Metagenome-guided culturomics of healthy gut microbes, Denmark
498 samples from healthy adult controls in Copenhagen, Denmark, used to combine whole-metagenome sequencing with culturomics to selectively enrich targeted gut microbial taxa and functions via medium modifications. machine-written summary
498 samples · 498 runs · DK · Age unknown · 2024 · 2.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 996 sample values (country, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,494 sample values (antibiotic exposure, health condition, health condition detail) · PMC11733127 |
| ○ 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 436 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 | 498 | 100% | ||||
| country | 498 | 100% | 498 | |||
| health_condition | 498 | 100% | 498 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 498 | 100% | 498 | |||
| detailed_location | 498 | 100% | ||||
| health_condition_detail | 498 | 100% | 498 | |||
| location_locality | 498 | 100% | 498 |
- Metagenome-guided culturomics for the targeted enrichment of gut microbes. 2025 PMID 39809763 PMC11733127 own_data
Archive description
Metagenome-guided culturomics for the targeted enrichment of gut microbes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.53. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
- body site study.description · “enrichment of gut microbes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43164958 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not having undergone antibiotic, antiviral, antifungal |
| SAMN43164958 | country | DK | R1 | 0.90 | sample.attr.geo_loc_name | Denmark: Copenhagen |
| SAMN43164958 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | selected to be considered healthy individual |
| SAMN43164958 | health_condition_detail | healthy individual, self-declared, no chronic condition | R3 | 0.70 | paper.fulltext.methods | selected to be considered healthy individual |
| SAMN43164958 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geo_loc_name | Denmark: Copenhagen |
Sequencing
498 runs over 498 samples · mean 2.38 Gbp per run (median 2.01 Gbp, total 1,185.78 Gbp; 498 runs with a base count) · layout PAIRED 498 · platform ILLUMINA 498 · models Illumina NovaSeq 6000 (498) · 88% of runs with a Sandpiper profile · first public 2024-12-05
Authors (5)
Armetta J first · Li SS · Vaaben TH · Vazquez-Uribe R · Sommer MOA last
Downloads
PRJNA1077691.csv.gz (11.4 KB) · parquet (87.3 KB) — all 498 samples, every field with route and confidence · PRJNA1077691_determinations.csv.gz (12.1 KB) — 2,490 evidence rows