PRJEB57770 ERP142769
Gut metagenomics in Parkinson's disease, Taiwan (case-control)
Gut metagenomic sequencing in Parkinson's disease
117 gut metagenome samples from adults in Taiwan, studied in a case-control design examining Parkinson's disease and its relationship to gut microbiota. machine-written summary
117 samples · 117 runs · Adult · 2024 · 9.25 Gbp / sample
Sources
✓Sequence archive 468✓Abstract / description 117✓Full text 117○Supplementary tables✓External resources 234–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 468 sample values (collection date, latitude, location region, longitude) |
| ✓ Abstract / description | 117 sample values (subject id) |
| ✓ Full text | 117 sample values (location site) · PMC10721883, PMC12022887 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 234 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
1 sampling locations · 0 countries
Age
adult117
Condition
neurological_psychiatric117
Body site
primary117
Sequencing depth per sample · this project all projects
! Self-contradictory metadata
country: sequence archive and GMrepo disagree for 117 samples (e.g. TW vs CN) — withheld.
The sources disagree on 117 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 117)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA114119291 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119292 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119293 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119294 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119295 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119296 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119297 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119298 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119299 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119300 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119301 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119302 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119303 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119304 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119305 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119306 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119307 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119308 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119309 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119310 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119311 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119312 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119313 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119314 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119315 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119316 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119317 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119318 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119319 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119320 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119321 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119322 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119323 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119324 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119325 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119326 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119327 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119328 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119329 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
| SAMEA114119330 | country | TW (sequence archive) | CN (GMrepo) | withheld: neither value published |
Community composition
Prevotella 18.4%Phocaeicola 15.3%Bacteroides 14.7%Alistipes 5.0%Faecalibacterium 3.2%Roseburia 2.3%Parabacteroides 2.2%Sutterella 1.6%Mediterraneibacter 1.3%Ruminococcoides 1.1%Lachnospira 1.1%Acetatifactor 1.0%not assigned to a genus 3.2%other genera 29.7%
Genera, mean relative abundance over 108 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 117 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 117 | 100% | 117 | |||
| subject_id | 117 | 100% | 117 | |||
| collection_date | 117 | 100% | 117 | |||
| detailed_location | 117 | 100% | ||||
| health_condition_detail | 117 | 100% | 117 | |||
| latitude | 117 | 100% | 117 | |||
| location_region | 117 | 100% | 117 | |||
| location_site | 117 | 100% | 117 | |||
| longitude | 117 | 100% | 117 |
Papers (2)
- Plasma metabolites of aromatic amino acids associate with clinical severity and gut microbiota of Parkinson's disease. 2023 PMID 38097625 PMC10721883 own_data
- Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism. 2025 PMID 40273394 PMC12022887 own_data
Details
Archive description
To explore the association between gut microbiome and Parkinson's disease.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut metagenomic sequencing in”
- body site study.description · “the association between gut microbiome and Parkinson's”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114119291 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMEA114119291 | health_condition | neurological_psychiatric | R2 | 0.75 | external.gmrepo source | phenotype: Parkinson Disease |
| SAMEA114119291 | health_condition_detail | Parkinson Disease | R2 | 0.75 | external.gmrepo source | phenotype: Parkinson Disease |
| SAMEA114119291 | latitude | 25.0412 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 25.04118 121.51924 |
| SAMEA114119291 | location_region | Taipei | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 25.04118 121.51924 |
| SAMEA114119291 | location_site | National Taiwan University Hospital movement disorder clinic | R3 | 0.70 | paper.fulltext.methods | enrolled from the movement disorder clinic of National Taiwan University Hospital |
| SAMEA114119291 | longitude | 121.5192 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 25.04118 121.51924 |
| SAMEA114119291 | subject_id | SAMEA114119291 | R4 | 0.60 | design.one_sample_per_subject:abstract | Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort |
Sequencing
117 runs over 117 samples · mean 11.19 Gbp per run (median 9.25 Gbp, total 1,309.78 Gbp; 117 runs with a base count) · layout PAIRED 117 · platform ILLUMINA 117 · models Illumina NovaSeq 6000 (117) · 92% of runs with a Sandpiper profile · first public 2024-01-01
Authors (16)
Chen SJ first · Wu YJ · Chen CC · Wu YW · Liou JM · Wu MS · Kuo CH · Lin CH last · Chiu JY · Tan AH · Toh TS · Lim SY · Tan EK · Pettersson S · Hsu CC · Hsu CL
Downloads
PRJEB57770.csv.gz (4.1 KB) · parquet (75.8 KB) — all 117 samples, every field with route and confidence · PRJEB57770_determinations.csv.gz (7.1 KB) — 936 evidence rows
Samples (117 · every field this project has values for · hover a cell for its source)
Loading the sample table…