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PRJEB57228 ERP142200

Diet intervention in Parkinson's patients and spouses, Germany

Dietary intervention of people with Parkinson's disease

44 gut metagenome samples from Germany, from Parkinson's disease patients and healthy spouse controls, studying a 4-week fibre-rich diet with lactulose in a prospective controlled pilot intervention study. machine-written summary

44 samples · 44 runs · DE · Adult · 2024 · 18.18 Gbp / sample

Sources
✓Sequence archive 616○Abstract / description✓Full text 88○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 archive616 sample values (age, collection date, country, diet, diet detail, family id, health condition, health condition detail)
○ Abstract / descriptionread; no usable statement
✓ Full text88 sample values (family role, location site) · PMC11968880
○ 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
Interventions

intervention — arms not resolved

Controlled / prescribed diet or feeding regimen Prebiotic / dietary fibre supplement design single_arm_before_after · population neurological_psychiatric · 4-week high-fibre diet with lactulose prebiotic

“4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose” — abstract:40180909 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 sampling locations · 1 country
Age
adult23
elderly21
Condition
neurological_psychiatric23
healthy_control21
Sex
female22
male22
Country
DE44
Body site
primary44
Collected 2017–2019
2017: 32 samples2018: 8 samples2019: 4 samples20172019
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 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 1 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 40 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 3 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 18.18 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalhouseholdspartners / couples

20 of 22 people sampled more than once (42 samples; median 2, up to 3 per person) · follow-up median 28 d (max 3 mo) · median interval between samples 28 d (time from collection dates). Schedule stated by the source: “faecal samples at baseline and 4 weeks after diet” (time origin: baseline); stated follow-up 28 d.

CO11CO11 (partner): day 0CO11 (partner): day 28PD11PD11 (partner): day 0PD11 (partner): day 28CO12CO12 (partner): day 0CO12 (partner): day 35PD12PD12 (partner): day 0PD12 (partner): day 35CO14CO14 (partner): day 0CO14 (partner): day 28PD14PD14 (partner): day 0PD14 (partner): day 28CO2CO2 (partner): day 0CO2 (partner): day 28PD2PD2 (partner): day 0PD2 (partner): day 28CO3CO3 (partner): day 0CO3 (partner): day 28PD3PD3 (partner): day 0PD3 (partner): day 28PD4PD4 (partner): day 0PD4 (partner): day 28PD4 (partner): day 105CO4CO4 (partner): day 0CO4 (partner): day 28PD6PD6 (partner): day 0PD6 (partner): day 35PD6 (partner): day 90CO6CO6 (partner): day 0CO6 (partner): day 35CO7CO7 (partner): day 0CO7 (partner): day 28PD7PD7 (partner): day 0PD7 (partner): day 28CO8CO8 (partner): day 0CO8 (partner): day 35PD8PD8 (partner): day 0PD8 (partner): day 35CO9CO9 (partner): day 0CO9 (partner): day 41PD9PD9 (partner): day 0PD9 (partner): day 410 d26 d52 d3 mo3 mo

Each row is one person (20 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).

11 couples: Parkinson's patient + healthy spouse control, sampled before/after a 4-week fibre diet · 11 families with 22 sampled people.

partnerPtpartnerPt
11 × partner×2
partner: CO10, PD10CO10 — partner · 1 samplePtCO10PD10 — partner · 1 samplePtPD10
partner: CO11, PD11CO11 — partner · 2 samplesPtCO11PD11 — partner · 2 samplesPtPD11
partner: CO12, PD12CO12 — partner · 2 samplesPtCO12PD12 — partner · 2 samplesPtPD12
partner: CO14, PD14CO14 — partner · 2 samplesPtCO14PD14 — partner · 2 samplesPtPD14
partner: CO2, PD2CO2 — partner · 2 samplesPtCO2PD2 — partner · 2 samplesPtPD2
partner: CO3, PD3CO3 — partner · 2 samplesPtCO3PD3 — partner · 2 samplesPtPD3
partner: CO4, PD4CO4 — partner · 2 samplesPtCO4PD4 — partner · 3 samplesPtPD4
partner: CO6, PD6CO6 — partner · 2 samplesPtCO6PD6 — partner · 3 samplesPtPD6
partner: CO7, PD7CO7 — partner · 2 samplesPtCO7PD7 — partner · 2 samplesPtPD7
partner: CO8, PD8CO8 — partner · 2 samplesPtCO8PD8 — partner · 2 samplesPtPD8
partner: CO9, PD9CO9 — partner · 2 samplesPtCO9PD9 — partner · 2 samplesPtPD9

partner · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 11 linked groups from explicit relations. 22 people in the project overall.

