US gut microbiome and cardiometabolic risk, cross-sectional
Cross-sectional study of 1,271 gut metagenome samples from adults in the USA (677 samples), examining the gut microbiome in relation to cardiometabolic risk within the Framingham Heart Study cohort. machine-written summary
1,271 samples · 1,271 runs · US · Adult · 2021 · 1.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 677 sample values (country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 594 sample values (country) · PMC10551180, PMC8680346 |
| ○ 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 1,157 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 | 1,271 | 100% | ||||
| country | 1,271 | 100% | 677 | 594 | ||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease. 2021 PMID 34915914 PMC8680346 own_data
- A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength. 2023 PMID 37810879 PMC10551180 own_data
Archive description
The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits</p><p>Available data sets:</p><p>1. Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol. This data set, consisting of metagenome FASTQ data from 594 of the 624 FHS participants used for analysis, was released in conjunction with PMID: 32544460. The reduced number posted is due to consent restrictions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “gut microbiome and relation to cardiometabolic risk”
- life stage study.description · “Framingham Heart Study (FHS) is a multi-generational observational study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34893827 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN21018939 | country | US | R3 | 0.70 | paper.fulltext.methods | recruited at six clinical sites in the U.S |
Sequencing
1,271 runs over 1,271 samples · mean 1.18 Gbp per run (median 1.13 Gbp, total 1,498.20 Gbp; 1,271 runs with a base count) · layout PAIRED 1,271 · platform ILLUMINA 1,271 · models Illumina HiSeq 2500 (1,271) · 91% of runs with a Sandpiper profile · first public 2021-09-23 – 2023-06-05
Authors (22)
Walker RL first · Vlamakis H · Lee JWJ · Besse LA · Xanthakis V · Vasan RS · Shaw SY · Xavier RJ last · Okoro PC first · Orwoll ES · Huttenhower C · Morgan X · Kuntz TM · McIver LJ · Dufour AB · Bouxsein ML · Langsetmo L · Farsijani S · Kado DM · Pacifici R · Sahni S · Kiel DP last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA758252.csv.gz (26.9 KB) · parquet (111.4 KB) — all 1,271 samples, every field with route and confidence · PRJNA758252_determinations.csv.gz (4.9 KB) — 1,271 evidence rows