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PRJEB53403 ERP138199

PD and control shotgun metagenomes, Denver, case-control

PD Shotgun Metagenomics Data

192 stool shotgun metagenome samples from a Denver, Colorado cohort (RUMC), comparing Parkinson's disease/neurological patients and healthy controls in a case-control design. machine-written summary

192 samples · 192 runs · US · Adult · 2022 · 2.98 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 1,597✓Abstract / description 250○Full text○Supplementary tables✓External resources 318–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive1,597 sample values (age, bmi, country, family role, health condition, health condition detail, latitude, location locality)
✓ Abstract / description250 sample values (health condition detail, location site)
○ Full textread; no usable statement or table · PMC12059030
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources318 sample values (age, antibiotic exposure, bmi, sex) · from curatedMetagenomicData 3 (cMD 3), Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult136
elderly56
Condition
healthy_control79
neurological_psychiatric55
Sex
male76
female45
Country
US192
Body site
primary192
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 62 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 3 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 8 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 12 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 11 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 96 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 2.98 Gbp per sample0130Gbp
! Self-contradictory metadata

antibiotic exposure: curatedMetagenomicData and Meta2DB disagree for 2 samples (e.g. yes vs no) — withheld.

The sources disagree on 2 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (2)
samplefieldvalueother valuehandling
SAMEA110061326antibiotic exposureyes (curatedMetagenomicData)no (Meta2DB)withheld: neither value published
SAMEA110061389antibiotic exposureyes (curatedMetagenomicData)no (Meta2DB)withheld: neither value published
Sampling design and relatedness

households — not resolved

30 household-control samples (people living with PD patients); index-patient pairing not deposited.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 8.4%Akkermansia 4.8%Phocaeicola 4.1%Roseburia 3.8%Faecalibacterium 3.4%Blautia_A 3.3%Vescimonas 3.1%Alistipes 2.9%Fimenecus 2.6%Ruminococcoides 2.5%Gemmiger 2.3%Dialister 1.8%not assigned to a genus 17.7%other genera 39.3%

Genera, mean relative abundance over 101 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category192 100%
country192 100%192
health_condition134 70%134
subject_id192 100%192
detailed_location192 100%
health_condition_detail192 100%13458
latitude192 100%192
location_locality192 100%192
location_region192 100%192
location_site192 100%192
longitude192 100%192
age_at_collection_days121 63%4972
sex121 63%4972
bmi112 58%4963
antibiotic_exposure111 58%111
family_role30 16%30
Papers (2)
  • Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030 unsure
  • Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease 2023 unsure
Details
Archive description

Shotgun metagenomic analysis of Parkinson's Disease and household and healthy control stool samples - Rush University Medical Center (RUMC) Cohort.

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.description · “and healthy control stool samples - Rush”
  • body site external_curation.infant_catalog · “body_site_call gut”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA110061210age_at_collection_days24106.5R10.90sample.attr.host_age66
SAMEA110061325age_at_collection_days18993.0R20.75external.cmd sourceage: 52; age_unit: Year; age_group: Adult
SAMEA110061369age_at_collection_days18993.0R20.70external.meta2db sourcehost_age: 52
SAMEA110061210antibiotic_exposurenoR20.75external.cmd sourceantibiotics_current_use: No
SAMEA110061336antibiotic_exposurenoR20.70external.meta2db sourceantibiotics: FALSE
SAMEA110061210bmi33.41R10.90sample.attr.host_body_mass_index33.41
SAMEA110061325bmi33.9R20.75external.cmd sourcebmi: 33.9
SAMEA110061210countryUSR10.90sample.attr.geo_loc_nameUSA:CO:Denver
SAMEA110061328family_rolehousehold_memberR10.85biosample.attribute:DESCRIPTIONDESCRIPTION=Household Control PDC004; donor_group=HC
SAMEA110061210health_conditionhealthy_controlR10.70sample.name_rule:descriptionPopulation Control 211468
SAMEA110061328health_conditionhealthy_controlR10.90biosample_attrHC
SAMEA110061210health_condition_detailPopulation ControlR10.70sample.name_rule:descriptionPopulation Control 211468
SAMEA110061259health_condition_detailmixed_case_control: PD patients vs household and healthy controlsR40.50study.descriptionParkinson's Disease and household and healthy control
SAMEA110061210latitude39.7300R10.90biosample.attribute:latitude+longitude39.73 -104.98
SAMEA110061210location_localityDenverR10.85biosample.attribute:geo_loc_nameUSA:CO:Denver
SAMEA110061210location_regionColoradoR10.75biosample.attribute:geo_loc_nameUSA:CO:Denver
SAMEA110061210location_siteRush University Medical CenterR40.45ena.study_descriptionRush University Medical Center (RUMC) Cohort
SAMEA110061210longitude-104.9800R10.90biosample.attribute:latitude+longitude39.73 -104.98
SAMEA110061210sexfemaleR10.90sample.attr.sexfemale
SAMEA110061325sexmaleR20.75external.cmd sourcesex: Male
SAMEA110061210subject_id211468R10.85sample.attr.host_subject_id211468
Sequencing

192 runs over 192 samples · mean 2.13 Gbp per run (median 2.98 Gbp, total 409.20 Gbp; 192 runs with a base count) · layout PAIRED 192 · platform ILLUMINA 192 · models Illumina NovaSeq 6000 (192) · 53% of runs with a Sandpiper profile · first public 2022-06-08

Authors (7)

Romano S first · Wirbel J · Ansorge R · Schudoma C · Ducarmon QR · Narbad A · Zeller G last

Downloads

PRJEB53403.csv.gz (7.3 KB) · parquet (81.5 KB) — all 192 samples, every field with route and confidence · PRJEB53403_determinations.csv.gz (20.9 KB) — 2,165 evidence rows

Samples (192 · every field this project has values for · hover a cell for its source)
Loading the sample table…