Fecal Shotgun Metagenomics in Parkinson's Disease, USA
58 fecal microbiome samples from the USA, comparing Parkinson's disease subjects (41) and healthy controls (17) in a case-control design. machine-written summary
58 samples · 58 runs · US · Age unknown · 2020 · 1.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 290 sample values (collection date, country, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10352622, PMC9163076 |
| ✓ Supplementary tables | 41 sample values (age, antibiotic exposure, bmi, sex) |
| – 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 |
longitudinal — not resolved
18 of 40 people sampled more than once (36 samples; median 2, up to 2 per person). Schedule stated by the source: “Unclear; no explicit timepoint labels given, but 18 of 40 subjects have more than one sample (likely repeat/replicate sampling of same individuals).”.
Genera, mean relative abundance over 49 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 | 5 | 9% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 58 | 100% | 58 | |||
| subject_id | 58 | 100% | 58 | |||
| collection_date | 58 | 100% | 58 | |||
| health_condition_detail | 58 | 100% | 58 | |||
| sex | 19 | 33% | 19 | |||
| antibiotic_exposure | 13 | 22% | 13 | |||
| age_at_collection_days | 5 | 9% | 5 | |||
| bmi | 4 | 7% | 4 |
- Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. 2022 PMID 35654877 PMC9163076 unsure
- SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline. 2022 PMID 37469625 PMC10352622 unsure
Archive description
Shotgun Metagenomics raw sequences. Fecal microbiome data in PD subjects and healthy control subjects.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Fecal Microbiome Dysbiosis in Parkinsons Disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14614881 | age_at_collection_days | 21184.5 | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip::Supplementary_Data/input/Indian_metadata.csv[age] | 58 |
| SAMN14614850 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip::Supplementary_Data/input/Indian_metadata.csv[antibiotics] | No |
| SAMN14614881 | bmi | 22.22 | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip::Supplementary_Data/input/Indian_metadata.csv[BMI] | 22.22 |
| SAMN14614830 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN14614830 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN14614830 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy Control |
| SAMN14614830 | health_condition_detail | Healthy Control | R1 | 0.90 | sample.attr.host_disease | Healthy Control |
| SAMN14614846 | sex | male | R2 | 0.75 | paper.supp.41598_2022_13313_MOESM2_ESM.zip::Supplementary_Data/input/Indian_metadata.csv[gender] | M |
| SAMN14614830 | subject_id | OLF001 | R1 | 0.70 | sample.name_rule:sample_alias | OLF001_136_S275604506 |
Sequencing
58 runs over 58 samples · mean 2.16 Gbp per run (median 1.16 Gbp, total 125.44 Gbp; 58 runs with a base count) · layout PAIRED 58 · platform ILLUMINA 58 · models Illumina HiSeq 4000 (58) · 84% of runs with a Sandpiper profile · first public 2020-04-21
Authors (33)
Stockdale SR first · Harrington RS · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O'Reagan O · Nolan JA · Sheehan D · Lavelle A · Draper LA · Shanahan F · Ross RP · Hill C last · Krapohl J first · Pickett BE last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last
Downloads
PRJNA626004.csv.gz (2.5 KB) · parquet (72.1 KB) — all 58 samples, every field with route and confidence · PRJNA626004_determinations.csv.gz (3.2 KB) — 331 evidence rows