Gut metagenome case-control study of multiple sclerosis in Japan
106 fecal samples from Japanese adults and elderly individuals, including healthy participants, relapsing-remitting MS patients, and secondary progressive MS patients, in a case-control design. machine-written summary
106 samples · 109 runs · JP · Adult · 2024 · 13.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 607 sample values (age, country, health condition, health condition detail, sex, subject id) |
| ✓ Abstract / description | 29 sample values (subject id) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
Genera, mean relative abundance over 96 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 | 106 | 100% | ||||
| country | 106 | 100% | 106 | |||
| health_condition | 106 | 100% | 106 | |||
| subject_id | 106 | 100% | 77 | 29 | ||
| age_at_collection_days | 106 | 100% | 106 | |||
| health_condition_detail | 106 | 100% | 106 | |||
| sex | 106 | 100% | 106 |
- Horizontal gene transfer shapes pathogenic bacteria in multiple sclerosis 2023 own_data
- Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis. 2024 PMID 39341204 own_data
Archive description
Novaseq reads derived from fecal samples of 29 Japanese healthy participants, 62 patients with relapsing-remitting multiple sclerosis, and 15 patients with secondary progressive multiple sclerosis are deposited. Sequel II HiFi reads derived from fecal samples of 2 patients with relapsing-remitting multiple sclerosis, and 1 patient with secondary progressive multiple sclerosis are also deposited.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “29 Japanese healthy participants”
- body site study.description · “Novaseq reads derived from fecal samples”
- life stage sample.attr.age · “35 (n=103/106)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00154041 | age_at_collection_days | 14971.0 | R1 | 0.85 | sample.attr.age | 41 |
| SAMD00154041 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00154041 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:title | RR-CMS001 |
| SAMD00154041 | health_condition_detail | RR-CMS | R1 | 0.70 | sample.name_rule:title | RR-CMS001 |
| SAMD00154041 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMD00154041 | subject_id | RR-CMS001 | R1 | 0.85 | sample.attr.host_subject_id | RR-CMS001 |
| SAMD00724851 | subject_id | SAMD00724851 | R4 | 0.60 | design.one_sample_per_subject:description | fecal samples of 29 Japanese healthy participants, 62 patients with relapsing-remitting multiple sclerosis, and 15 patients with secondary progressive multiple sclerosis |
Sequencing
109 runs over 106 samples · mean 15.13 Gbp per run (median 13.29 Gbp, total 1,649.39 Gbp; 109 runs with a base count) · layout PAIRED 106, SINGLE 3 · platform ILLUMINA 106, PACBIO_SMRT 3 · models Illumina NovaSeq 6000 (106), Sequel II (3) · 88% of runs with a Sandpiper profile · first public 2024-10-24 – 2024-10-27
Authors (0)
No author record.
Downloads
PRJDB17221.csv.gz (4.1 KB) · parquet (74.7 KB) — all 106 samples, every field with route and confidence · PRJDB17221_determinations.csv.gz (5.5 KB) — 636 evidence rows