Home › Studies › PRJNA834801
PRJNA834801 SRP373424

PD vs healthy gut microbiome, shotgun metagenomics, USA

Characterizing dysbiosis of the Parkinson's disease gut microbiome using shotgun metagenomics

725 fecal samples from Parkinson's disease and neurologically healthy adults/elderly, mostly in Alabama and nearby Southeastern US states, analyzed by shotgun metagenomics in a case-control design. machine-written summary

725 samples · 725 runs · US · Adult · 2022 · 6.64 Gbp / sample · cohort Comparison of phage and plasmid populations in the

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 9,593○Abstract / description✓Full text 234○Supplementary tables–External resources–User contribution–Human verified

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

what each source gave
✓ Sequence archive9,593 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, latitude)
○ Abstract / descriptionread; no usable statement
✓ Full text234 sample values (subject id) · PMC11099085, PMC11109112, PMC11334437, PMC11671694, PMC12012184, PMC12042535, PMC12059030, PMC12219260, PMC12339375, PMC12413466, PMC12757628, PMC12807719, PMC13021664, PMC9663292
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
96 sampling locations · 1 country
Age
elderly469
adult256
Condition
neurological_psychiatric488
healthy_control194
autoimmune_inflammatory2
crohns_disease1
Sex
male380
female345
Country
US725
Body site
primary725
Collected 2018–2020
2018: 97 samples2019: 519 samples2020: 109 samples20182020
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 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 4 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 597 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 120 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 4 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 6.64 Gbp per sample0130Gbp
! Self-contradictory metadata

antibiotic exposure: two sequence archives disagree for 145 samples (e.g. no vs yes) — withheld; health condition: two sequence archives disagree for 40 samples (e.g. healthy_control vs type2_diabetes) — withheld.

The sources disagree on 175 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 185)
samplefieldvalueother valuehandling
SAMN28061630antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061634antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061648antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061653antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061660antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061661antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061664antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061672antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061675antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061676antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061682antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061688antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061691antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061694antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061699antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061701antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061711antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061718antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061726antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061730antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061735antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061739antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061742antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061746antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061752antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061753antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061754antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061756antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061759antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061782antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061791antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061792antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061798antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061800antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061814antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061815antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061820antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061822antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061823antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
SAMN28061827antibiotic exposureno (sequence archive)yes (sequence archive)withheld: neither value published
Community composition
Bacteroides 9.8%Blautia_A 7.0%Phocaeicola 5.2%Alistipes 4.5%Bifidobacterium 4.4%Faecalibacterium 4.3%Roseburia 3.4%Ruminococcoides 2.3%Collinsella 2.3%Akkermansia 2.2%Mediterraneibacter 2.0%Streptococcus 1.9%not assigned to a genus 6.9%other genera 43.8%

Genera, mean relative abundance over 649 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category725 100%
country725 100%725
health_condition685 94%685
subject_id234 32%234
age_at_collection_days725 100%725
collection_date725 100%725
detailed_location725 100%
health_condition_detail725 100%725
location_region725 100%725
sex725 100%725
latitude724 100%724
longitude724 100%724
bmi721 99%721
smoking_status703 97%703
stool_consistency_bristol687 95%687
antibiotic_exposure561 77%561
medication438 60%438
Papers (16)
  • Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms. 2022 PMID 36376318 PMC9663292 own_data
  • Enrichment of gut-derived metabolites in a Parkinson's disease subtype with REM sleep behavior disorder. 2025 PMID 40593920 PMC12219260 own_data
  • Gut microbial production of imidazole propionate drives Parkinson's pathologies. 2025 PMID 40913049 PMC12413466 own_data
  • Genome-wide identification of tissue-specific fitness genes in murine models of <i>Staphylococcus aureus</i> infection. 2026 PMID 41488771 PMC12757628 own_data
  • Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration. 2024 PMID 38755164 PMC11099085 unsure
11 more
  • Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease. 2024 PMID 38773112 PMC11109112
  • Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. 2024 PMID 39078158 PMC11334437
  • Rapid species-level metagenome profiling and containment estimation with sylph. 2025 PMID 39379646 PMC12339375
  • Predicting phage-host interactions via feature augmentation and regional graph convolution. 2024 PMID 39727002 PMC11671694
  • Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls. 2025 PMID 40258842 PMC12012184
  • Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders. 2025 PMID 40307949 PMC12042535
  • Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030
  • gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
  • Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems. 2026 PMID 41720792 PMC13035836
  • Examination of shared gut microbiome signatures in aging and Parkinson's disease. 2026 PMID 41907847 PMC13021664
  • Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease 2023
Details
Archive description

