95
Body site
primary95
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all 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 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 11 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 84 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all 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 4.07 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolvedFMT donor → recipient

12 of 12 people sampled more than once (95 samples; median 6, up to 14 per person). Schedule stated by the source: “Samples collected at Day 1, 2, 15, and 36 within each cycle (C0, C1, C2), plus screening visits S1-S3, per subject.”.

single stool donor SD01; 6 donor dose lots sequenced and linked to 12 recipient FMT courses via fmt_dose (13 donor->recipient links).

donor: PM01, PM02, PM03, PM04, PM05, PM06, PM07, PM08, PM09, PM13, SD01SD01 donor of PM01SD01 donor of PM02SD01 donor of PM03SD01 donor of PM03SD01 donor of PM04SD01 donor of PM04SD01 donor of PM05SD01 donor of PM06SD01 donor of PM07SD01 donor of PM07SD01 donor of PM08SD01 donor of PM09SD01 donor of PM13PM01 — recipient · 7 samplesRPM01PM02 — recipient · 5 samplesRPM02PM03 — recipient · 13 samplesRPM03PM04 — recipient · 9 samplesRPM04PM05 — recipient · 9 samplesRPM05PM06 — recipient · 5 samplesRPM06PM07 — recipient · 14 samplesRPM07PM08 — recipient · 11 samplesRPM08PM09 — recipient · 6 samplesRPM09PM13 — recipient · 5 samplesRPM13SD01 — donor · 6 samplesDSD01

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: 1 linked group from explicit relations. 12 people in the project overall.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 26.9%Phocaeicola 13.8%Escherichia 5.1%Parabacteroides 3.8%Alistipes 3.5%Akkermansia 3.5%Klebsiella 3.0%Faecalibacterium 2.2%Enterocloster 2.0%Mediterraneibacter 2.0%Prevotella 1.4%Phascolarctobacterium 1.4%not assigned to a genus 7.0%other genera 24.3%

Genera, mean relative abundance over 90 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category95 100%
country95 100%95
health_condition89 94%89
subject_id95 100%95
age_at_collection_days95 100%95
detailed_location95 100%
health_condition_detail95 100%95
intervention95 100%95
intervention_detail95 100%95
latitude95 100%95
location_locality95 100%95
location_region95 100%95
longitude95 100%95
sex95 100%95
timepoint_label95 100%95
Papers (2)
  • Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. 2023 PMID 37910603 PMC10821315 unsure
  • Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Details
Archive description

Randomized clinical trial of fecal microbiota transplant (FMT) for eradication of intestinal multi-drug resistant organism (MDRO) colonization after infection.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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.description · “clinical trial of fecal microbiota transplant (FMT)”
  • body site external_curation.infant_catalog · “body_site_call stool”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage sample.attr.host_age · “74 (n=44/95)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN19760871age_at_collection_days22280.2R10.70sample.attr.host_age61
SAMN19760871countryUSR10.90sample.attr.geo_loc_nameUSA: Atlanta, GA
SAMN19760871health_conditiontype2_diabetesR10.90biosample_attrDiabetes
SAMN19760871health_condition_detailmdro: yesR10.85sample.attr.mdro_statusPositive
SAMN19760871interventionfmtR10.90biosample.attribute:GroupGroup: FMT
SAMN19760875interventionno_interventionR10.80biosample.attribute:VisitVisit: S1
SAMN19760871intervention_detailFMT treatment armR10.90biosample.attribute:GroupGroup: FMT
SAMN19760875intervention_detailscreening visit before randomisationR10.80biosample.attribute:VisitVisit: S1
SAMN19760871latitude33.7900R10.90biosample.attribute:lat_lon33.79 N 84.32 W
SAMN19760871location_localityAtlantaR10.85biosample.attribute:geo_loc_nameUSA: Atlanta, GA
SAMN19760871location_regionGeorgiaR10.75biosample.attribute:geo_loc_nameUSA: Atlanta, GA
SAMN19760871longitude-84.3200R10.90biosample.attribute:lat_lon33.79 N 84.32 W
SAMN19760871sexfemaleR10.90sample.attr.host_sexfemale
SAMN19760871subject_idPM01R10.85sample.attr.host_subject_idPM01
SAMN19760871timepoint_labelC1D01R10.85sample.attr.visitC1D01
Sequencing

155 runs over 95 samples · mean 2.46 Gbp per run (median 2.77 Gbp, total 381.37 Gbp; 155 runs with a base count) · layout PAIRED 155 · platform ILLUMINA 155 · models Illumina NovaSeq 6000 (82), NextSeq 550 (45), Illumina MiSeq (28) · 91% of runs with a Sandpiper profile · first public 2022-07-06

Authors (35)

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 · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last

Downloads

PRJNA728680.csv.gz (3.7 KB) · parquet (75.1 KB) — all 95 samples, every field with route and confidence · PRJNA728680_determinations.csv.gz (8.8 KB) — 1,229 evidence rows

Samples (95 · every field this project has values for · hover a cell for its source)
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