PD, IBD, and control gut metagenomes, Florida, case-control
96 shotgun metagenome samples from PD, IBD, and healthy control individuals recruited at University of Florida clinics, case-control design comparing gut microbiome features across the two diseases. machine-written summary
96 samples · 96 runs · US · Age unknown · 2024 · 0.64 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,009 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| ✓ Abstract / description | 96 sample values (location site) |
| ✓ Full text | 288 sample values (antibiotic exposure, location locality, subject id) · PMC11923181 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
health condition: two sequence archives disagree for 4 samples (e.g. pregnancy_postpartum vs healthy_control) — withheld.
The sources disagree on 4 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 (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN40759275 | health condition | pregnancy_postpartum (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN40759292 | health condition | autoimmune_inflammatory (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN40759303 | health condition | healthy_control (sequence archive) | neurological_psychiatric (sequence archive) | withheld: neither value published |
| SAMN40759311 | health condition | healthy_control (sequence archive) | malnutrition (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 91 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 | 96 | 100% | ||||
| country | 96 | 100% | 96 | |||
| health_condition | 92 | 96% | 92 | |||
| subject_id | 96 | 100% | 96 | |||
| age_at_collection_days | 96 | 100% | 96 | |||
| antibiotic_exposure | 96 | 100% | 96 | |||
| collection_date | 96 | 100% | 96 | |||
| detailed_location | 96 | 100% | ||||
| health_condition_detail | 96 | 100% | 96 | |||
| latitude | 96 | 100% | 96 | |||
| location_locality | 96 | 100% | 96 | |||
| location_region | 96 | 100% | 96 | |||
| location_site | 96 | 100% | 96 | |||
| longitude | 96 | 100% | 96 | |||
| sex | 96 | 100% | 96 | |||
| medication | 81 | 84% | 81 | |||
| smoking_status | 68 | 71% | 68 |
- Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion. 2025 PMID 40108151 PMC11923181 own_data
Archive description
Parkinson's disease (PD) is a progressive neurodegenerative disease which currently cannot be prevented or cured. Epidemiological studies have revealed that a diagnosis of inflammatory bowel disease (IBD) is associated with an increased risk of developing PD later in life. The presence of gut dysbiosis has been documented in both PD and IBD patients, but it is currently unknown how alterations in the gut microbiome may contribute to the epidemiological link between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we performed the first joint analysis of 54 PD, 26 IBD, and 16 healthy control gut metagenomes recruited from clinics at the University of Florida. We collected stool and metadata, and conducted shallow shotgun metagenomic sequencing of fecal DNA. Raw sequences and metadata are provided here.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “We collected stool and metadata”
- life stage sample.attr.age · “67 (n=49/96)”
- life stage sample.attr.age · “63 (n=47/96)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40759226 | age_at_collection_days | 24471.8 | R1 | 0.70 | sample.attr.age | 67 |
| SAMN40759226 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | treatment with immunosuppressants or antibiotics within one month |
| SAMN40759226 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN40759226 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Florida |
| SAMN40759226 | health_condition | neurological_psychiatric | R1 | 0.60 | biosample_attr | PD |
| SAMN40759250 | health_condition | other_cancer | R1 | 0.90 | sample.attr.cancer_type | Prostate |
| SAMN40759226 | health_condition_detail | PD | R1 | 0.90 | sample.attr.diagnosis_by_ibd_type | PD |
| SAMN40759226 | latitude | 29.6520 | R1 | 0.90 | biosample.attribute:lat_lon | 29.6520 N 82.3250 W |
| SAMN40759226 | location_locality | University of Florida | R3 | 0.70 | paper.fulltext.methods | conducted at the University of Florida by a team |
| SAMN40759226 | location_region | Florida | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Florida |
| SAMN40759226 | location_site | University of Florida clinics | R4 | 0.45 | ena.study_description | recruited from clinics at the University of Florida |
| SAMN40759226 | longitude | -82.3250 | R1 | 0.90 | biosample.attribute:lat_lon | 29.6520 N 82.3250 W |
| SAMN40759226 | medication | nsaid_or_aspirin | R1 | 0.90 | biosample.attribute:nsaids | Y |
| SAMN40759228 | medication | other_medication | R1 | 0.90 | biosample.attribute:anti_inflammatories_non_nsaid | Y |
| SAMN40759230 | medication | laxative;nsaid_or_aspirin | R1 | 0.90 | biosample.attribute:laxatives | Y |
| SAMN40759226 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN40759227 | smoking_status | never | R1 | 0.90 | biosample.attribute:smoking | never |
| SAMN40759226 | subject_id | SAMN40759226 | R3 | 0.70 | design.one_sample_per_subject:fulltext | 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes |
Sequencing
96 runs over 96 samples · mean 0.77 Gbp per run (median 0.64 Gbp, total 73.83 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models Illumina NovaSeq X (96) · 95% of runs with a Sandpiper profile · first public 2024-05-26
Authors (9)
Krueger ME first · Boles JS · Simon ZD · Alvarez SD · McFarland NR · Okun MS · Zimmermann EM · Forsmark CE · Tansey MG last
Downloads
PRJNA1096686.csv.gz (4.5 KB) · parquet (77.2 KB) — all 96 samples, every field with route and confidence · PRJNA1096686_determinations.csv.gz (11.7 KB) — 1,393 evidence rows