Parkinson's disease (PD) is a common, progressive and debilitating neurodegenerative disease which currently cannot be prevented or cured. It is well-established that the overall composition of the gut microbiome is altered in PD, but little is still known about the nature of the dysbiosis and the key players. To characterize the dysbiosis at species, gene family, and metabolic pathway resolution, we enrolled 490 PD and 234 age and geographically matched neurologically healthy individuals, collected stool and metadata, and conducted deep shotgun metagenomic sequencing of fecal DNA. Sequences and metadata are provided here.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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.title · “the Parkinson's disease gut microbiome using shotgun”
  • body site study.description · “composition of the gut microbiome is altered”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage sample.attr.age_at_collection · “68 (n=449/725)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN28061624age_at_collection_days26298.0R10.70sample.attr.age_at_collection72
SAMN28061624antibiotic_exposurenoR10.90biosample_attrN
SAMN28061624bmi32.28R10.90sample.attr.bmi32.27731864
SAMN28061624collection_date2018-11-05R10.90biosample.attribute:collection_date2018-11-05
SAMN28061624countryUSR10.90sample.attr.geo_loc_nameUSA: Alabama
SAMN28061625health_conditionhealthy_controlR10.80biosample_attrControl
SAMN28061629health_conditionhealthy_controlR10.80sample.attr.case_statusControl
SAMN28061624health_condition_detailControlR10.90sample.attr.case_statusControl
SAMN28061624latitude30.5230R10.90biosample.attribute:lat_lon30.5230 N 87.9033 W
SAMN28061624location_regionAlabamaR10.85biosample.attribute:geo_loc_nameUSA: Alabama
SAMN28061624longitude-87.9033R10.90biosample.attribute:lat_lon30.5230 N 87.9033 W
SAMN28061625medicationnsaid_or_aspirinR10.90biosample.attribute:anti_inflammatory_drugsY
SAMN28061626medicationlaxative;nsaid_or_aspirinR10.90biosample.attribute:laxativesY
SAMN28061629medicationother_medicationR10.90biosample.attribute:indigestion_drugsY
SAMN28061624sexmaleR10.90sample.attr.sexmale
SAMN28061624smoking_statusneverR10.80biosample.attribute:do_you_smokeN
SAMN28061624stool_consistency_bristol5R10.90biosample.attribute:bristol_stool_chart5
SAMN28061624subject_idSAMN28061624R30.75design.one_sample_per_subject:fulltextEach subject provided one stool sample at one time point; hence each data point represents a unique individual.
Sequencing

725 runs over 725 samples · mean 7.62 Gbp per run (median 6.64 Gbp, total 5,528.08 Gbp; 725 runs with a base count) · layout PAIRED 725 · platform ILLUMINA 725 · models Illumina NovaSeq 6000 (725) · 90% of runs with a Sandpiper profile · first public 2022-10-27

Authors (39)

Wei A first · Xiao Z · Fu L · Zhao W · Jiang X last · Duru IC first · Lecomte A · Laine P · Shishido TK · Suppula J · Paulin L · Scheperjans F · Pereira PAB · Auvinen P last · Lee JY first · Jo S · Lee J · Choi M · Kim K · Lee S · Kim HS · Bae JW · Chung SJ last · Romano S first · Wirbel J · Ansorge R · Schudoma C · Ducarmon QR · Narbad A · Zeller G last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last

Downloads

PRJNA834801.csv.gz (32.6 KB) · parquet (114.1 KB) — all 725 samples, every field with route and confidence · PRJNA834801_determinations.csv.gz (90.9 KB) — 9,827 evidence rows

Samples (725 · every field this project has values for · hover a cell for its source)
Loading the sample table…