Gut virome in ME/CFS vs household controls (case-control)
12 stool samples combining VLP-derived DNA viromes and whole metagenomes from ME/CFS patients and household-matched healthy controls, analyzed in a case-control design; no sample locations given. machine-written summary
12 samples · 12 runs · GB · Age unknown · 2023 · 13.33 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 | 48 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 24 sample values (collection date, country) · PMC10744171 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 — not resolved
ME/CFS patients paired with household-matched healthy controls; DESCRIPTION field labels controls as "same household healthy controls (SHHC)"..
Genera, mean relative abundance over 11 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 | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 12 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| health_condition_detail | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 |
- 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
Whole metagenome sequencing of stools samples of ME/CFS patients and household-matched healthy controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “stools samples of ME/CFS patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112184150 | collection_date | 2017/2019 | R3 | 0.70 | paper.fulltext.methods | recruited to the study between 2017 and 2019 |
| SAMEA112184150 | country | GB | R3 | 0.70 | paper.fulltext.methods | St. Helier Hospital, Surrey, UK |
| SAMEA112184150 | health_condition | ibs | R1 | 0.70 | sample.name_rule:sample_description | Diagnosed with IBS and severe ME/CFS |
| SAMEA112184150 | health_condition_detail | Diagnosed with IBS and severe ME/CFS | R1 | 0.70 | sample.name_rule:sample_description | Diagnosed with IBS and severe ME/CFS |
| SAMEA112184150 | sex | female | R1 | 0.90 | sample.attr.sex | F |
| SAMEA112184150 | subject_id | S1 | R1 | 0.70 | biosample.name_rule:alias | S1-wms |
Sequencing
12 runs over 12 samples · mean 13.83 Gbp per run (median 13.33 Gbp, total 165.99 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina NovaSeq 6000 (12) · 92% 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
PRJEB57953.csv.gz (1.3 KB) · parquet (69.8 KB) — all 12 samples, every field with route and confidence · PRJEB57953_determinations.csv.gz (1.3 KB) — 72 evidence rows