Gut metagenomes in Parkinson's disease, Japan, case-control
167 gut shotgun metagenome samples from Japan (Nagoya and collaborating sites), comparing Parkinson's disease patients (94 samples) with healthy controls (73 samples) in a case-control design. machine-written summary
167 samples · 167 runs · JP · Age unknown · 2023 · 2.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,336 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 167 sample values (subject id) |
| ✓ Full text | 167 sample values (antibiotic exposure) · PMC11109112 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 167 sample values (age) · 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 149 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 | 161 | 96% | ||||
| country | 167 | 100% | 167 | |||
| health_condition | 167 | 100% | 167 | |||
| subject_id | 167 | 100% | 167 | |||
| age_at_collection_days | 167 | 100% | 167 | |||
| antibiotic_exposure | 167 | 100% | 167 | |||
| collection_date | 167 | 100% | 167 | |||
| detailed_location | 167 | 100% | ||||
| health_condition_detail | 167 | 100% | 167 | |||
| latitude | 167 | 100% | 167 | |||
| location_locality | 167 | 100% | 167 | |||
| location_region | 167 | 100% | 167 | |||
| longitude | 167 | 100% | 167 |
- Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease. 2024 PMID 38773112 PMC11109112 own_data
Archive description
This is shotgun metagenome sequencing in the gut of Parkinson's disease patients. The sample size is 73 for healthy controls and 94 for Parkinson's disease. All studies were approved by the Ethical Review Committees of the Nagoya University Graduate School of Medicine (approval #2016-0151), Iwate Medical College Hospital (H28-123), Okayama Kyokuto Hospital (approval #kyoIR-2016002), and Fukuoka Medical College (approval #2016M027). We obtained written informed consent from all PD patients and healthy controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host study.description · “Parkinson's disease patients”
- host run.host_tax_id · “9606”
- body site study.title · “Shotgun data in the gut”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00618036 | age_at_collection_days | 20819.25 | R2 | 0.75 | external.cmd source | age: 57; age_unit: Year; age_group: Adult |
| SAMD00618036 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods_results | We also excluded subjects who claimed to have taken antibiotics in the last four weeks. |
| SAMD00618036 | collection_date | 2018-03-01 | R1 | 0.90 | biosample.attribute:collection_date | 2018-03-01 |
| SAMD00618036 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan:Nagoya |
| SAMD00618036 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_title | I-C002AG |
| SAMD00618036 | health_condition_detail | I-C002AG | R1 | 0.70 | sample.name_rule:sample_title | I-C002AG |
| SAMD00618036 | latitude | 35.1815 | R1 | 0.90 | biosample.attribute:lat_lon | 35.1815 N 136.9066 E |
| SAMD00618036 | location_locality | Nagoya | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Nagoya |
| SAMD00618036 | location_region | Aichi | R1 | 0.60 | biosample.attribute:lat_lon | 35.1815 N 136.9066 E |
| SAMD00618036 | longitude | 136.9066 | R1 | 0.90 | biosample.attribute:lat_lon | 35.1815 N 136.9066 E |
| SAMD00618036 | subject_id | SAMD00618036 | R4 | 0.60 | design.one_sample_per_subject:description | The sample size is 73 for healthy controls and 94 for Parkinson's disease. |
Sequencing
167 runs over 167 samples · mean 2.49 Gbp per run (median 2.47 Gbp, total 415.89 Gbp; 167 runs with a base count) · layout PAIRED 167 · platform ILLUMINA 167 · models Illumina HiSeq 2500 (167) · 89% of runs with a Sandpiper profile · first public 2023-07-13 – 2023-07-16
Authors (0)
No author record.
Downloads
PRJDB15956.csv.gz (6.2 KB) · parquet (79.2 KB) — all 167 samples, every field with route and confidence · PRJDB15956_determinations.csv.gz (16.8 KB) — 1,837 evidence rows