Gut microbiome in first-episode psychosis, Helsinki, Finland
A case-control study of 66 samples from adults in Helsinki, Finland, comparing gut (and oral) microbiome composition between first-episode psychosis patients (n=26) and healthy controls (n=23). machine-written summary
66 samples · 66 runs · FI · Adult · 2024 · 1.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 347 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 17 sample values (health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 98 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: sequence archive and GMrepo disagree for 49 samples (e.g. FI vs US) — withheld.
The sources disagree on 49 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 49)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN38372396 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372397 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372398 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372399 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372400 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372401 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372402 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372403 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372404 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372405 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372406 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372407 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372408 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372409 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372410 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372411 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372412 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372413 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372414 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372415 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372416 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372417 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372418 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372419 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372420 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372421 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372422 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372423 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372424 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372425 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372426 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372427 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372428 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372429 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372430 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372431 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372432 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372433 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372434 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
| SAMN38372435 | country | FI (sequence archive) | US (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 47 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 | 66 | 100% | ||||
| country | 17 | 26% | 17 | |||
| health_condition | 49 | 74% | 49 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 66 | 100% | 66 | |||
| detailed_location | 66 | 100% | ||||
| health_condition_detail | 66 | 100% | 49 | 17 | ||
| latitude | 66 | 100% | 66 | |||
| location_locality | 66 | 100% | 66 | |||
| location_region | 66 | 100% | 66 | |||
| longitude | 66 | 100% | 66 |
- Dysregulation of Microbiota in Patients With First-Episode Psychosis Is Associated With Symptom Severity and Treatment Response. 2024 PMID 38061464 own_data
Archive description
The goal was to assess the compositional and functional differences of the gastrointestinal microbiome in first episode psychosis patients compared to healthy controls at baseline.
How this project entered the registry
Classified as human gut / stool / oral cavity / nasal / nasopharyngeal shotgun DNA metagenome of adult 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 · “Human oral and gut microbiome in first”
- body site study.description · “differences of the gastrointestinal microbiome in first”
- body site study.title · “Human oral and gut microbiome”
- body site sample.attr.isolation_source · “throat swab (n=17/66)”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38372396 | collection_date | 2013/2016 | R1 | 0.90 | biosample.attribute:collection_date | 2013/2016 |
| SAMN38372445 | country | FI | R1 | 0.90 | sample.attr.geo_loc_name | Finland: Helsinki |
| SAMN38372396 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN38372396 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN38372445 | health_condition_detail | mixed_case_control: first-episode psychosis patients vs healthy controls | R4 | 0.50 | study.description | first episode psychosis patients compared to healthy controls |
| SAMN38372396 | latitude | 60.1699 | R1 | 0.90 | biosample.attribute:lat_lon | 60.1699 N 24.9384 E |
| SAMN38372396 | location_locality | Helsinki | R1 | 0.85 | biosample.attribute:geo_loc_name | Finland: Helsinki |
| SAMN38372396 | location_region | Uusimaa | R1 | 0.60 | biosample.attribute:lat_lon | 60.1699 N 24.9384 E |
| SAMN38372396 | longitude | 24.9384 | R1 | 0.90 | biosample.attribute:lat_lon | 60.1699 N 24.9384 E |
Sequencing
66 runs over 66 samples · mean 1.63 Gbp per run (median 1.58 Gbp, total 107.37 Gbp; 66 runs with a base count) · layout SINGLE 66 · platform ILLUMINA 66 · models Illumina HiSeq 4000 (66) · 95% of runs with a Sandpiper profile · first public 2024-06-14
Authors (6)
Sen P first · Prandovszky E · Honkanen JK · Chen O · Yolken R · Suvisaari J last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, subject_id. Share metadata
Downloads
PRJNA1044118.csv.gz (2.6 KB) · parquet (73.1 KB) — all 66 samples, every field with route and confidence · PRJNA1044118_determinations.csv.gz (3.8 KB) — 462 evidence rows