Longitudinal gut microbiome in T2D development, Finland
332 stool samples from the Finnish METSIM cohort (archive notes 139 samples from 55 individuals at 2–3 time-points), studying microbiome stability and metabolic changes linked to type 2 diabetes development in a longitudinal design. machine-written summary
332 samples · 1,327 runs · FI · Age unknown · 2023 · 10.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,328 sample values (collection date, country, latitude, longitude) |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “139 stool samples from 55 individuals collected at 2–3 time-points per person”.
Genera, mean relative abundance over 309 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 | 332 | 100% | 332 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 332 | 100% | 332 | |||
| latitude | 332 | 100% | 332 | |||
| longitude | 332 | 100% | 332 |
Archive description
Microbiome stability and resilience are essential ecological characteristics that can be quantified via a serial collection of sequencing data. Longitudinal characterization of the host microbiome is essential to capture dynamic variance within an individual and to identify microbiome-mediated metabolic changes that could lead to a disease state. The samples include 139 human stool samples collected at two to three time-points in a subset of 55 individuals from the population-based METSIM cohort.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host study.description · “139 human stool samples”
- body site study.description · “139 human stool samples”
- body site run.scientific_name · “human oral metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114006769 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMEA114006769 | country | FI | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Finland |
| SAMEA114006769 | latitude | 62.8000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 62.8 27.6 |
| SAMEA114006769 | longitude | 27.6000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 62.8 27.6 |
Sequencing
1,327 runs over 332 samples · mean 2.51 Gbp per run (median 2.60 Gbp, total 3,332.36 Gbp; 1,327 runs with a base count) · layout PAIRED 1,327 · platform ILLUMINA 1,327 · models Illumina NovaSeq 6000 (1,327) · 84% of runs with a Sandpiper profile · first public 2023-07-24 – 2023-08-08
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB61646.csv.gz (8.1 KB) · parquet (81.2 KB) — all 332 samples, every field with route and confidence · PRJEB61646_determinations.csv.gz (6.6 KB) — 1,328 evidence rows