Gut microbiome in gallstone patients, Shanghai, China
Case-control metagenomic study of 1 sample from a gallstone disease (cholelithiasis) patient at Huadong Hospital, Shanghai, China, comparing intestinal microbiota to healthy individuals. machine-written summary
1 samples · 1 runs · CN · Adult · 2023 · 15.19 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 | 6 sample values (collection date, country, latitude, location region, location site, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2 sample values (antibiotic exposure, location locality) · PMC10453932 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1 | 100% | ||||
| country | 1 | 100% | 1 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 1 | 100% | 1 | |||
| collection_date | 1 | 100% | 1 | |||
| detailed_location | 1 | 100% | ||||
| latitude | 1 | 100% | 1 | |||
| location_locality | 1 | 100% | 1 | |||
| location_region | 1 | 100% | 1 | |||
| location_site | 1 | 100% | 1 | |||
| longitude | 1 | 100% | 1 |
- Identification of Intestinal Microbial Community in Gallstone Patients with Metagenomic Next-Generation Sequencing. 2023 PMID 37627971 PMC10453932 own_data
Archive description
Gallstone disease is a significant health problem worldwide. It can result in pancreatitis, cholangitis and even gallbladder carcinoma. Nowadays, the prevalence of gallstone disease kept a continuously rising tendency. However, the process of gallstones 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. In this study, the metagenomic sequencing was used to analyze the diversity and functions of the intestinal microbiota in patients with gallstone disease. The results of our research revealed that the intestinal tract of cholelithiasis patients harbored a particular microbial community. By comparison with the healthy individuals, we discovered the differential intestinal microbes and the corresponding functions in cholelithiasis subjects. Our study broaden the insight into the potential mechanism of how intestinal microbes affect the progression of gallstones to some extent. Meanwhile, our study also provide potential targets for prevention, diagnosis or treatment of gallstone disease.
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 microbiome of gallstone”
- 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 |
|---|---|---|---|---|---|---|
| SAMN34376379 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods_results | None of the patients had taken antibiotics or probiotics within the previous 3 months prior to this study. |
| SAMN34376379 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN34376379 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN34376379 | latitude | 31.2100 | R1 | 0.90 | biosample.attribute:lat_lon | 31.21 N 121.44 E |
| SAMN34376379 | location_locality | Shanghai | R3 | 0.70 | paper.body.methods_results | Huadong Hospital affiliated with Fudan University, Shanghai, China. |
| SAMN34376379 | location_region | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN34376379 | location_site | Huadong hospital | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shanghai,Huadong hospital |
| SAMN34376379 | longitude | 121.4400 | R1 | 0.90 | biosample.attribute:lat_lon | 31.21 N 121.44 E |
Sequencing
1 runs over 1 samples · mean 15.19 Gbp per run (median 15.19 Gbp, total 15.19 Gbp; 1 runs with a base count) · layout PAIRED 1 · platform ILLUMINA 1 · models HiSeq X Ten (1) · 0% of runs with a Sandpiper profile · first public 2023-06-21
Authors (0)
No author record.
Downloads
PRJNA961998.csv.gz (907 B) · parquet (69.8 KB) — all 1 samples, every field with route and confidence · PRJNA961998_determinations.csv.gz (868 B) — 8 evidence rows