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PRJNA446038 SRP136685

FMT virome dynamics in C. difficile patients, Finland

viral metagenome Raw sequence reads

134 samples from Finland examining viral/bacteriophage transfer following faecal microbiota transplantation (FMT) from donors to recipients treated for recurrent Clostridium difficile infection; intervention study tracking colonisation over time. machine-written summary

134 samples · 134 runs · FI · Age unknown · 2019 · 0.77 Gbp / sample

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Sources
✓Sequence archive 524○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 archive524 sample values (country, intervention, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC6288847
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention · arms resolved

before · no interventionbefore · no interventi33 samplesFMTFMT97 samples
single arm: samples before and on the intervention

Faecal microbiota transplantation design single_arm_before_after · population gi_infection_or_diarrhoea · FMT from 3 donors to 14 recipients (recurrent C. difficile infection), viral tracking

“viral transfer following FMT from 3 donors to 14 patients” — abstract:30526683 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 country
Age
unknown134
Country
FI134
Body site
primary134
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 %)this project, 0.03–0.1 Gbp: 2 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 11 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 85 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 36 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 0.77 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolvedFMT donor → recipient

17 of 17 people sampled more than once (130 samples; median 7, up to 16 per person). Schedule stated by the source: “pre-FMT and at intervals up to 1-year post-FMT” (time origin: transplant); stated follow-up 12 mo.

FMT virome study: 3 sampled donors -> 14 recipients (rCDI); donor per recipient from Table S1.

donor: D3, P10, P11, P12, P14, P6, P8, P9D3 donor of P6D3 donor of P8D3 donor of P9D3 donor of P10D3 donor of P11D3 donor of P12D3 donor of P14D3 — donor · 16 samplesDD3P10 — recipient · 8 samplesRP10P11 — recipient · 7 samplesRP11P12 — recipient · 8 samplesRP12P14 — recipient · 7 samplesRP14P6 — recipient · 8 samplesRP6P8 — recipient · 7 samplesRP8P9 — recipient · 6 samplesRP9
donor: D2, P1, P13, P2, P3, P4, P5D2 donor of P1D2 donor of P2D2 donor of P3D2 donor of P4D2 donor of P5D2 donor of P13D2 — donor · 9 samplesDD2P1 — recipient · 6 samplesRP1P13 — recipient · 8 samplesRP13P2 — recipient · 7 samplesRP2P3 — recipient · 7 samplesRP3P4 — recipient · 4 samplesRP4P5 — recipient · 7 samplesRP5
donor: D1, P7D1 donor of P7D1 — donor · 8 samplesDD1P7 — recipient · 7 samplesRP7

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: 3 linked groups from explicit relations. 17 people in the project overall.

How longitudinal and relatedness information is derived

Community composition
Aphodocola 30.7%Nanosynbacter 16.5%UMGS1271 7.8%UMGS995 3.5%CAG-628 3.4%CAG-302 3.1%Caccenecus 2.9%CAG-433 2.6%Akkermansia 2.3%Onthocola_B 2.2%CAG-914 2.1%Saccharimonas 1.9%not assigned to a genus 17.4%other genera 3.5%

Genera, mean relative abundance over 29 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country134 100%134
health_condition0 0%
subject_id130 97%130
intervention130 97%130
timepoint_label130 97%130
Papers (1)
  • Long-term colonisation with donor bacteriophages following successful faecal microbial transplantation. 2018 PMID 30526683 PMC6288847 own_data
Details
Archive description

FMT Virome Analysis

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN08805293countryFIR10.90sample.attr.geo_loc_nameFinland
SAMN08805293interventionfmtR10.70sample.name_rule:aliasP
SAMN08805293subject_idP9R10.70sample.name_rule:aliasP9
SAMN08805293timepoint_labelF5R10.70sample.name_rule:aliasF5
Sequencing

134 runs over 134 samples · mean 0.77 Gbp per run (median 0.77 Gbp, total 103.81 Gbp; 134 runs with a base count) · layout PAIRED 134 · platform ILLUMINA 134 · models Illumina HiSeq 2500 (134) · 44% of runs with a Sandpiper profile · first public 2019-07-27

Authors (21)

Draper LA first · Ryan FJ · Smith MK · Jalanka J · Mattila E · Arkkila PA · Ross RP · Satokari R · Hill C last · Zeng S first · Almeida A · Li S · Ying J · Wang H · Qu Y · Paul Ross R · Stanton C · Zhou Z · Niu X · Mu D · Wang S last

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJNA446038.csv.gz (3.9 KB) · parquet (73.6 KB) — all 134 samples, every field with route and confidence · PRJNA446038_determinations.csv.gz (3.9 KB) — 524 evidence rows

Samples (134 · every field this project has values for · hover a cell for its source)
Loading the sample table…