Gut metagenomes, SCAPIS Sweden cohort, cross-sectional
9,817 gut metagenome samples from adults aged 50–65 in Sweden (SCAPIS Uppsala and Malmo), a cross-sectional study examining associations between physical activity, sedentary behavior, and gut microbiota composition and function. machine-written summary
9,819 samples · 9,977 runs · SE · Adult · 2023 · 7.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 54,065 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 2 sample values (collection date) |
| ✓ Full text | 9,819 sample values (subject id) · PMC10399955, PMC10410248, PMC10844941, PMC12234806, PMC12987725, PMC13099378, PMC13377033, PMC4744991, PMC9508139 |
| ○ 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 8,898 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 | 9,819 | 100% | ||||
| country | 9,819 | 100% | 9,819 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 9,819 | 100% | 9,819 | |||
| collection_date | 9,819 | 100% | 9,817 | 2 | ||
| detailed_location | 9,817 | 100% | ||||
| latitude | 9,817 | 100% | 9,817 | |||
| location_region | 9,817 | 100% | 9,817 | |||
| longitude | 9,817 | 100% | 9,817 | |||
| location_locality | 4,978 | 51% | 4,978 |
- The Swedish CArdioPulmonary BioImage Study: objectives and design. 2015 PMID 26096600 PMC4744991 own_data
- An online atlas of human plasma metabolite signatures of gut microbiome composition. 2022 PMID 36151114 PMC9508139 own_data
- OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study. 2023 PMID 36925044 PMC10410248 own_data
- Streptococcus Species Abundance in the Gut Is Linked to Subclinical Coronary Atherosclerosis in 8973 Participants From the SCAPIS Cohort. 2023 PMID 37435755 PMC10399955 own_data
- Accelerometer-based physical activity is associated with the gut microbiota in 8416 individuals in SCAPIS. 2024 PMID 38301483 PMC10844941 own_data
7 more
- The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study. 2025 PMID 40624247 PMC12234806
- Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation. 2026 PMID 41688638 PMC12987725
- Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals. 2026 PMID 41814006 PMC13099378
- Obstructive sleep apnea is associated with specific gut microbiota species and functions in the population-based Swedish CardioPulmonary bioImage Study (SCAPIS) 2022
- The association between the gut microbiome and 24-hour blood pressure measurements in the SCAPIS study 2023
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data. 2026 PMID 42103726 PMC13377033
- Streptococcus species abundance in the gut is linked to subclinical coronary atherosclerosis in 8973 participants from the SCAPIS cohort 2022
Archive description
SCAPIS is a prospective population-based study of 30,154 men and women, aged 50–65 years, living in six municipality regions in Sweden. It was designed with the main aim to improve risk prediction and understanding of cardiovascular disease, chronic pulmonary obstructive disease, and related metabolic disorders. After a pilot study in 2012, recruitment was initiated in 2014 and completed in 2018. Individuals were randomly recruited from the population register, with a participation rate of 50%. Fecal samples were obtained for 9,819 participants at SCAPIS-Uppsala and SCAPIS-Malmo. More information can be found at: https://doi.org/10.1111/joim.12384 and https://doi.org/10.1038/s41467-022-33050-0
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 study.title · “Human gut metagenomes of SCAPIS”
- body site study.description · “rate of 50%. Fecal samples were obtained”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “study of 30,154 men and women, aged”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113534647 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA113549008 | collection_date | 2014/2018 | R4 | 0.45 | ena.study_description | recruitment was initiated in 2014 and completed in 2018 |
| SAMEA113534647 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA113534647 | latitude | 55.6058 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.605833 13.035833 |
| SAMEA113534647 | location_locality | Malmö | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Malmö |
| SAMEA113534647 | location_region | Skane | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.605833 13.035833 |
| SAMEA113534647 | longitude | 13.0358 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.605833 13.035833 |
| SAMEA113534647 | subject_id | SAMEA113534647 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal metagenomics data were available for 4839 participants from Uppsala and 4980 from Malmö |
Sequencing
9,977 runs over 9,819 samples · mean 7.78 Gbp per run (median 7.50 Gbp, total 77,651.45 Gbp; 9,977 runs with a base count) · layout PAIRED 9,977 · platform ILLUMINA 9,977 · models Illumina NovaSeq 6000 (9,977) · 91% of runs with a Sandpiper profile · first public 2023-05-20 – 2023-06-18
Authors (70)
Bergström G first · Berglund G · Blomberg A · Brandberg J · Engström G · Engvall J · Eriksson M · de Faire U · Flinck A · Hansson MG · Hedblad B · Hjelmgren O · Janson C · Jernberg T · Johnsson · Johnsson Å · Johansson L · Lind L · Löfdahl CG · Melander O · Östgren CJ · Persson A · Persson M · Sandström A · Schmidt C · Söderberg S · Sundström J · Toren K · Waldenström A · Wedel H · Vikgren J · Fagerberg B · Rosengren A last · Dekkers KF first · Sayols-Baixeras S · Baldanzi G · Nowak C · Hammar U · Nguyen D · Varotsis G · Brunkwall L · Nielsen N · Eklund AC · Bak Holm J · Nielsen HB · Ottosson F · Lin YT · Ahmad S · Smith JG · Ärnlöv J · Orho-Melander M · Fall T last · Holm JB · Larsson A · Graells T · Gazolla Volpiano C · Meric G · Järhult JD · Tängdén T · Ludvigsson JF · Michaëlsson K · Kennedy B · Goulet L first · Plaza Oñate F · Famechon A · Quinquis B · Belda E · Prifti E · Le Chatelier E · Gautreau G last
Downloads
PRJEB51353.csv.gz (225.0 KB) · parquet (501.2 KB) — all 9,819 samples, every field with route and confidence · PRJEB51353_determinations.csv.gz (381.5 KB) — 63,886 evidence rows