Gut microbiome and cholesterol metabolism in Kelowna, Canada
61 gut samples from adults and elderly individuals in Kelowna, Canada, examining mucus, microbiome, and metabolites in relation to luminal cholesterol metabolism and Akkermansia muciniphila. machine-written summary
61 samples · 81 runs · CA · Adult · 2023 · 0.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 366 sample values (age, bmi, collection date, country, location locality, sex) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 19 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 | 61 | 100% | ||||
| country | 61 | 100% | 61 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 61 | 100% | 61 | |||
| bmi | 61 | 100% | 61 | |||
| collection_date | 61 | 100% | 61 | |||
| detailed_location | 61 | 100% | ||||
| location_locality | 61 | 100% | 61 | |||
| sex | 61 | 100% | 61 |
Archive description
Our study delved into the gut's environment, encompassing the mucus, microbiome, and metabolites to explore its relationship with cholesterol metabolism.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “gut's environment, encompassing the mucus”
- life stage sample.attr.age · “29 (n=41/61)”
- life stage sample.attr.age · “69 (n=20/61)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39092986 | age_at_collection_days | 17166.8 | R1 | 0.70 | sample.attr.age | 47 |
| SAMN39092986 | bmi | 24.2 | R1 | 0.90 | sample.attr.bmi | 24.2 |
| SAMN39092986 | collection_date | 2020-09-13 | R1 | 0.90 | biosample.attribute:collection_date | 2020-09-13 |
| SAMN39092986 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Kelowna |
| SAMN39092986 | location_locality | Kelowna | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Kelowna |
| SAMN39092986 | sex | male | R1 | 0.90 | sample.attr.sex | male |
Sequencing
81 runs over 61 samples · mean 0.82 Gbp per run (median 0.18 Gbp, total 66.80 Gbp; 81 runs with a base count) · layout PAIRED 81 · platform ILLUMINA 81 · models Illumina MiSeq (61), NextSeq 2000 (20) · 23% of runs with a Sandpiper profile · first public 2023-12-24 – 2024-06-16
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1056258.csv.gz (2.9 KB) · parquet (72.3 KB) — all 61 samples, every field with route and confidence · PRJNA1056258_determinations.csv.gz (3.5 KB) — 366 evidence rows