Gut microbiome, visceral fat, sleeve gastrectomy, Shanghai
76 stool samples from adults in Shanghai, China, comparing obese patients, healthy controls, and obese patients after sleeve gastrectomy, in a case-control study of gut microbiome and visceral fat. machine-written summary
76 samples · 76 runs · CN · Age unknown · 2020 · 6.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 758 sample values (collection date, country, health condition, health condition detail, intervention, intervention detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 76 sample values (location site) · PMC7528071 |
| ✓ Supplementary tables | 118 sample values (age, bmi, sex) |
| – 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population obesity · Laparoscopic sleeve gastrectomy, sampled pre- and post-surgery
“14 subjects underwent laparoscopic sleeve gastrectomy” — abstract:33033580 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
14 of 62 people sampled more than once (28 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 70 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 | 76 | 100% | ||||
| country | 76 | 100% | 76 | |||
| health_condition | 76 | 100% | 76 | |||
| subject_id | 76 | 100% | 76 | |||
| collection_date | 76 | 100% | 76 | |||
| detailed_location | 76 | 100% | ||||
| health_condition_detail | 76 | 100% | 76 | |||
| latitude | 76 | 100% | 76 | |||
| location_locality | 76 | 100% | 76 | |||
| location_region | 76 | 100% | 76 | |||
| location_site | 76 | 100% | 76 | |||
| longitude | 76 | 100% | 76 | |||
| sex | 58 | 76% | 58 | |||
| timepoint_label | 46 | 61% | 46 | |||
| age_at_collection_days | 30 | 39% | 30 | |||
| bmi | 30 | 39% | 30 | |||
| intervention | 14 | 18% | 14 | |||
| intervention_detail | 14 | 18% | 14 |
- A metagenome-wide association study of gut microbiome and visceral fat accumulation. 2020 PMID 33033580 PMC7528071 own_data
- MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations. 2025 PMID 40171165 PMC11958714 unsure
Archive description
Stool samples from 31 patients with obesity, 30 healthy controls and 14 subjects after sleeve gastrectomy were collected and performed metagenomic shotgun sequencing. The gut microbiome was analysed for investigating the relationship with visceral fate and sleeve gastrectomy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “31 patients with obesity”
- body site study.description · “Stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13684584 | age_at_collection_days | 11323 | R2 | 0.85 | paper.supp.mmc9.xlsx[32obese30healthy!age] | 31 |
| SAMN13684584 | bmi | 18.6 | R2 | 0.85 | paper.supp.mmc9.xlsx[32obese30healthy!BMI] | 18.6 |
| SAMN13684538 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN13684538 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN13684538 | health_condition | obesity | R1 | 0.90 | biosample_attr | Obesity |
| SAMN13684539 | health_condition | obesity | R1 | 0.70 | sample.name_rule:attr:grouping | After |
| SAMN13684538 | health_condition_detail | Obesity | R1 | 0.90 | sample.attr.grouping | Obesity |
| SAMN13684539 | intervention | surgery | R1 | 0.90 | biosample.attribute:grouping | grouping: After |
| SAMN13684539 | intervention_detail | sample taken after sleeve gastrectomy | R1 | 0.90 | biosample.attribute:grouping | grouping: After |
| SAMN13684538 | latitude | 31.1800 | R1 | 0.90 | biosample.attribute:lat_lon | 31.18 N 121.42 E |
| SAMN13684538 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN13684538 | location_region | Shanghai Shi | R1 | 0.60 | biosample.attribute:lat_lon | 31.18 N 121.42 E |
| SAMN13684538 | location_site | Shanghai Jiao Tong University Affiliated Sixth People's Hospital | R3 | 0.70 | paper.fulltext.methods | recruited at Shanghai Jiao Tong University Affiliated Sixth People's Hospital |
| SAMN13684538 | longitude | 121.4200 | R1 | 0.90 | biosample.attribute:lat_lon | 31.18 N 121.42 E |
| SAMN13684538 | sex | female | R2 | 0.75 | paper.supp.mmc9.xlsx[pre- and post-operative ][Gender] | female |
| SAMN13684538 | subject_id | 434 | R1 | 0.70 | sample.name_rule:alias | DS434S1 |
| SAMN13684538 | timepoint_label | S1 | R1 | 0.70 | sample.name_rule:alias | DS434S1 |
Sequencing
76 runs over 76 samples · mean 6.84 Gbp per run (median 6.77 Gbp, total 519.46 Gbp; 76 runs with a base count) · layout PAIRED 76 · platform ILLUMINA 76 · models Illumina HiSeq 1500 (76) · 92% of runs with a Sandpiper profile · first public 2020-10-01
Authors (27)
Nie X first · Chen J · Ma X · Ni Y · Shen Y · Yu H · Panagiotou G · Bao Y last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Shi H first · Li J last
Downloads
PRJNA597839.csv.gz (3.4 KB) · parquet (75.9 KB) — all 76 samples, every field with route and confidence · PRJNA597839_determinations.csv.gz (8.1 KB) — 952 evidence rows