Families (11)
familymemberssamples
4partner×2SAMEA111547180 · SAMEA111547181 · SAMEA111547201 · SAMEA111547202 · SAMEA111547203
6partner×2SAMEA111547182 · SAMEA111547183 · SAMEA111547204 · SAMEA111547205 · SAMEA111547206
11partner×2SAMEA111547170 · SAMEA111547171 · SAMEA111547191 · SAMEA111547192
12partner×2SAMEA111547172 · SAMEA111547173 · SAMEA111547193 · SAMEA111547194
14partner×2SAMEA111547174 · SAMEA111547175 · SAMEA111547195 · SAMEA111547196
2partner×2SAMEA111547176 · SAMEA111547177 · SAMEA111547197 · SAMEA111547198
3partner×2SAMEA111547178 · SAMEA111547179 · SAMEA111547199 · SAMEA111547200
7partner×2SAMEA111547184 · SAMEA111547185 · SAMEA111547207 · SAMEA111547208
8partner×2SAMEA111547186 · SAMEA111547187 · SAMEA111547209 · SAMEA111547210
9partner×2SAMEA111547188 · SAMEA111547189 · SAMEA111547211 · SAMEA111547212
10partner×2SAMEA111547169 · SAMEA111547190

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 8.5%Faecalibacterium 6.7%Blautia_A 5.1%Alistipes 3.9%Roseburia 3.7%Vescimonas 3.3%Bacteroides 3.2%Ruminococcoides 3.1%Prevotella 2.7%Phocaeicola 2.3%Collinsella 2.1%Gemmiger 2.1%not assigned to a genus 3.8%other genera 49.6%

Genera, mean relative abundance over 41 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category44 100%
country44 100%44
health_condition44 100%44
subject_id44 100%44
age_at_collection_days44 100%44
collection_date44 100%44
detailed_location44 100%
diet44 100%44
diet_detail44 100%44
family_id44 100%44
family_role44 100%44
health_condition_detail44 100%44
latitude44 100%44
location_region44 100%44
location_site44 100%44
longitude44 100%44
sex44 100%44
timepoint_label44 100%44
Papers (1)
  • A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease. 2025 PMID 40180909 PMC11968880 own_data
Details
Archive description

Placeholder

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 external_curation.infant_catalog · “body_site_call gut”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
  • life stage sample.attr.host_age · “74 (n=18/44)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA111547169age_at_collection_days24106.5R10.70sample.attr.host_age66
SAMEA111547169collection_date2017-10-25R10.90biosample.attribute:collection_date2017-10-25
SAMEA111547169countryDER10.90sample.attr.geographic_location_country_and_or_seaGermany
SAMEA111547169dietomnivoreR10.90biosample.attribute:host_dietOmnivore [ecocore_00000082]
SAMEA111547169diet_detailOmnivore [ecocore_00000082]R10.90biosample.attribute:host_dietOmnivore [ecocore_00000082]
SAMEA111547169family_id10R10.85biosample.attribute:host family relationshiphost family relationship: 10
SAMEA111547169family_rolepartnerR30.60paper.body.Study design and participants[text] + biosample.attribute:host family relationshipN = 11 PD patients and their n = 11 healthy spouses (CO group)
SAMEA111547169health_conditionhealthy_controlR10.90biosample_attrHealthy [NCIT:C115935]
SAMEA111547169health_condition_detailHealthy [NCIT:C115935]R10.90sample.attr.host_disease_statusHealthy [NCIT:C115935]
SAMEA111547169latitude50.7014R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude50.701415 7.103049
SAMEA111547169location_regionNorth Rhine-WestphaliaR10.60biosample.attribute:geographic_location_latitude+geographic_location_longitude50.701415 7.103049
SAMEA111547169location_siteDepartment of Neurology, University of BonnR30.70paper.fulltext.methodsrecruited from the Department of Neurology, University of Bonn
SAMEA111547169longitude7.1030R10.90biosample.attribute:geographic_location_latitude+geographic_location_longitude50.701415 7.103049
SAMEA111547169sexfemaleR10.90sample.attr.host_sexfemale
SAMEA111547169subject_idCO10R10.85sample.attr.host_subject_idCO10
SAMEA111547169timepoint_labelT0R10.70sample.name_rule:aliasC10T0
Sequencing

44 runs over 44 samples · mean 19.10 Gbp per run (median 18.18 Gbp, total 840.41 Gbp; 44 runs with a base count) · layout PAIRED 44 · platform ILLUMINA 44 · models Illumina NovaSeq 6000 (44) · 93% of runs with a Sandpiper profile · first public 2024-07-30

Authors (11)

Bedarf JR first · Romano S · Heinzmann SS · Duncan A · Traka MH · Ng D · Segovia-Lizano D · Simon MC · Narbad A · Wüllner U · Hildebrand F last

Downloads

PRJEB57228.csv.gz (2.6 KB) · parquet (74.2 KB) — all 44 samples, every field with route and confidence · PRJEB57228_determinations.csv.gz (6.5 KB) — 704 evidence rows

Samples (44 · every field this project has values for · hover a cell for its source)
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