Fecal metagenomes in L-DOPA-naive Parkinson's patients, Germany
59 fecal samples from Germany, comparing 31 early-stage, L-DOPA-naive Parkinson's disease patients to 28 age-matched healthy controls using shotgun metagenomics, in a case-control design. machine-written summary
59 samples · 364 runs · DE · Adult · 2017 · 5.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 413 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10199500, PMC10246480, PMC10588041, PMC10609969, PMC11009399, PMC11109112, PMC11402979, PMC12059030, PMC12390848, PMC13021664, PMC13035836, PMC13106387, PMC5408370, PMC6856723, PMC7038607, PMC7890817, PMC8201803, PMC8528855, PMC8813618, PMC9052204 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 157 sample values (antibiotic exposure, bmi, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: curatedMetagenomicData and Meta2DB disagree for 6 samples (e.g. yes vs no) — withheld.
The sources disagree on 6 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 (6)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA103958114 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
| SAMEA103958126 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
| SAMEA103958133 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
| SAMEA103958156 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
| SAMEA103958160 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
| SAMEA103958161 | antibiotic exposure | yes (curatedMetagenomicData) | no (Meta2DB) | withheld: neither value published |
Genera, mean relative abundance over 59 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 | 59 | 100% | ||||
| country | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 59 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 59 | 100% | 59 | |||
| detailed_location | 59 | 100% | ||||
| health_condition_detail | 59 | 100% | 59 | |||
| latitude | 59 | 100% | 59 | |||
| location_region | 59 | 100% | 59 | |||
| longitude | 59 | 100% | 59 | |||
| sex | 59 | 100% | 59 | |||
| antibiotic_exposure | 53 | 90% | 53 | |||
| bmi | 45 | 76% | 45 |
- Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. 2017 PMID 28449715 PMC5408370 own_data
- Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease. 2019 PMID 31722195 PMC6856723 own_data
- Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease. 2023 PMID 37208728 PMC10199500 own_data
- Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. 2020 PMID 32093762 PMC7038607 unsure
- PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. 2021 PMID 33597026 PMC7890817 unsure
17 more
- Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 2021 PMID 34079079 PMC8528855
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803
- Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts. 2022 PMID 35087227 PMC8813618
- Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. 2022 PMID 35258340 PMC9052204
- Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
- Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
- Gut Microbiota Composition in Patients with Neurodegenerative Disorders (Parkinson's and Alzheimer's) and Healthy Controls: A Systematic Review. 2023 PMID 37892440 PMC10609969
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399
- Meta-analysis of shotgun sequencing of gut microbiota in Parkinson's disease. 2024 PMID 38773112 PMC11109112
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. 2025 PMID 40335465 PMC12059030
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- 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
- A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production. 2026 PMID 42039832 PMC13106387
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease 2023
Archive description
Parkinson’s disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both, the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker.We thus compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD subjects to 28 age matched controls by metagenomic analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “compared the fecal microbiomes”
- life stage study.description · “age matched controls by metagenomic analysis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA103958109 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA103958109 | bmi | 24.78 | R2 | 0.75 | external.cmd source | bmi: 24.7842575173938 |
| SAMEA103958109 | collection_date | 2013/2015 | R1 | 0.90 | biosample.attribute:collection_date | 2013/2015 |
| SAMEA103958109 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA103958109 | health_condition | neurological_psychiatric | R1 | 0.90 | biosample_attr | parkinson |
| SAMEA103958109 | health_condition_detail | parkinson | R1 | 0.90 | sample.attr.host_disease_status | parkinson |
| SAMEA103958109 | latitude | 50.9429 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.942911 6.967314 |
| SAMEA103958109 | location_region | North Rhine-Westphalia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.942911 6.967314 |
| SAMEA103958109 | longitude | 6.9673 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 50.942911 6.967314 |
| SAMEA103958109 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
Sequencing
364 runs over 59 samples · mean 0.87 Gbp per run (median 0.61 Gbp, total 317.46 Gbp; 364 runs with a base count) · layout PAIRED 182, SINGLE 182 · platform ILLUMINA 364 · models Illumina HiSeq 2500 (364) · 62% of runs with a Sandpiper profile · first public 2017-04-06
Authors (69)
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 · Nishiwaki H first · Ueyama J · Ito M · Hamaguchi T · Takimoto K · Maeda T · Kashihara K · Tsuboi Y · Mori H · Kurokawa K · Katsuno M · Hirayama M · Ohno K last · 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 · Tng TJW first · Vanan S · Tan EK · Zeng L · Goh WWB · Wong SH · Lim KL last · Sola L first · Candeliere F · Busi E · Raimondi S · Amaretti A · Rossi M last
Downloads
PRJEB17784.csv.gz (2.6 KB) · parquet (72.7 KB) — all 59 samples, every field with route and confidence · PRJEB17784_determinations.csv.gz (6.1 KB) — 570 evidence rows