Gut metagenome in Parkinson's disease, Xiangyang, China
78 fecal shotgun metagenome samples from Xiangyang, China, in a case-control study comparing Parkinson's disease patients (39) with healthy spousal controls (39) to characterize gut microbiome composition and function. machine-written summary
78 samples · 78 runs · CN · Adult · 2021 · 12.23 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 546 sample values (collection date, country, family id, family role, health condition, health condition detail, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 156 sample values (location region, subject id) · PMC11109112, PMC11706413, PMC12059030, PMC8506127, PMC9846222 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 156 sample values (age, antibiotic exposure, sex) · from BugSigDB, curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
partners / couples
39 couples: Parkinson’s disease patient + healthy spouse (alias PD<n>/Spouse<n>).
partner · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 39 linked groups from explicit relations. 78 people in the project overall.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 78 | 100% | ||||
| country | 78 | 100% | 78 | |||
| health_condition | 78 | 100% | 78 | |||
| subject_id | 78 | 100% | 78 | |||
| antibiotic_exposure | 78 | 100% | 78 | |||
| collection_date | 78 | 100% | 78 | |||
| detailed_location | 78 | 100% | ||||
| family_id | 78 | 100% | 78 | |||
| family_role | 78 | 100% | 78 | |||
| health_condition_detail | 78 | 100% | 78 | |||
| location_locality | 78 | 100% | 78 | |||
| location_region | 78 | 100% | 78 | |||
| age_at_collection_days | 39 | 50% | 39 | |||
| sex | 39 | 50% | 39 |
- Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China. 2021 PMID 34650532 PMC8506127 own_data
- High levels of Bifidobacteriaceae are associated with the pathogenesis of Parkinson's disease. 2022 PMID 36686268 PMC9846222 own_data
- Deep learning-based differential gut flora for prediction of Parkinson's. 2025 PMID 39774383 PMC11706413 own_data
- Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease. 2024 PMID 38773112 PMC11109112 unsure
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030 unsure
1 more
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease 2023
Archive description
Intestinal microbiome disorderplays play an important role in the occurrence and development of Parkinson's disease, and the purpose of this study is to accurately, comprehensively and in detail assess the composition of the intestinal microbiome in patients with Parkinson's disease in central China.
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 · “Cross-sectional study of intestinal flora in Parkinson's”
- body site study.description · “Intestinal microbiome disorderplays play”
- 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 |
|---|---|---|---|---|---|---|
| SAMN13221582 | age_at_collection_days | 21915.0 | R2 | 0.75 | external.cmd source | age: 60; age_unit: Year; age_group: Adult |
| SAMN13221582 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMN13221582 | collection_date | 2017-01 | R1 | 0.90 | biosample.attribute:collection_date | 2017-01 |
| SAMN13221582 | country | CN | R1 | 0.85 | biosample.attribute:geo_loc_name | geo_loc_name: China:Xiangyang |
| SAMN13221582 | family_id | 1 | R1 | 0.60 | sample.name_rule:alias | 1PD1CL100071231L01_65 |
| SAMN13221582 | family_role | partner | R1 | 0.70 | sample.name_rule:alias | 1PD1CL100071231L01_65 |
| SAMN13221582 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:alias | 1PD1CL100071231L01_65 |
| SAMN13221582 | health_condition_detail | PD | R1 | 0.70 | sample.name_rule:alias | 1PD1CL100071231L01_65 |
| SAMN13221582 | location_locality | Xiangyang | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Xiangyang |
| SAMN13221582 | location_region | Central China | R3 | 0.70 | paper.fulltext.methods | gut microbiota of Parkinson's disease patients in the Central China region |
| SAMN13221582 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN13221582 | subject_id | SAMN13221582 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected |
Sequencing
78 runs over 78 samples · mean 12.96 Gbp per run (median 12.23 Gbp, total 1,011.04 Gbp; 78 runs with a base count) · layout PAIRED 78 · platform BGISEQ 78 · models BGISEQ-500 (78) · 0% of runs with a Sandpiper profile · first public 2021-09-14
Authors (35)
Mao L first · Zhang Y · Tian J · Sang M · Zhang G · Zhou Y · Wang P last · Zuo S first · Wang H · Zhao Q · Tang J · Wang M · Nishiwaki H first · Ueyama J · Ito M · Hamaguchi T · Takimoto K · Maeda T · Kashihara K · Tsuboi Y · Mori H · Kurokawa K · Katsuno M · Hirayama M · Ohno K last · Yu B first · Zhang H · Zhang M last · Romano S first · Wirbel J · Ansorge R · Schudoma C · Ducarmon QR · Narbad A · Zeller G last
Downloads
PRJNA588035.csv.gz (3.4 KB) · parquet (74.6 KB) — all 78 samples, every field with route and confidence · PRJNA588035_determinations.csv.gz (9.3 KB) — 858 evidence rows