Gut metagenomes in T2D and T2D-CVD patients, Beijing, China
150 gut metagenome samples from adults in Beijing, China, comparing healthy, T2D, and T2D-CVD patients in a case-control design, linking Klebsiella pneumoniae virulence factors to T2D-CVD. machine-written summary
150 samples · 150 runs · CN · Adult · 2024 · 8.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 872 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 150 sample values (health condition detail) |
| – 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 138 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 | 150 | 100% | ||||
| country | 150 | 100% | 150 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 150 | 100% | 150 | |||
| detailed_location | 150 | 100% | ||||
| health_condition_detail | 150 | 100% | 150 | |||
| latitude | 150 | 100% | 150 | |||
| location_locality | 150 | 100% | 150 | |||
| longitude | 150 | 100% | 150 | |||
| location_region | 122 | 81% | 122 |
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979 unsure
Archive description
Human gut microbiota have been proved to associate with multiple human chronic disease. The gut microbiota has been found associated with pre-diabetes and type 2 diabetes, however the association between gut microbiota and the development of cardiovascular disease in T2D patients is not clear. By comparing the metagenomes of healthy, T2D and T2D-CVD patients, we found the enrichment of K. pneumoniae strains were associated with T2D-CVD patients by producing TMA and virulence factors.
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.description · “Human gut microbiota have been”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38862507 | collection_date | 2018-09 | R1 | 0.90 | biosample.attribute:collection_date | 2018-09 |
| SAMN38862507 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Beijing |
| SAMN38862507 | health_condition_detail | mixed_case_control: healthy individuals vs type 2 diabetes patients vs type 2 diabetes with cardiovascular disease | R4 | 0.40 | study.description | healthy, T2D and T2D-CVD patients |
| SAMN38862507 | latitude | 39.5400 | R1 | 0.90 | biosample.attribute:lat_lon | 39.54 N 116.23 E |
| SAMN38862507 | location_locality | Beijing | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Beijing |
| SAMN38862510 | location_region | Beijing | R1 | 0.60 | biosample.attribute:lat_lon | 39.54 N 116.26 E |
| SAMN38862507 | longitude | 116.2300 | R1 | 0.90 | biosample.attribute:lat_lon | 39.54 N 116.23 E |
Sequencing
150 runs over 150 samples · mean 9.01 Gbp per run (median 8.39 Gbp, total 1,351.37 Gbp; 150 runs with a base count) · layout PAIRED 150 · platform ILLUMINA 150 · models HiSeq X Ten (150) · 92% of runs with a Sandpiper profile · first public 2024-07-29
Authors (14)
Dong W first · Fan X · Guo Y · Wang S · Jia S · Lv N · Yuan T · Pan Y · Xue Y · Chen X · Xiong Q · Yang R · Zhao W · Zhu B last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1053635.csv.gz (5.0 KB) · parquet (76.9 KB) — all 150 samples, every field with route and confidence · PRJNA1053635_determinations.csv.gz (8.5 KB) — 1,022 evidence rows