Adult-onset T1D vs healthy gut metagenome, China
218 gut metagenome samples from adults in Changsha and Pingjiang, China, comparing adult-onset type 1 diabetes patients with healthy controls, in a case-control design. machine-written summary
218 samples · 218 runs · CN · Adult · 2023 · 6.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,436 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 436 sample values (antibiotic exposure, subject id) · PMC10430172 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 308 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 201 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 | 218 | 100% | ||||
| country | 218 | 100% | 218 | |||
| health_condition | 218 | 100% | 64 | 154 | ||
| subject_id | 218 | 100% | 218 | |||
| antibiotic_exposure | 218 | 100% | 218 | |||
| collection_date | 218 | 100% | 218 | |||
| detailed_location | 218 | 100% | ||||
| health_condition_detail | 218 | 100% | 64 | 154 | ||
| latitude | 218 | 100% | 218 | |||
| location_locality | 218 | 100% | 218 | |||
| location_region | 218 | 100% | 218 | |||
| longitude | 218 | 100% | 218 |
- Distinct signatures of gut microbiota and metabolites in different types of diabetes: a population-based cross-sectional study. 2023 PMID 37593224 PMC10430172 own_data
Archive description
Patients with adult-onset T1D showed distinct changes in the composition and function of gut microbiome.
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 · “human gut metagenome Raw sequence”
- body site study.description · “and function of gut microbiome.”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “Patients with adult -onset T1D showed”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31421935 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of probiotics, prebiotics or antibiotics within one month |
| SAMN31421935 | collection_date | 2021-10-09 | R1 | 0.90 | biosample.attribute:collection_date | 2021-10-09 |
| SAMN31421935 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Pingjiang |
| SAMN31421935 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:library_names | H1 |
| SAMN31421999 | health_condition | type1_diabetes | R2 | 0.75 | external.gmrepo source | phenotype: Diabetes Mellitus, Type 1 |
| SAMN31421935 | health_condition_detail | H | R1 | 0.70 | sample.name_rule:library_names | H1 |
| SAMN31421999 | health_condition_detail | Diabetes Mellitus, Type 1 | R2 | 0.75 | external.gmrepo source | phenotype: Diabetes Mellitus, Type 1 |
| SAMN31421935 | latitude | 28.7100 | R1 | 0.90 | biosample.attribute:lat_lon | 28.71 N 113.58 E |
| SAMN31421935 | location_locality | Pingjiang | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Pingjiang |
| SAMN31421935 | location_region | Hunan | R1 | 0.60 | biosample.attribute:lat_lon | 28.71 N 113.58 E |
| SAMN31421935 | longitude | 113.5800 | R1 | 0.90 | biosample.attribute:lat_lon | 28.71 N 113.58 E |
| SAMN31421935 | subject_id | SAMN31421935 | R3 | 0.70 | design.one_sample_per_subject:fulltext | A total of 218 study subjects were recruited from February 2019 to April 2022 |
Sequencing
218 runs over 218 samples · mean 6.13 Gbp per run (median 6.05 Gbp, total 1,336.84 Gbp; 218 runs with a base count) · layout PAIRED 218 · platform ILLUMINA 218 · models Illumina NovaSeq 6000 (218) · 92% of runs with a Sandpiper profile · first public 2023-09-30
Authors (18)
Hu J first · Ding J · Li X · Li J · Zheng T · Xie L · Li C · Tang Y · Guo K · Huang J · Liu S · Yan J · Peng W · Hou C · Wen L · Xu A · Zhou Z · Xiao Y last
Downloads
PRJNA893406.csv.gz (6.8 KB) · parquet (80.9 KB) — all 218 samples, every field with route and confidence · PRJNA893406_determinations.csv.gz (16.4 KB) — 2,180 evidence rows