Gut metagenomes in Parkinson's disease vs controls, Finland
134 fecal metagenome samples from Finland (68 Parkinson's disease, 66 healthy control) in a case-control design, analyzed by deep shotgun sequencing and metagenome-assembled genome construction. machine-written summary
134 samples · 134 runs · FI · Age unknown · 2024 · 7.22 Gbp / sample · cohort Comparison of phage and plasmid populations in the
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 798 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 134 sample values (subject id) · PMC11324757, PMC12012184 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 140 sample values (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 125 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 | 134 | 100% | 134 | |||
| health_condition | 134 | 100% | 64 | 70 | ||
| subject_id | 134 | 100% | 134 | |||
| collection_date | 134 | 100% | 134 | |||
| detailed_location | 134 | 100% | ||||
| health_condition_detail | 134 | 100% | 64 | 70 | ||
| latitude | 134 | 100% | 134 | |||
| location_region | 134 | 100% | 134 | |||
| longitude | 134 | 100% | 134 |
- Metagenome-assembled microbial genomes from Parkinson's disease fecal samples. 2024 PMID 39143178 PMC11324757 own_data
- Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls. 2025 PMID 40258842 PMC12012184 own_data
- Examination of shared gut microbiome signatures in aging and Parkinson's disease. 2026 PMID 41907847 PMC13021664 unsure
Archive description
This study includes deep shotgun DNA sequencing of 136 patient’s fecal samples (68 Parkinson vs 68 Control).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.title · “136 patient’s fecal samples”
- body site study.title · “fecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112439700 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMEA112439700 | country | FI | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Finland |
| SAMEA112439768 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:TITLE | TITLE: P100 |
| SAMEA112439700 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA112439768 | health_condition_detail | P | R1 | 0.70 | sample.name_rule:TITLE | TITLE: P100 |
| SAMEA112439700 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA112439700 | latitude | 60.1921 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.192059 24.945831 |
| SAMEA112439700 | location_region | Uusimaa | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.192059 24.945831 |
| SAMEA112439700 | longitude | 24.9458 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.192059 24.945831 |
| SAMEA112439700 | subject_id | SAMEA112439700 | R3 | 0.75 | design.one_sample_per_subject:fulltext | Since we performed an independent assembly for each subject’s sample, we encountered highly similar MAGs across subjects. |
Sequencing
134 runs over 134 samples · mean 8.78 Gbp per run (median 7.22 Gbp, total 1,176.27 Gbp; 134 runs with a base count) · layout PAIRED 134 · platform ILLUMINA 134 · models Illumina NovaSeq 6000 (134) · 93% of runs with a Sandpiper profile · first public 2024-08-22
Authors (16)
Duru IC first · Lecomte A · Shishido TK · Laine P · Suppula J · Paulin L · Scheperjans F · Pereira PAB · Auvinen P last · Tng TJW first · Vanan S · Tan EK · Zeng L · Goh WWB · Wong SH · Lim KL last
Downloads
PRJEB59350.csv.gz (4.4 KB) · parquet (76.0 KB) — all 134 samples, every field with route and confidence · PRJEB59350_determinations.csv.gz (9.1 KB) — 1,072 evidence rows