Gut bacteriome and virome in LADA, Denmark, case-control
239 gut samples from adults in Denmark, comparing individuals with LADA to non-diabetic controls and individuals with type 1 or type 2 diabetes, using a case-control design. machine-written summary
239 samples · 239 runs · DK · Adult · 2024 · 1.79 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 478 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11003976 |
| ○ 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 197 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 | 239 | 100% | ||||
| country | 239 | 100% | 239 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 239 | 100% | 239 |
- Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults. 2024 PMID 38594375 PMC11003976 own_data
Archive description
Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.
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 · “Characterization of the gut bacteriome and virome”
- body site study.description · “have an altered gut microbiota relative to”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “autoimmune diabetes in adults (LADA) is a”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114605061 | collection_date | 2013-03-01 | R1 | 0.90 | biosample.attribute:collection_date | 2013-03-01 |
| SAMEA114605061 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
Sequencing
239 runs over 239 samples · mean 1.78 Gbp per run (median 1.79 Gbp, total 425.86 Gbp; 239 runs with a base count) · layout PAIRED 239 · platform ILLUMINA 239 · models NextSeq 500 (239) · 84% of runs with a Sandpiper profile · first public 2024-01-15
Authors (15)
Poulsen CS first · Hesse D · Fernandes GR · Hansen TH · Kern T · Linneberg A · Van Espen L · Jørgensen T · Nielsen T · Alibegovic AC · Matthijnssens J · Pedersen O · Vestergaard H · Hansen T · Andersen MK last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB68363.csv.gz (6.5 KB) · parquet (78.4 KB) — all 239 samples, every field with route and confidence · PRJEB68363_determinations.csv.gz (3.7 KB) — 478 evidence rows