Gut microbiota before type 2 diabetes onset, China (case-control)
126 fecal samples from normoglycemic adults in China, nested case-control design, comparing baseline gut microbiota of those who later developed type 2 diabetes or prediabetes versus matched controls. machine-written summary
126 samples · 126 runs · CN · Age unknown · 2021 · 7.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 504 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 126 sample values (health condition detail) |
| ✓ Full text | 252 sample values (antibiotic exposure, location locality) · PMC7930378 |
| ○ 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 117 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 | 126 | 100% | ||||
| country | 126 | 100% | 126 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 126 | 100% | 126 | |||
| collection_date | 126 | 100% | 126 | |||
| detailed_location | 126 | 100% | ||||
| health_condition_detail | 126 | 100% | 126 | |||
| latitude | 126 | 100% | 126 | |||
| location_locality | 126 | 100% | 126 | |||
| longitude | 126 | 100% | 126 |
- The Fecal Microbiota Is Already Altered in Normoglycemic Individuals Who Go on to Have Type 2 Diabetes. 2021 PMID 33680988 PMC7930378 own_data
Archive description
Patients with type 2 diabetes have alterations in intestinal microbial composition. To investigate whether these changes occur before the impaired glucose regulation, we characterize gut microbiota in normoglycemic individuals who go on to develop type 2 diabetes. In a nested case-control study, we enrolled individuals with a similar living environment. In total, 341 normoglycemic individuals were followed for 5 years, including 30 who developed type 2 diabetes, 33 who developed prediabetes, and their matched controls. Fecal samples (126) collected at baseline underwent metagenomics sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host study.description · “341 normoglycemic individuals were followed”
- body site study.description · “Fecal samples (126) collected at baseline”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5335500 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | taken antibiotics within the past 3 months |
| SAMEA5335500 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMEA5335500 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA5335500 | health_condition_detail | mixed_case_control: Nested case-control study with three groups: incident T2D (n=30), incident prediabetes (n=33), and m | R4 | 0.50 | paper.abstract | 30 who developed T2D, 33 who developed prediabetes, and their matched controls |
| SAMEA5335500 | latitude | 22.5000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.5 114 |
| SAMEA5335500 | location_locality | Xi'an | R3 | 0.60 | paper.fulltext.results | residents of Xi'an, Shaanxi province in China |
| SAMEA5335500 | longitude | 114.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 22.5 114 |
Sequencing
126 runs over 126 samples · mean 7.69 Gbp per run (median 7.69 Gbp, total 968.99 Gbp; 126 runs with a base count) · layout PAIRED 126 · platform ILLUMINA 126 · models HiSeq X Ten (126) · 93% of runs with a Sandpiper profile · first public 2021-02-02
Authors (14)
Wang L first · Yu X · Xu X · Ming J · Wang Z · Gao B · Xing Y · Zhou J · Fu J · Liu T · Liu X · Garstka MA · Wang X · Ji Q last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB30611.csv.gz (4.0 KB) · parquet (75.0 KB) — all 126 samples, every field with route and confidence · PRJEB30611_determinations.csv.gz (5.3 KB) — 882 evidence rows