ME/CFS fecal metagenomics case-control study, USA
100 fecal metagenome samples from adults in the USA, comparing patients with another condition (ME/CFS-related subgroup) to healthy controls (50 each) in a case-control design. machine-written summary
100 samples · 100 runs · US · Age unknown · 2018 · 5.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 500 sample values (bmi, collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10154212, PMC13260335, PMC13526866, PMC5405467, PMC8485520, PMC9465070 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 300 sample values (age, antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 88 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 | 100 | 100% | ||||
| country | 100 | 100% | 100 | |||
| health_condition | 100 | 100% | 50 | 50 | ||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 100 | 100% | 100 | |||
| antibiotic_exposure | 100 | 100% | 100 | |||
| bmi | 100 | 100% | 100 | |||
| collection_date | 100 | 100% | 100 | |||
| health_condition_detail | 100 | 100% | 50 | 50 | ||
| sex | 100 | 100% | 100 |
- Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome. 2017 PMID 28441964 PMC5405467 own_data
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive. 2026 PMID 42277027 PMC13260335 own_data
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520 unsure
- Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex. 2022 PMID 35536747 PMC9465070 unsure
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
1 more
- Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis. 2026 PMID 42289444 PMC13526866
Archive description
Fecal metagenomic profiles in subgroups of patients with Myalgic Encephalomyelitis/ Chronic Fatigue Syndrome
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal metagenomic profiles in subgroups”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06619222 | age_at_collection_days | 18627.75 | R2 | 0.75 | external.cmd source | age: 51; age_unit: Year; age_group: Adult |
| SAMN06619222 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN06619222 | bmi | 22.09 | R1 | 0.90 | sample.attr.bmi | 22.09428571 |
| SAMN06619222 | collection_date | 2014-06-22 | R1 | 0.90 | biosample.attribute:collection_date | 2014-06-22 |
| SAMN06619222 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN06619226 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:desc | Control |
| SAMN06619222 | health_condition | other_disease | R2 | 0.75 | external.cmd source | disease: Chronic Fatigue Syndrome |
| SAMN06619226 | health_condition_detail | Control | R1 | 0.85 | biosample.attribute:desc | Control |
| SAMN06619222 | health_condition_detail | Chronic Fatigue Syndrome | R2 | 0.75 | external.cmd source | disease: Chronic Fatigue Syndrome |
| SAMN06619222 | sex | female | R1 | 0.90 | sample.attr.sex | female |
Sequencing
100 runs over 100 samples · mean 6.05 Gbp per run (median 5.23 Gbp, total 605.37 Gbp; 100 runs with a base count) · layout PAIRED 100 · platform ILLUMINA 100 · models Illumina HiSeq 4000 (100) · 88% of runs with a Sandpiper profile · first public 2018-02-27 – 2018-03-03
Authors (45)
Shao L first · Liao J · Qian J · Chen W · Fan X last · Gotoh Y first · Atsuta Y · Taniguchi T · Nishida R · Nakamura K · Ogura Y · Misawa N · Hayashi T last · Ghosh TS first · Shanahan F · O'Toole PW last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Wacker EM first · Rühlemann MC · Franke A · Ellinghaus D last · Masuoka H first · Miyatake T · Park J · Negishi H · Kurokawa R · Tsuchihashi H · Makino S · Suda W last
Downloads
PRJNA379741.csv.gz (3.9 KB) · parquet (74.9 KB) — all 100 samples, every field with route and confidence · PRJNA379741_determinations.csv.gz (8.4 KB) — 800 evidence rows