Gut metagenome in gallstone disease vs controls, Shanghai
62 fecal samples from adults in Shanghai, China (Huadong hospital), comparing gut microbiota composition and function between gallstone disease patients (n=42) and healthy controls (n=20) in a case-control design. machine-written summary
62 samples · 62 runs · CN · Adult · 2023 · 12.32 Gbp / sample · cohort Identification of Intestinal Microbial Community i
One study deposited as 2 BioProjects (63 catalog samples together): PRJNA961998 · PRJNA999028 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 456 sample values (collection date, country, health condition, health condition detail, latitude, location region, location site, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 124 sample values (location locality, subject id) · PMC10453932 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 40 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 58 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 | 62 | 100% | ||||
| country | 62 | 100% | 62 | |||
| health_condition | 62 | 100% | 42 | 20 | ||
| subject_id | 62 | 100% | 62 | |||
| collection_date | 62 | 100% | 62 | |||
| detailed_location | 62 | 100% | ||||
| health_condition_detail | 62 | 100% | 42 | 20 | ||
| latitude | 62 | 100% | 62 | |||
| location_locality | 62 | 100% | 62 | |||
| location_region | 62 | 100% | 62 | |||
| location_site | 62 | 100% | 62 | |||
| longitude | 62 | 100% | 62 |
- Identification of Intestinal Microbial Community in Gallstone Patients with Metagenomic Next-Generation Sequencing. 2023 PMID 37627971 PMC10453932 own_data
Archive description
Gallstone disease (GD), also known as cholelithiasis, is a common disease which can stimulate the gallbladder mucosa and result in the acute/chronic cholecystitis or even the gallbladder carcinoma. Nowadays, the prevalence of GD still keeps a continuously rising tendency. However, the process of gallstone formation still remains unclear. The microecosystem of the human intestinal tract has been reported to participate in regulating the biological metabolism in human bodies. In recent years, some researches have suggested intestinal microbes might play an important role in gallstone pathogenesis, but few of them laid emphasis on the detailed function of those differential microbiota. The aim of this study is to figure out the composition and function of the intestinal microbiota in patients with GD. The results of our research revealed that the intestinal tract of GD patients harbored a particular microbial community. By comparison with the healthy individuals, we discovered the differential intestinal microbes and their functions in cholelithiasis subjects. Our study broaden the insight into the potential mechanism of how intestinal microbes affect the progression of gallstone to some extent. Meanwhile, our study also provide potential targets for prevention, diagnosis or treatment of GD.
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 · “Intestinal microbial community of”
- body site study.description · “of the human intestinal tract has been”
- 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 |
|---|---|---|---|---|---|---|
| SAMN36718900 | collection_date | 2018-06-10 | R1 | 0.90 | biosample.attribute:collection_date | 2018-06-10 |
| SAMN36718900 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN36718900 | health_condition | other_disease | R1 | 0.70 | sample.name_rule:alias | D1 |
| SAMN36718942 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN36718900 | health_condition_detail | Other disease / condition [sample-name token 'D'] | R1 | 0.70 | sample.name_rule:alias | D1 |
| SAMN36718942 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN36718900 | latitude | 31.2100 | R1 | 0.90 | biosample.attribute:lat_lon | 31.21 N 121.44 E |
| SAMN36718900 | location_locality | Shanghai | R3 | 0.70 | paper.fulltext.methods | Huadong Hospital affiliated with Fudan University, Shanghai, China |
| SAMN36718900 | location_region | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN36718900 | location_site | Huadong hospital | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN36718900 | longitude | 121.4400 | R1 | 0.90 | biosample.attribute:lat_lon | 31.21 N 121.44 E |
| SAMN36718900 | subject_id | SAMN36718900 | R3 | 0.70 | design.one_sample_per_subject:fulltext | A total of 62 fecal samples from 42 GD patients (16 males/26 females) and 20 healthy individuals (12 males/8 females) were included in our study. |
Sequencing
62 runs over 62 samples · mean 12.66 Gbp per run (median 12.32 Gbp, total 784.75 Gbp; 62 runs with a base count) · layout PAIRED 62 · platform ILLUMINA 62 · models HiSeq X Ten (62) · 94% of runs with a Sandpiper profile · first public 2023-07-28
Authors (12)
Ding L first · Wang S · Jiang W · Miao Y · Liu W · Yang F · Zhang J · Chi W · Liu T · Liu Y · Zhang Y · Zhao H last
Downloads
PRJNA999028.csv.gz (2.8 KB) · parquet (73.1 KB) — all 62 samples, every field with route and confidence · PRJNA999028_determinations.csv.gz (5.4 KB) — 620 evidence rows