Gut microbiome, bone density, postmenopausal women, China
Cross-sectional study of 385 gut metagenome samples from women in Shenzhen, China, investigating links between the gut microbiome and bone mineral density after menopause. machine-written summary
385 samples · 385 runs · CN · Adult · 2020 · 6.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,075 sample values (age, bmi, collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,155 sample values (antibiotic exposure, location site, sex) · PMC9631969 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: two sequence archives disagree for 4 samples (e.g. 59.3 vs 21659.3) — withheld.
The sources disagree on 4 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11311457 | age | 59.3 (sequence archive) | 21659.3 (sequence archive) | withheld: neither value published |
| SAMN11311466 | age | 59.3 (sequence archive) | 21659.3 (sequence archive) | withheld: neither value published |
| SAMN11311676 | age | 59.3 (sequence archive) | 21659.3 (sequence archive) | withheld: neither value published |
| SAMN11311781 | age | 59.3 (sequence archive) | 21659.3 (sequence archive) | withheld: neither value published |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 385 | 100% | ||||
| country | 385 | 100% | 385 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 385 | 100% | 385 | |||
| collection_date | 385 | 100% | 385 | |||
| detailed_location | 385 | 100% | ||||
| latitude | 385 | 100% | 385 | |||
| location_locality | 385 | 100% | 385 | |||
| location_region | 385 | 100% | 385 | |||
| location_site | 385 | 100% | 385 | |||
| longitude | 385 | 100% | 385 | |||
| sex | 385 | 100% | 385 | |||
| bmi | 384 | 100% | 384 | |||
| age_at_collection_days | 381 | 99% | 381 |
- Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women. 2021 PMID 36824343 PMC9631969 own_data
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery. 2026 PMID 41980943 PMC13079874 unsure
Archive description
The process that reabsorb calcium and phosphate from the bones instead of keeping these minerals just make our bones weaker, finally reach to the osteoporosis stage . The osteoporosis is a severe and common disease in elderly group, and it is the most common reason for fracture among the aged . Here we</p><p>carried out metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of gut microbiota change withe the bone loss .
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage study.title · “361 post-menopause women”
- life stage study.description · “osteoporosis is a severe and common disease in elderly group”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11311452 | age_at_collection_days | 20045.0 | R1 | 0.85 | sample.attr.host_age | 54.6 |
| SAMN11311452 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | none of the volunteers used antibiotics within one month prior |
| SAMN11311452 | bmi | 24.78 | R1 | 0.90 | sample.attr.host_body_mass_index | 24.77679525 |
| SAMN11311452 | collection_date | 2017-03-20 | R1 | 0.90 | biosample.attribute:collection_date | 2017-03-20 |
| SAMN11311452 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shenzhen |
| SAMN11311452 | latitude | 22.2700 | R1 | 0.90 | biosample.attribute:lat_lon | 22.27 N 113.46 E |
| SAMN11311452 | location_locality | Shenzhen | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shenzhen |
| SAMN11311452 | location_region | Guangdong | R1 | 0.60 | biosample.attribute:lat_lon | 22.27 N 113.46 E |
| SAMN11311452 | location_site | Shenzhen People's Hospital | R3 | 0.70 | paper.fulltext.methods | medical center of Shenzhen People's Hospital |
| SAMN11311452 | longitude | 113.4600 | R1 | 0.90 | biosample.attribute:lat_lon | 22.27 N 113.46 E |
| SAMN11311452 | sex | female | R3 | 0.70 | paper.fulltext.abstract | recruited 361 Chinese post-menopausal women |
Sequencing
385 runs over 385 samples · mean 7.04 Gbp per run (median 6.69 Gbp, total 2,711.53 Gbp; 385 runs with a base count) · layout SINGLE 385 · platform BGISEQ 385 · models BGISEQ-500 (385) · 0% of runs with a Sandpiper profile · first public 2020-01-06 – 2020-02-08
Authors (14)
Wang Q first · Sun Q · Li X · Wang Z · Zheng H · Ju Y · Guo R · Peng S · Jia H last · Kim J first · Kim N · Cha JH · Ma J · Lee I last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA530339.csv.gz (13.2 KB) · parquet (87.9 KB) — all 385 samples, every field with route and confidence · PRJNA530339_determinations.csv.gz (33.0 KB) — 4,230 evidence rows