PREDICT 3 US22A: gut microbiome, US adults, cross-sectional
Cross-sectional cohort of 8,468 gut microbiome samples from adults in the USA, part of a multinational study (PREDICT 3) examining diet-pattern (omnivore, vegetarian, vegan) signatures in the gut microbiome. machine-written summary
8,469 samples · 8,469 runs · US · Adult · 2024 · 4.72 Gbp / sample · cohort Gut micro-organisms associated with health, nutrit
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16,938 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 8,469 sample values (subject id) · PMC11602726, PMC11726441, PMC12893911 |
| ○ 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 |
Genera, mean relative abundance over 7,619 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 | 8,469 | 100% | ||||
| country | 8,469 | 100% | 8,469 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 8,469 | 100% | 8,469 | |||
| collection_date | 8,469 | 100% | 8,469 |
- Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. 2024 PMID 39558133 PMC11602726 unsure
- Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals. 2025 PMID 39762435 PMC11726441 unsure
- Gut micro-organisms associated with health, nutrition and dietary interventions. 2026 PMID 41372407 PMC12893911 unsure
Archive description
PREDICT 3 US22A
How this project entered the registry
Classified as human gut / stool 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 external_curation.infant_catalog · “body_site_call gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA117311710 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMEA117311710 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA117311710 | subject_id | SAMEA117311710 | R3 | 0.70 | design.one_sample_per_subject:fulltext | n = 8,470 participants from the USA aged 18–90 years |
Sequencing
8,469 runs over 8,469 samples · mean 4.93 Gbp per run (median 4.72 Gbp, total 41,763.39 Gbp; 8,469 runs with a base count) · layout PAIRED 8,469 · platform ILLUMINA 8,469 · models unspecified (8,469) · 90% of runs with a Sandpiper profile · first public 2024-11-21 – 2024-11-23
Authors (45)
Manghi P first · Bhosle A · Wang K · Marconi R · Selma-Royo M · Ricci L · Asnicar F · Golzato D · Ma W · Hang D · Thompson KN · Franzosa EA · Nabinejad A · Tamburini S · Rimm EB · Garrett WS · Sun Q · Chan AT · Valles-Colomer M · Arumugam M · Bermingham KM · Giordano F · Davies R · Hadjigeorgiou G · Wolf J · Strowig T · Berry SE · Huttenhower C · Spector TD · Segata N · Song M last · Fackelmann G first · Carlino N · Heidrich V · Piccinno G · Piperni E · Arrè A · Bakker E · Creedon AC · Francis L · Capdevila Pujol J · Baldanzi G · Mladenovic K · Amati F · Ganesh S
Downloads
PRJEB75463.csv.gz (201.4 KB) · parquet (435.7 KB) — all 8,469 samples, every field with route and confidence · PRJEB75463_determinations.csv.gz (140.3 KB) — 25,407 evidence rows