PREDICT 3 US cardiometabolic gut microbiome cohort (US21)
11,795 gut metagenome samples from participants in the USA, part of a cross-sectional study (PREDICT 3 US21) examining diet, anthropometric and health markers in relation to the gut microbiome. machine-written summary
11,797 samples · 11,797 runs · US · Age unknown · 2024 · 4.92 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 | 23,594 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 11,797 sample values (subject id) · PMC11602726, 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 10,603 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 | 0 | 0% | ||||
| country | 11,797 | 100% | 11,797 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 11,797 | 100% | 11,797 | |||
| collection_date | 11,797 | 100% | 11,797 |
- Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. 2024 PMID 39558133 PMC11602726 unsure
- Gut micro-organisms associated with health, nutrition and dietary interventions. 2026 PMID 41372407 PMC12893911 unsure
Archive description
PREDICT 3 US21
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115677894 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMEA115677894 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA115677894 | subject_id | SAMEA115677894 | R3 | 0.70 | design.one_sample_per_subject:fulltext | PREDICT3 US21 ( n = 11,798 participants from the USA aged 18–87 years |
Sequencing
11,797 runs over 11,797 samples · mean 5.29 Gbp per run (median 4.92 Gbp, total 62,414.92 Gbp; 11,797 runs with a base count) · layout PAIRED 11,797 · platform ILLUMINA 11,797 · models unspecified (11,797) · 90% of runs with a Sandpiper profile · first public 2024-06-10 – 2025-04-12
Authors (40)
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 · Baldanzi G · Bakker E · Piccinno G · Piperni E · Mladenovic K · Amati F · Arrè A · Ganesh S
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB75462.csv.gz (277.1 KB) · parquet (580.0 KB) — all 11,797 samples, every field with route and confidence · PRJEB75462_determinations.csv.gz (192.7 KB) — 35,391 evidence rows