Metagenomes in Parkinson's disease, Chicago, case-control
70 fecal metagenome samples from Parkinson's disease patients on levodopa and age-matched household healthy controls in Chicago, IL, studying gut bacterial tyrosine decarboxylase activity and levodopa bioavailability; case-control design. machine-written summary
70 samples · 70 runs · US · Adult · 2023 · 6.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 490 sample values (collection date, country, health condition, health condition detail, location locality, location region, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
households — not resolved
19 PD patients and 16 age-matched household spousal healthy controls (spouse/partner pairs living together).
Genera, mean relative abundance over 29 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 | 70 | 100% | ||||
| country | 70 | 100% | 70 | |||
| health_condition | 70 | 100% | 70 | |||
| subject_id | 70 | 100% | 70 | |||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| health_condition_detail | 70 | 100% | 70 | |||
| location_locality | 70 | 100% | 70 | |||
| location_region | 70 | 100% | 70 |
- High Throughput Assessment of Gut Bacterial Tyrosine Decarboxylase Activity for Predicting Peripheral Levodopa Loss in Parkinson's Disease 2023 own_data
Archive description
Small intestinal bacteria harboring tyrosine decarboxylase (TDC) activity have been shown to reduce levels of the main treatment for Parkinsons disease (PD), levodopa. However, it remains obscure whether the relative abundance of faecal bacterial-TDC contributes to the reduced plasma levodopa bioavailability and the frequency of dosage regimen of levodopa treatment. Shotgun metagenomic sequencing of fecal samples collected from 19 PD patients requiring various levodopa dosage regimens (consumed between 2 and 7 times per day dosage range between 300-1400 mg) and 16 age-matched household spousal healthy control subjects was employed. The composition of TDC- harboring bacteria was significantly different between PD patients compared to their controls. Independently, in vitro TDC-bacterial activity was determined and showed significant negative correlation with the plasma levels of the total absorbed levodopa measured over five hours in all PD patients, while TDC-bacterial relative abundance correlated positively with the total daily levodopa dosage in PD patients. Overall, the data infers a significant contribution of TDC-bacterial species to the decreased levodopa bioavailability in PD patients, thus representing significant progress toward improving the treatment of PD.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- life stage study.description · “age-matched household spousal healthy control”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN28557424 | collection_date | 2019/2020 | R1 | 0.90 | biosample.attribute:collection_date | 2019/2020 |
| SAMN28557424 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Chicago, IL |
| SAMN28557424 | health_condition | neurological_psychiatric | R1 | 0.90 | biosample_attr | PD subject |
| SAMN28557424 | health_condition_detail | PD subject | R1 | 0.90 | sample.attr.host_disease | PD subject |
| SAMN28557424 | location_locality | Chicago | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28557424 | location_region | Illinois | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Chicago, IL |
| SAMN28557424 | subject_id | SMS_01 | R1 | 0.85 | sample.attr.host_subject_id | SMS_01 |
Sequencing
70 runs over 70 samples · mean 5.76 Gbp per run (median 6.69 Gbp, total 403.53 Gbp; 70 runs with a base count) · layout PAIRED 70 · platform ILLUMINA 70 · models Illumina NovaSeq 6000 (70) · 86% of runs with a Sandpiper profile · first public 2023-06-22 – 2023-06-23
Authors (0)
No author record.
Downloads
PRJNA838841.csv.gz (2.7 KB) · parquet (72.7 KB) — all 70 samples, every field with route and confidence · PRJNA838841_determinations.csv.gz (3.6 KB) — 490 evidence rows