Gut microbiota in lean/obese adults with T2D, Shanghai
Cross-sectional study of 182 gut metagenome samples from adult subjects in Shanghai, China, comparing lean and abdominally obese individuals with and without type 2 diabetes. machine-written summary
182 samples · 182 runs · CN · Adult · 2021 · 4.72 Gbp / sample · cohort Risk assessment with gut microbiome and metabolite
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,638 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 364 sample values (antibiotic exposure, location site) · PMC11730835, PMC12522779, PMC12763994, PMC8373164, PMC9746350 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 167 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 | 182 | 100% | ||||
| country | 182 | 100% | 182 | |||
| health_condition | 182 | 100% | 182 | |||
| subject_id | 182 | 100% | 182 | |||
| antibiotic_exposure | 182 | 100% | 182 | |||
| collection_date | 182 | 100% | 182 | |||
| detailed_location | 182 | 100% | ||||
| health_condition_detail | 182 | 100% | 182 | |||
| latitude | 182 | 100% | 182 | |||
| location_locality | 182 | 100% | 182 | |||
| location_region | 182 | 100% | 182 | |||
| location_site | 182 | 100% | 182 | |||
| longitude | 182 | 100% | 182 |
- Decreased Abundance of Akkermansia muciniphila Leads to the Impairment of Insulin Secretion and Glucose Homeostasis in Lean Type 2 Diabetes. 2021 PMID 34085773 PMC8373164 own_data
- Risk assessment with gut microbiome and metabolite markers in NAFLD development. 2022 PMID 35675435 PMC9746350 unsure
- Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease. 2025 PMID 39810263 PMC11730835 unsure
- Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome. 2025 PMID 41087898 PMC12522779 unsure
- Characterization of the gut virome in patients with nonalcoholic fatty liver disease. 2025 PMID 41316248 PMC12763994 unsure
Archive description
Numerous studies have revealed the association of gut microbiota to the development of two human metabolic disorders, obesity and type 2 diabetes (T2D). Medical research has found a positive correlation between the two diseases, and previous metagenomic studies have reported potential metagenomic markers linked with them. However, few metagenomic studies have been designed to investigate two related diseases interactively. Our objective here is to investigate how the gut microbiota contribute to the development and the differentiation of people into different metabolic status of obesity and T2D, by looking into 182 subjects from lean individuals with normal glucose tolerance (NL), abdominally obese individuals with normal glucose tolerance (NAO), lean individuals with T2D (TL) and abdominally obese individuals with T2D (TAO).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Human gut microbiota”
- body site run.scientific_name · “gut metagenome”
- body site study.title · “Human gut microbiota”
- life stage study.description · “lean individuals with normal glucose tolerance”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17126167 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic treatment within 3 months before sample collection |
| SAMN17126167 | collection_date | 2016-04 | R1 | 0.90 | biosample.attribute:collection_date | 2016-04 |
| SAMN17126167 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN17126167 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | NGT-lean (NL) group |
| SAMN17126167 | health_condition_detail | NGT-lean (NL) group | R1 | 0.85 | biosample.attribute:description | NGT-lean (NL) group |
| SAMN17126167 | latitude | 31.1883 | R1 | 0.90 | biosample.attribute:lat_lon | 31.1883 N 121.4368 E |
| SAMN17126167 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN17126167 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.1883 N 121.4368 E |
| SAMN17126167 | location_site | Shanghai Nicheng cohort study | R3 | 0.70 | paper.fulltext.methods | Shanghai Nicheng cohort study |
| SAMN17126167 | longitude | 121.4368 | R1 | 0.90 | biosample.attribute:lat_lon | 31.1883 N 121.4368 E |
| SAMN17126167 | subject_id | NL_104 | R1 | 0.70 | sample.name_rule:title | Subject ID NL_104 from NGT-lean (NL) group |
Sequencing
182 runs over 182 samples · mean 4.76 Gbp per run (median 4.72 Gbp, total 866.64 Gbp; 182 runs with a base count) · layout PAIRED 182 · platform ILLUMINA 182 · models Illumina HiSeq 4000 (182) · 92% of runs with a Sandpiper profile · first public 2021-05-02
Authors (49)
Zhang J first · Ni Y · Qian L · Fang Q · Zheng T · Zhang M · Gao Q · Zhang Y · Ni J · Hou X · Bao Y · Kovatcheva-Datchary P · Xu A · Li H · Panagiotou G · Jia W last · Leung H first · Long X · Nychas E · Siliceo SL · Pohl D · Hanhineva K · Liu Y · Nielsen HB · Belda E · Clément K · Loomba R · Marfil-Sánchez A · Chen X · Mirhakkak M · Nieuwdorp M · Zheng N first · Wang D · Xing G · Gao Y · Li S · Liu J · Kang J · Sha S · Cheng L · Fan S · Yu J · Yan Q · Jiang C last · Wang L first · Liu M · Yuan Q · Chen H · Mao S
Downloads
PRJNA686835.csv.gz (5.8 KB) · parquet (78.7 KB) — all 182 samples, every field with route and confidence · PRJNA686835_determinations.csv.gz (14.5 KB) — 2,002 evidence rows