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PRJNA525458 SRP187482

Pediatric fecal transplant for recurrent C. difficile

Fecal transplant in children with Clostridioides difficile

40 stool samples from pediatric recipients (adolescent, child, infant) and adult donors in a fecal microbiota transplant (FMT) intervention study for recurrent Clostridioides difficile infection, with pre- and post-FMT shotgun metagenomic sequencing. machine-written summary

40 samples · 40 runs · Child · 2020 · 1.28 Gbp / sample

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Sources
✓Sequence archive 193○Abstract / description✓Full text 15○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 archive193 sample values (age, health condition, health condition detail, intervention, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
✓ Full text15 sample values (family id) · PMC10465488, PMC12180181, PMC6790402
○ Supplementary tablesfiles read; no table could be matched to the samples
– 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 not resolved

Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · Fecal microbiota transplantation for recurrent C. difficile in children

“Nine children with recurrent CDI underwent FMT” — abstract:31660343 (study level; per-sample arms are in the intervention column below)

Samples at a glance
Age
adolescent15
child14
infant7
adult4
Condition
gi_infection_or_diarrhoea31
healthy_control9
Body site
primary40
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 %)this project, 0.3–1 Gbp: 1 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 39 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)all 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 1.28 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolvedfamiliesFMT donor → recipient

9 of 9 people sampled more than once (31 samples; median 4, up to 4 per person). Schedule stated by the source: “Stool at pre-FMT and longitudinally post-FMT up to 24 weeks, analyzed in windows of 2-7, 8-13, 14-19, 20-24 weeks”; stated follow-up 6 mo.

9 FMT donor->recipient pairs (donor + recipient pre/post-FMT stool); 3 pairs used related donors (Table 1), 6 stool-bank donors · 3 families with 6 sampled people.

unknown?unknown?
3 × unknown×2
donor: SAMN11052987, SAMN11052988, SAMN11052989, SAMN11052990, SAMN11052991SAMN11052987 donor of SAMN11052988SAMN11052987 donor of SAMN11052989SAMN11052987 donor of SAMN11052990SAMN11052987 donor of SAMN11052991SAMN11052987 — donor · 1 sampleD87SAMN11052988 — recipient · 1 sampleR88SAMN11052989 — recipient · 1 sampleR89SAMN11052990 — recipient · 1 sampleR90SAMN11052991 — recipient · 1 sampleR91SAMN110529…
donor: SAMN11052992, SAMN11052993, SAMN11052994, SAMN11052995, SAMN11052996SAMN11052992 donor of SAMN11052993SAMN11052992 donor of SAMN11052994SAMN11052992 donor of SAMN11052995SAMN11052992 donor of SAMN11052996SAMN11052992 — donor · 1 sampleD2SAMN11052993 — recipient · 1 sampleR3SAMN11052994 — recipient · 1 sampleR4SAMN11052995 — recipient · 1 sampleR5SAMN11052996 — recipient · 1 sampleR6SAMN1105299…
donor: SAMN11052997, SAMN11052998, SAMN11052999, SAMN11053000, SAMN11053001SAMN11052997 donor of SAMN11052998SAMN11052997 donor of SAMN11052999SAMN11052997 donor of SAMN11053000SAMN11052997 donor of SAMN11053001SAMN11052997 — donor · 1 sampleD2997SAMN11052998 — recipient · 1 sampleR2998SAMN11052999 — recipient · 1 sampleR2999SAMN11053000 — recipient · 1 sampleR3000SAMN11053001 — recipient · 1 sampleR3001SAMN1105…
donor: SAMN11053002, SAMN11053003, SAMN11053004, SAMN11053005, SAMN11053006SAMN11053002 donor of SAMN11053003SAMN11053002 donor of SAMN11053004SAMN11053002 donor of SAMN11053005SAMN11053002 donor of SAMN11053006SAMN11053002 — donor · 1 sampleD2SAMN11053003 — recipient · 1 sampleR3SAMN11053004 — recipient · 1 sampleR4SAMN11053005 — recipient · 1 sampleR5SAMN11053006 — recipient · 1 sampleR6SAMN1105300…
donor: SAMN11053007, SAMN11053008, SAMN11053009, SAMN11053010, SAMN11053011SAMN11053007 donor of SAMN11053008SAMN11053007 donor of SAMN11053009SAMN11053007 donor of SAMN11053010SAMN11053007 donor of SAMN11053011SAMN11053007 — donor · 1 sampleD07SAMN11053008 — recipient · 1 sampleR08SAMN11053009 — recipient · 1 sampleR09SAMN11053010 — recipient · 1 sampleR10SAMN11053011 — recipient · 1 sampleR11SAMN110530…
donor: SAMN11053015, SAMN11053016, SAMN11053017, SAMN11053018SAMN11053015 donor of SAMN11053016SAMN11053015 donor of SAMN11053017SAMN11053015 donor of SAMN11053018SAMN11053015 — donor · 1 sampleD5SAMN11053016 — recipient · 1 sampleR6SAMN11053017 — recipient · 1 sampleR7SAMN11053018 — recipient · 1 sampleR8SAMN1105301…
donor: SAMN11053019, SAMN11053020, SAMN11053021, SAMN11053022SAMN11053019 donor of SAMN11053020SAMN11053019 donor of SAMN11053021SAMN11053019 donor of SAMN11053022SAMN11053019 — donor · 1 sampleD19SAMN11053020 — recipient · 1 sampleR20SAMN11053021 — recipient · 1 sampleR21SAMN11053022 — recipient · 1 sampleR22SAMN110530…
donor: SAMN11053023, SAMN11053024, SAMN11053025, SAMN11053026SAMN11053023 donor of SAMN11053024SAMN11053023 donor of SAMN11053025SAMN11053023 donor of SAMN11053026SAMN11053023 — donor · 1 sampleD3SAMN11053024 — recipient · 1 sampleR4SAMN11053025 — recipient · 1 sampleR5SAMN11053026 — recipient · 1 sampleR6SAMN1105302…
donor: SAMN11053012, SAMN11053013, SAMN11053014SAMN11053012 donor of SAMN11053013SAMN11053012 donor of SAMN11053014SAMN11053012 — donor · 1 sampleD2SAMN11053013 — recipient · 1 sampleR3SAMN11053014 — recipient · 1 sampleR4SAMN1105301…
family 1family 1nan — member · 1 samplenanIR1 — member · 4 samplesIR1
family 6family 6nan — member · 1 samplenanR06 — member · 4 samplesR06
family 7family 7nan — member · 1 samplenanR07 — member · 4 samplesR07

