Gut virome in C. difficile infection, FMT vs vancomycin
83 virus metagenome samples from stool of C. difficile-infected patients and healthy household controls, studying enteric virome and bacteriophage (Caudovirales) changes with fecal microbiota transplantation or vancomycin treatment. machine-written summary
83 samples · 83 runs · Age unknown · 2017 · 6.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 337 sample values (collection date, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5868238 |
| ✓ Supplementary tables | 265 sample values (age, family id, family role, intervention, sex, shared setting id, shared setting type) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy Faecal microbiota transplantation design non_randomized_controlled · population gi_infection_or_diarrhoea · FMT vs vancomycin for recurrent C. difficile infection
“treated with FMT and five treated with vancomycin” — abstract:28539351 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipienthouseholds
14 of 44 people sampled more than once (53 samples; median 4, up to 6 per person) · follow-up median 2 mo (max 6 mo) · median interval between samples 24 d (time from collection dates). Schedule stated by the source: “Baseline stool for all 44 subjects (24 CDI, 20 controls); 14 CDI subjects had serial post-treatment stool samples up to last follow-up (last stool collection time point).” (time origin: intervention_start).
Each row is one person (14 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
16 households with >=2 sampled people (CDI patient + household control/donor); 8 FMT donor->recipient links (Suppl. Table 1) · 16 families with 32 sampled people · 16 shared settings.
household memberdonorrecipientmember · 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 · 8 families · 8 of 16 shared settings. 44 people in the project overall.
Families (16)
Genera, mean relative abundance over 77 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 18 | 22% | ||||
| country | 0 | 0% | ||||
| health_condition | 44 | 53% | 44 | |||
| subject_id | 83 | 100% | 83 | |||
| collection_date | 83 | 100% | 83 | |||
| timepoint_label | 83 | 100% | 83 | |||
| family_id | 57 | 69% | 57 | |||
| family_role | 57 | 69% | 57 | |||
| shared_setting_id | 57 | 69% | 57 | |||
| shared_setting_type | 57 | 69% | 57 | |||
| health_condition_detail | 44 | 53% | 44 | |||
| age_at_collection_days | 18 | 22% | 18 | |||
| sex | 18 | 22% | 18 | |||
| intervention | 1 | 1% | 1 |
- Bacteriophage transfer during faecal microbiota transplantation in <i>Clostridium difficile</i> infection is associated with treatment outcome. 2018 PMID 28539351 PMC5868238 own_data
Archive description
virus Metagenome for c.difficile infected patients. Referenced in "Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome" as PRJNA3535980.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “virus Metagenome for c.difficile infected patients”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06019293 | age_at_collection_days | 31411.5 | R2 | 0.80 | paper.supp.gutjnl-2017-313952supp001.pdf[page7_t1!Age] | Age: 86 |
| SAMN06019293 | collection_date | 2015-01-19 | R1 | 0.90 | biosample.attribute:collection_date | 2015-01-19 |
| SAMN06019293 | family_id | A | R2 | 0.85 | paper.supp.gutjnl-2017-313952supp001.pdf[Supplementary Table 1!Household(famiy_ID)] | C1W0 cross-sectional CDI NA A0198ST1 19-Jan-15 A |
| SAMN06019293 | family_role | household_member | R2 | 0.85 | paper.supp.gutjnl-2017-313952supp001.pdf[Supplementary Table 1!Household(famiy_ID)] | C1W0 cross-sectional CDI NA A0198ST1 19-Jan-15 A |
| SAMN06019293 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:ecotype | CDI |
| SAMN06019293 | health_condition_detail | CDI | R1 | 0.85 | biosample.attribute:ecotype | CDI |
| SAMN06019312 | intervention | fmt | R2 | 0.80 | paper.supp.gutjnl-2017-313952supp001.pdf[page7_t1!FMT_n umber] | FMT_n umber: FMT1 |
| SAMN06019293 | sex | female | R2 | 0.80 | paper.supp.gutjnl-2017-313952supp001.pdf[page7_t1!Sex] | Sex: F |
| SAMN06019293 | shared_setting_id | A | R2 | 0.85 | paper.supp.gutjnl-2017-313952supp001.pdf[Supplementary Table 1!Household(famiy_ID)] | C1W0 cross-sectional CDI NA A0198ST1 19-Jan-15 A |
| SAMN06019293 | shared_setting_type | household | R2 | 0.85 | paper.supp.gutjnl-2017-313952supp001.pdf[Supplementary Table 1!Household(famiy_ID)] | C1W0 cross-sectional CDI NA A0198ST1 19-Jan-15 A |
| SAMN06019293 | subject_id | C1 | R1 | 0.70 | sample.name_rule:alias | C1W0_VLP |
| SAMN06019293 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | C1W0_VLP |
Sequencing
83 runs over 83 samples · mean 6.34 Gbp per run (median 6.74 Gbp, total 525.89 Gbp; 83 runs with a base count) · layout PAIRED 83 · platform ILLUMINA 83 · models Illumina HiSeq 4000 (83) · 94% of runs with a Sandpiper profile · first public 2017-06-15
Authors (14)
Zuo T first · Wong SH · Lam K · Lui R · Cheung K · Tang W · Ching JYL · Chan PKS · Chan MCW · Wu JCY · Chan FKL · Yu J · Sung JJY · Ng SC last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, country. Share metadata
Downloads
PRJNA353598.csv.gz (3.8 KB) · parquet (75.3 KB) — all 83 samples, every field with route and confidence · PRJNA353598_determinations.csv.gz (7.6 KB) — 602 evidence rows