Gut virome in ME/CFS vs household controls, case-control
20 stool VLP-enriched virome samples from ME/CFS patients, household-matched healthy controls, and processing controls, profiled by DNA virome sequencing in a case-control design. machine-written summary
20 samples · 20 runs · Age unknown · 2023 · 9.30 Gbp / sample · cohort Investigating the Human Intestinal DNA Virome and
One study deposited as 2 BioProjects (32 catalog samples together): PRJEB57952 · PRJEB57953 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 50 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| ✓ Supplementary tables | 64 sample values (family id, family role, shared setting id, shared setting type) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
households
8 ME/CFS patient + same-household healthy control pairs (Table S1-1 household-matched pair 1–8); 1 unmatched patient · 8 families with 16 sampled people · 8 shared settings.
household membermember · 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 families · 8 shared settings. 17 people in the project overall.
Families (8)
| family | members | samples |
|---|---|---|
| 1 | household_member×2 | SAMEA112183596 · SAMEA112183597 |
| 2 | household_member×2 | SAMEA112183598 · SAMEA112183599 |
| 3 | household_member×2 | SAMEA112183600 · SAMEA112183601 |
| 4 | household_member×2 | SAMEA112183602 · SAMEA112183603 |
| 5 | household_member×2 | SAMEA112183604 · SAMEA112183605 |
| 6 | household_member×2 | SAMEA112183606 · SAMEA112183607 |
| 7 | household_member×2 | SAMEA112183609 · SAMEA112183610 |
| 8 | household_member×2 | SAMEA112183611 · SAMEA112183612 |
Genera, mean relative abundance over 16 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 8 | 40% | 8 | |||
| subject_id | 17 | 85% | 17 | |||
| sex | 17 | 85% | 17 | |||
| family_id | 16 | 80% | 16 | |||
| family_role | 16 | 80% | 16 | |||
| shared_setting_id | 16 | 80% | 16 | |||
| shared_setting_type | 16 | 80% | 16 | |||
| health_condition_detail | 8 | 40% | 8 |
- Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). 2023 PMID 38139096 PMC10744171 unsure
Archive description
Sequencing of VLP-enriched DNA virome collected from the stool samples of 9 ME/CFS patients, 8 household-matched healthy controls and 3 processing control samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.82. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “stool samples of 9 ME/CFS patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112183596 | family_id | 1 | R2 | 0.85 | paper.supp.ijms-24-17267-s001.zip/Table S1.pdf[Table S1-1!# Household-matched pair] | S1 Severe ME/CFS F 56-60 1M |
| SAMEA112183596 | family_role | household_member | R2 | 0.85 | paper.supp.ijms-24-17267-s001.zip/Table S1.pdf[Table S1-1!# Household-matched pair] | S1 Severe ME/CFS F 56-60 1M |
| SAMEA112183597 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | same household healthy controls (SHHC) |
| SAMEA112183597 | health_condition_detail | same household healthy controls (SHHC) | R1 | 0.85 | biosample.attribute:description | same household healthy controls (SHHC) |
| SAMEA112183596 | sex | female | R1 | 0.90 | sample.attr.sex | F |
| SAMEA112183596 | shared_setting_id | 1 | R2 | 0.85 | paper.supp.ijms-24-17267-s001.zip/Table S1.pdf[Table S1-1!# Household-matched pair] | S1 Severe ME/CFS F 56-60 1M |
| SAMEA112183596 | shared_setting_type | household | R2 | 0.85 | paper.supp.ijms-24-17267-s001.zip/Table S1.pdf[Table S1-1!# Household-matched pair] | S1 Severe ME/CFS F 56-60 1M |
| SAMEA112183596 | subject_id | S1 | R1 | 0.70 | biosample.name_rule:alias | S1-vlp |
Sequencing
20 runs over 20 samples · mean 9.47 Gbp per run (median 9.30 Gbp, total 189.42 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models HiSeq X Ten (20) · 80% of runs with a Sandpiper profile · first public 2023-07-30
Authors (12)
Hsieh SY first · Savva GM · Telatin A · Tiwari SK · Tariq MA · Newberry F · Seton KA · Booth C · Bansal AS · Wileman T · Adriaenssens EM · Carding SR last
Downloads
PRJEB57952.csv.gz (1.5 KB) · parquet (70.5 KB) — all 20 samples, every field with route and confidence · PRJEB57952_determinations.csv.gz (2.1 KB) — 114 evidence rows