Gut metagenome in type 1 diabetes with albuminuria, Denmark
Case-control study of 206 faecal samples from Denmark, comparing gut metagenomes of individuals with type 1 diabetes (stratified by albuminuria status) to healthy controls, using whole genome sequencing for taxonomic and functional profiling. machine-written summary
206 samples · 206 runs · DK · Age unknown · 2022 · 11.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,030 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 206 sample values (location site) |
| ✓ Full text | 206 sample values (antibiotic exposure) · PMC9755599 |
| ○ 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 187 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 | 206 | 100% | 206 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 206 | 100% | 206 | |||
| collection_date | 206 | 100% | 206 | |||
| detailed_location | 206 | 100% | ||||
| latitude | 206 | 100% | 206 | |||
| location_region | 206 | 100% | 206 | |||
| location_site | 206 | 100% | 206 | |||
| longitude | 206 | 100% | 206 |
- Multiomics signatures of type 1 diabetes with and without albuminuria. 2022 PMID 36531462 PMC9755599 own_data
Archive description
In a cross-sectional study we included 161 individuals with type 1 diabetes and 50 healthy control individuals. Individuals with type 1 diabetes were categorised into three groups according to historically measured albuminuria: (1) normoalbuminuria (<3.39 mg/mmol) (2) microalbuminuria (3.39–33.79 mg/mmol) and (3) macroalbuminuria (≥33.90 mg/ mmol). From faecal samples, the gut metagenome was analyzed by whole genome sequencing, comparing both taxonomical and functional profiles
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “From faecal samples, the gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8997067 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | treatment with systemic antibiotics in the 3 months prior to recruitment |
| SAMEA8997067 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA8997067 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
| SAMEA8997067 | latitude | 55.6933 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.69326 12.563258 |
| SAMEA8997067 | location_region | Capital Region | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.69326 12.563258 |
| SAMEA8997067 | location_site | Steno Diabetes Center Copenhagen | R4 | 0.50 | paper.abstract | One hundred and sixty-one individuals with T1D and 50 HC were recruited at the Steno Diabetes Center Copenhagen, Denmark. |
| SAMEA8997067 | longitude | 12.5633 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 55.69326 12.563258 |
Sequencing
206 runs over 206 samples · mean 11.13 Gbp per run (median 11.13 Gbp, total 2,292.19 Gbp; 206 runs with a base count) · layout PAIRED 206 · platform ILLUMINA 206 · models Illumina MiSeq (206) · 91% of runs with a Sandpiper profile · first public 2022-06-21
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
PRJEB46664.csv.gz (5.5 KB) · parquet (77.4 KB) — all 206 samples, every field with route and confidence · PRJEB46664_determinations.csv.gz (8.5 KB) — 1,442 evidence rows