donorrecipientmember · 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: 9 linked groups from explicit relations · 3 families. 9 people in the project overall.

Families (3)
familymemberssamples
1unknown×2SAMN11052997 · SAMN11052998 · SAMN11052999 · SAMN11053000 · SAMN11053001
6unknown×2SAMN11052987 · SAMN11052988 · SAMN11052989 · SAMN11052990 · SAMN11052991
7unknown×2SAMN11052992 · SAMN11052993 · SAMN11052994 · SAMN11052995 · SAMN11052996

How longitudinal and relatedness information is derived

Community composition
Bacteroides 10.7%Faecalibacterium 9.5%Klebsiella 7.1%Prevotella 5.5%Veillonella 5.2%Escherichia 4.5%Phocaeicola 3.5%Gemmiger 3.4%Roseburia 3.2%Anaerostipes 3.1%Blautia_A 2.3%Bifidobacterium 2.1%not assigned to a genus 8.2%other genera 31.8%

Genera, mean relative abundance over 31 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category40 100%
country0 0%
health_condition40 100%40
subject_id31 78%31
health_condition_detail40 100%40
timepoint_label40 100%40
age_at_collection_days33 82%33
family_id15 38%15
intervention9 22%9
Papers (3)
  • Fecal Transplant in Children With Clostridioides difficile Gives Sustained Reduction in Antimicrobial Resistance and Potential Pathogen Burden. 2019 PMID 31660343 PMC6790402 own_data
  • Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile. 2023 PMID 37644161 PMC10465488 unsure
  • Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Details
Archive description

Little is known regarding the changes in antimicrobial resistance (AMR) genes, pathogens, species and functional pathways that occur with fecal transplant, especially with an adult donor to child recipient. Fecal transplant for recurrent Clostridioides difficile infection (CDI) in children causes an overall significant sustained decrease in AMR genes and potential pathogens in addition to species level and functional changes. However certain AMR genes increased post-FMT and low levels of potential pathogens were found in donors.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of child and adult and adolescent by sonnet_x2 with confidence 0.68. Assay shotgun_dna.

  • host run.scientific_name · “Homo sapiens”
  • body site study.title · “Fecal transplant in children”
  • life stage study.title · “Fecal transplant in children”
  • life stage study.description · “adult donor to child recipient”
  • life stage sample.attr.age · “16 (n=7/40)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN11052987age_at_collection_days8766.0R10.85sample.attr.age24
SAMN11052987family_id6R30.70paper.body.Table 1[Study #; Donor Stool Source] + sample.name_rule:library_nameD06; Table 1 Study # 6: Donor Stool Source = Related
SAMN11052987health_conditionhealthy_controlR10.70sample.name_rule:descriptiondescription: Donor
SAMN11052987health_condition_detailstool donor (volunteer or stool bank)R10.70sample.name_rule:descriptiondescription: Donor
SAMN11052988health_condition_detail0111154, 8534R10.90sample.attr.disease0111154, 8534
SAMN11052987interventionno_interventionR10.70sample.name_rule:descriptiondescription: Donor
SAMN11052988subject_idR06R10.70sample.name_rule:aliasR06A
SAMN11052987timepoint_labelDonorR10.70sample.name_rule:descriptiondescription: Donor
Sequencing

40 runs over 40 samples · mean 1.27 Gbp per run (median 1.28 Gbp, total 50.65 Gbp; 40 runs with a base count) · layout PAIRED 40 · platform ILLUMINA 40 · models Illumina HiSeq 3000 (40) · 78% of runs with a Sandpiper profile · first public 2020-03-28

Authors (20)

Hourigan SK first · Ahn M · Gibson KM · Pérez-Losada M · Felix G · Weidner M · Leibowitz I · Niederhuber JE · Sears CL · Crandall KA · Oliva-Hemker M last · Koo H first · Morrow CD last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last

Downloads

PRJNA525458.csv.gz (2.1 KB) · parquet (71.4 KB) — all 40 samples, every field with route and confidence · PRJNA525458_determinations.csv.gz (3.3 KB) — 208 evidence rows

Samples (40 · every field this project has values for · hover a cell for its source)
Loading the sample table…