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PRJNA762484 SRP336652

Gut microbiota in Parkinson disease, case-control, Taiwan

Gut microbiota in patients with Parkinson disease

108 fecal metagenome samples from Taiwan, comparing patients with Parkinson disease (59 neurological/psychiatric) to healthy controls (49), in a case-control study linking gut microbiota and short-chain fatty acids to disease severity. machine-written summary

108 samples · 110 runs · Adult · 2022 · 8.69 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 788○Abstract / description✓Full text 324○Supplementary tables✓External resources 2–User contribution–Human verified

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

what each source gave
✓ Sequence archive788 sample values (age, collection date, health condition, health condition detail, latitude, location region, longitude, sex)
○ Abstract / descriptionread; no usable statement
✓ Full text324 sample values (antibiotic exposure, location site, subject id) · PMC8883514
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources2 sample values (health condition, health condition detail) · from GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
2 sampling locations · 0 countries
Age
elderly43
adult35
unknown30
Condition
neurological_psychiatric59
healthy_control49
Sex
male46
female32
Body site
primary108
Collected 2019–2020
2019: 15 samples2020: 93 samples20192020
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: 1 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 75 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 32 samplesall 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 8.69 Gbp per sample0130Gbp
! Self-contradictory metadata

country: sequence archive and GMrepo disagree for 108 samples (e.g. TW vs CN) — withheld.

The sources disagree on 108 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 108)
samplefieldvalueother valuehandling
SAMN21395805countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395806countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395807countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395808countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395809countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395810countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395811countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395812countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395813countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395814countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395815countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395816countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395817countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395818countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395819countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395820countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395821countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395822countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395823countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395824countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395825countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395826countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395827countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395828countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395829countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395830countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395831countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395832countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395833countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395834countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395835countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395836countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395837countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395838countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395839countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395840countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395841countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395842countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395843countryTW (sequence archive)CN (GMrepo)withheld: neither value published
SAMN21395844countryTW (sequence archive)CN (GMrepo)withheld: neither value published
Community composition
Prevotella 17.4%Phocaeicola 16.1%Bacteroides 15.6%Alistipes 4.6%Faecalibacterium 3.1%Parabacteroides 2.2%Roseburia 2.1%Sutterella 1.5%Mediterraneibacter 1.3%Lachnospira 1.0%Ruminococcoides 0.9%Akkermansia 0.9%not assigned to a genus 3.3%other genera 30.2%

Genera, mean relative abundance over 106 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category78 72%
country0 0%
health_condition108 100%1071
subject_id108 100%108
antibiotic_exposure108 100%108
collection_date108 100%108
detailed_location108 100%
health_condition_detail108 100%1071
latitude108 100%108
location_site108 100%108
longitude108 100%108
location_region94 87%94
age_at_collection_days78 72%78
sex78 72%78
Papers (1)
  • Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Parkinson Disease Patients. 2022 PMID 34996879 PMC8883514 own_data
Details
Archive description

We aimed to compare fecal microbiota in PD patients and healthy controls to delineate their interrelations and link to gut microbiota changes and clinical severity of PD

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.68. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.description · “fecal microbiota in PD patients”
  • life stage study.description · “clinical severity of PD”
  • life stage sample.attr.host_age · “68 (n=42/108)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN21395805age_at_collection_days27759.0R10.70sample.attr.host_age76
SAMN21395805antibiotic_exposurenoR30.70paper.fulltext.methodsuse of antibiotics or probiotic supplements within 3 months
SAMN21395805collection_date2020-02-01R10.90biosample.attribute:collection_date2020-02-01
SAMN21395805health_conditionhealthy_controlR10.80biosample_attrControl
SAMN21395912health_conditionneurological_psychiatricR20.75external.gmrepo sourcephenotype: Parkinson Disease
SAMN21395805health_condition_detailControlR10.90sample.attr.host_phenotypeControl
SAMN21395912health_condition_detailParkinson DiseaseR20.75external.gmrepo sourcephenotype: Parkinson Disease
SAMN21395805latitude25.1054R10.90biosample.attribute:lat_lon25.1054 N 121.5973 E
SAMN21395805location_regionTaipeiR10.60biosample.attribute:lat_lon25.1054 N 121.5973 E
SAMN21395805location_siteNational Taiwan University HospitalR30.70paper.fulltext.methodsrecruited from National Taiwan University Hospital
SAMN21395805longitude121.5973R10.90biosample.attribute:lat_lon25.1054 N 121.5973 E
SAMN21395805sexmaleR10.90sample.attr.host_sexmale
SAMN21395805subject_idSAMN21395805R30.75design.one_sample_per_subject:fulltextFinally, the cross-sectional study design precludes any inferences of a causal relationship between SCFAs and the disease process in PD.
Sequencing

110 runs over 108 samples · mean 8.97 Gbp per run (median 8.65 Gbp, total 986.87 Gbp; 110 runs with a base count) · layout PAIRED 110 · platform ILLUMINA 110 · models Illumina NovaSeq 6000 (110) · 98% of runs with a Sandpiper profile · first public 2022-01-15 – 2025-09-21

Authors (9)

Chen SJ first · Chen CC · Liao HY · Lin YT · Wu YW · Liou JM · Wu MS · Kuo CH · Lin CH last

Downloads

PRJNA762484.csv.gz (4.7 KB) · parquet (77.0 KB) — all 108 samples, every field with route and confidence · PRJNA762484_determinations.csv.gz (8.9 KB) — 1,114 evidence rows

Samples (108 · every field this project has values for · hover a cell for its source)
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