Gut virome in T2D and diabetic nephropathy, Sichuan, China
Case-control study of 132 fecal samples from adults in Sichuan province, China, comparing gut virome and 16S profiles across type 2 diabetes, diabetic nephropathy, and healthy controls. machine-written summary
132 samples · 132 runs · CN · Adult · 2023 · 10.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 578 sample values (collection date, country, health condition, health condition detail, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 396 sample values (antibiotic exposure, location site, subject id) · PMC10291934 |
| ✓ Supplementary tables | 82 sample values (health condition, health condition detail) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 119 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 | 132 | 100% | ||||
| country | 132 | 100% | 132 | |||
| health_condition | 132 | 100% | 91 | 41 | ||
| subject_id | 132 | 100% | 132 | |||
| antibiotic_exposure | 132 | 100% | 132 | |||
| collection_date | 132 | 100% | 132 | |||
| detailed_location | 132 | 100% | ||||
| health_condition_detail | 132 | 100% | 91 | 41 | ||
| location_region | 132 | 100% | 132 | |||
| location_site | 132 | 100% | 132 |
- Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy. 2023 PMID 37349979 PMC10291934 own_data
- Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut. 2025 PMID 40210629 PMC11986028 unsure
Archive description
Human gut virome and 16S sequencing
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”
- body site study.description · “Human gut virome and 16S”
- 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 |
|---|---|---|---|---|---|---|
| SAMN31628617 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | had received antibiotics, probiotics or immunosuppressive medications in the previous 3 months |
| SAMN31628617 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN31628617 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Sichuan province |
| SAMN31628617 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:library_names | Control-1 |
| SAMN31628659 | health_condition | type2_diabetes | R2 | 0.85 | paper.supp.Supplementary Table S1.xls[Table S1!Group] | T2D-Ne |
| SAMN31628617 | health_condition_detail | Control | R1 | 0.70 | sample.name_rule:library_names | Control-1 |
| SAMN31628659 | health_condition_detail | T2D-Ne | R2 | 0.85 | paper.supp.Supplementary Table S1.xls[Table S1!Group] | T2D-Ne |
| SAMN31628617 | location_region | Sichuan | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Sichuan province |
| SAMN31628617 | location_site | Affiliated Hospital of Chengdu University of Traditional Chinese Medicine | R3 | 0.70 | paper.fulltext.methods | Affiliated Hospital of Chengdu University of Traditional Chinese Medicine |
| SAMN31628617 | subject_id | SAMN31628617 | R3 | 0.70 | design.one_sample_per_subject:fulltext | A total of 132 participants were enrolled. |
Sequencing
132 runs over 132 samples · mean 10.51 Gbp per run (median 10.11 Gbp, total 1,387.00 Gbp; 132 runs with a base count) · layout PAIRED 132 · platform ILLUMINA 132 · models Illumina NovaSeq 6000 (132) · 90% of runs with a Sandpiper profile · first public 2023-06-25
Authors (30)
Fan G first · Cao F · Kuang T · Yi H · Zhao C · Wang L · Peng J · Zhuang Z · Xu T · Luo Y · Xie Y · Li H · Zhang K · Zeng Y · Zhang X · Peng S · Qiu X · Zhou D · Liang H · Yang B · Kang J · Liu Y · Zhang Y last · Park JW first · Yun YE · Cho JA · Yoon SI · In SA · Park EJ · Kim MS last
Downloads
PRJNA891875.csv.gz (4.6 KB) · parquet (76.6 KB) — all 132 samples, every field with route and confidence · PRJNA891875_determinations.csv.gz (7.4 KB) — 1,056 evidence rows