Oral/gut metagenome in Parkinson's disease, case-control
156 stool/oral whole genome shotgun metagenome samples from Parkinson's disease patients and healthy controls (spouses) in Seoul, Korea, in a case-control study of oral-gut microbiome composition and function. machine-written summary
156 samples · 156 runs · KR · Adult · 2021 · 2.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,092 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 76 sample values (antibiotic exposure, family role) · PMC11109112, PMC12059030, PMC13021664, PMC9262988 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 154 sample values (antibiotic exposure) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
partners / couples — not resolved
PD patients with their spouses as healthy controls (74 control samples tagged partner); patient–spouse pairs not identified per sample.
Genera, mean relative abundance over 139 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 | 156 | 100% | ||||
| country | 156 | 100% | 156 | |||
| health_condition | 156 | 100% | 156 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 156 | 100% | 154 | 2 | ||
| collection_date | 156 | 100% | 156 | |||
| detailed_location | 156 | 100% | ||||
| health_condition_detail | 156 | 100% | 156 | |||
| latitude | 156 | 100% | 156 | |||
| location_region | 156 | 100% | 156 | |||
| longitude | 156 | 100% | 156 | |||
| family_role | 74 | 47% | 74 |
- Oral and gut dysbiosis leads to functional alterations in Parkinson's disease. 2022 PMID 35798742 PMC9262988 own_data
- Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease. 2024 PMID 38773112 PMC11109112 unsure
- Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders. 2025 PMID 40307949 PMC12042535 unsure
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030 unsure
- Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836 unsure
2 more
- Examination of shared gut microbiome signatures in aging and Parkinson's disease. 2026 PMID 41907847 PMC13021664
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease 2023
Archive description
Stool whole genome shotgun metagenome of Parkinson's disease patients and their spouse
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Stool whole genome shotgun metagenome”
- life stage study.title · “Parkinson's disease patients and their spouse”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20058723 | antibiotic_exposure | no | R2 | 0.70 | external.meta2db source | antibiotics: FALSE |
| SAMN20058746 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | participants using antibiotics, steroids, or immunosuppressants |
| SAMN20058723 | collection_date | 2020-06 | R1 | 0.90 | biosample.attribute:collection_date | 2020-06 |
| SAMN20058723 | country | KR | R1 | 0.90 | sample.attr.geo_loc_name | Korea: Seoul |
| SAMN20058723 | family_role | partner | R3 | 0.60 | paper.body.text[Methods: Study participants] | patients with PD ... and their spouses as HCs |
| SAMN20058723 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Control No.001 |
| SAMN20058797 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:alias | S-SJC-P-001-3 |
| SAMN20058723 | health_condition_detail | C | R1 | 0.70 | sample.name_rule:alias | S-SJC-C-001-3 |
| SAMN20058723 | latitude | 37.5266 | R1 | 0.90 | biosample.attribute:lat_lon | 37.52658163 N 127.10872432 E |
| SAMN20058723 | location_region | Seoul | R1 | 0.85 | biosample.attribute:geo_loc_name | Korea: Seoul |
| SAMN20058723 | longitude | 127.1087 | R1 | 0.90 | biosample.attribute:lat_lon | 37.52658163 N 127.10872432 E |
Sequencing
156 runs over 156 samples · mean 2.58 Gbp per run (median 2.58 Gbp, total 403.07 Gbp; 156 runs with a base count) · layout PAIRED 156 · platform ILLUMINA 156 · models Illumina NovaSeq 6000 (156) · 89% of runs with a Sandpiper profile · first public 2021-07-05 – 2021-07-06
Authors (53)
Jo S first · Kang W · Hwang YS · Lee SH · Park KW · Kim MS · Lee H · Yoon HJ · Park YK · Chalita M · Lee JH · Sung H · Lee JY · Bae JW · Chung SJ last · Lee J · Choi M · Kim K · Lee S · Kim HS · Romano S first · Wirbel J · Ansorge R · Schudoma C · Ducarmon QR · Narbad A · Zeller G last · Mohammadzadeh R first · Mahnert A · Zurabishvili T · Wink L · Kumpitsch C · Habisch H · Sprengel J · Filek K · Mertelj P · Pernitsch D · Hingerl K · Durdevic M · Gorkiewicz G · Diener C · Loy A · Kolb D · Trautwein C · Madl T · Moissl-Eichinger C last · Tng TJW first · Vanan S · Tan EK · Zeng L · Goh WWB · Wong SH · Lim KL last
Downloads
PRJNA743718.csv.gz (4.5 KB) · parquet (75.9 KB) — all 156 samples, every field with route and confidence · PRJNA743718_determinations.csv.gz (11.3 KB) — 1,322 evidence rows