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PRJEB53401 ERP138197

PD vs household/healthy control stool metagenomics, Denver, USA

PD Shotgun Metagenomics - TBC

118 shotgun metagenome samples from Parkinson's disease, household, and healthy control stool donors in Denver, Colorado, USA; case-control design comparing gut microbiomes across 70 adult and 48 elderly samples. machine-written summary

118 samples · 118 runs · US · Adult · 2022 · 1.60 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 1,475○Abstract / description○Full text○Supplementary tables✓External resources 114–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,475 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location locality)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC12059030, PMC13035836
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources114 sample values (age, antibiotic exposure) · from curatedMetagenomicData 3 (cMD 3), Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance
1 sampling locations · 1 country
Age
adult70
elderly48
Condition
neurological_psychiatric48
healthy_control27
Sex
female60
male58
Country
US118
Body site
primary118
Collected 2016–2019
2016: 7 samples2017: 50 samples2018: 5 samples2019: 56 samples20162019
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 5 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 113 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)all 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 1.60 Gbp per sample0130Gbp
! Self-contradictory metadata

health condition: sequence archive and GMrepo disagree for 43 samples (e.g. healthy_control vs neurological_psychiatric) — withheld.

The sources disagree on 43 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 (40 of 43)
samplefieldvalueother valuehandling
SAMEA110061094health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061097health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061100health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061103health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061105health conditionhealthy_control (sequence archive)neurological_psychiatric (curatedMetagenomicData)withheld: neither value published
SAMEA110061106health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061109health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061112health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061114health conditionhealthy_control (sequence archive)neurological_psychiatric (curatedMetagenomicData)withheld: neither value published
SAMEA110061115health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061118health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061121health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061124health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061127health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061130health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061133health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061136health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061139health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061142health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061145health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061148health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061151health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061154health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061157health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061160health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061162health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061164health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061166health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061168health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061170health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061172health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061174health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061176health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061178health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061180health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061183health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061185health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061187health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061197health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
SAMEA110061200health conditionhealthy_control (sequence archive)neurological_psychiatric (GMrepo)withheld: neither value published
Sampling design and relatedness

households — not resolved

PD patients (n=48), household controls (n=29), and population controls (n=41); household controls linked to PD patients' homes.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 16.9%Phocaeicola 9.7%Alistipes 8.0%Parabacteroides 3.0%Prevotella 2.7%Roseburia 2.5%Akkermansia 2.1%Blautia_A 2.0%Faecalibacterium 1.8%Lachnospira 1.7%Vescimonas 1.6%Fimenecus 1.5%not assigned to a genus 10.0%other genera 36.6%

Genera, mean relative abundance over 103 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category118 100%
country118 100%118
health_condition75 64%75
subject_id118 100%118
age_at_collection_days118 100%1171
collection_date118 100%118
detailed_location118 100%
health_condition_detail118 100%118
latitude118 100%118
location_locality118 100%118
location_region118 100%118
longitude118 100%118
sex118 100%118
stool_consistency_bristol116 98%116
antibiotic_exposure113 96%113
bmi105 89%105
Papers (3)
  • Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030 unsure
  • Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836 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 - the BioCollective (TBC) 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 - the”
  • 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
SAMEA110061092age_at_collection_days23741.2R10.90sample.attr.host_age65
SAMEA110061110age_at_collection_days20454.0R20.70external.meta2db sourcehost_age: 56
SAMEA110061092antibiotic_exposurenoR20.75external.cmd sourceantibiotics_current_use: No
SAMEA110061096antibiotic_exposurenoR20.70external.meta2db sourceantibiotics: FALSE
SAMEA110061092bmi23.05R10.90sample.attr.host_body_mass_index23.05362654
SAMEA110061092collection_date2019-02-05R10.85biosample.attribute:collection_timestampcollection_timestamp: 2019-02-05
SAMEA110061092countryUSR10.90sample.attr.geo_loc_nameUSA:CO:Denver
SAMEA110061092health_conditionneurological_psychiatricR10.90biosample_attrPD Patient
SAMEA110061092health_condition_detailPD PatientR10.85biosample.attribute:donor_groupdonor_group: PD Patient
SAMEA110061092latitude39.7300R10.90biosample.attribute:latitude+longitude39.73 -104.98
SAMEA110061092location_localityDenverR10.85biosample.attribute:geo_loc_nameUSA:CO:Denver
SAMEA110061092location_regionColoradoR10.75biosample.attribute:geo_loc_nameUSA:CO:Denver
SAMEA110061092longitude-104.9800R10.90biosample.attribute:latitude+longitude39.73 -104.98
SAMEA110061092sexmaleR10.90sample.attr.sexmale
SAMEA110061092stool_consistency_bristol5R10.90biosample.attribute:bristol_stool_scale5
SAMEA110061092subject_idBC002158R10.85sample.attr.host_subject_idBC002158
Sequencing

118 runs over 118 samples · mean 1.66 Gbp per run (median 1.60 Gbp, total 195.31 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models NextSeq 550 (118) · 87% of runs with a Sandpiper profile · first public 2022-06-08

Authors (26)

Romano S first · Wirbel J · Ansorge R · Schudoma C · Ducarmon QR · Narbad A · Zeller G last · Mohammadzadeh R first · Mahnert A · Zurabishvili T · Wink L · Kumpitsch C · Habisch H · Sprengel J · Filek K · Mertelj P · Pernitsch D · Hingerl K · Durdevic M · Gorkiewicz G · Diener C · Loy A · Kolb D · Trautwein C · Madl T · Moissl-Eichinger C last

Downloads

PRJEB53401.csv.gz (5.6 KB) · parquet (78.4 KB) — all 118 samples, every field with route and confidence · PRJEB53401_determinations.csv.gz (16.3 KB) — 1,589 evidence rows

Samples (118 · every field this project has values for · hover a cell for its source)
Loading the sample table…