Gut microbiome and bone density in elderly, Shaanxi China
Cross-sectional study of 57 fecal samples from older men and women in Shaanxi, China, comparing gut microbiome composition and function across normal BMD, osteopenia, and osteoporosis groups. machine-written summary
57 samples · 57 runs · CN · Adult · 2019 · 6.66 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 285 sample values (country, health condition, health condition detail, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 228 sample values (antibiotic exposure, location locality, location site, subject id) · PMC9008261 |
| ○ 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 49 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 | 57 | 100% | ||||
| country | 57 | 100% | 57 | |||
| health_condition | 57 | 100% | 57 | |||
| subject_id | 57 | 100% | 57 | |||
| antibiotic_exposure | 57 | 100% | 57 | |||
| detailed_location | 57 | 100% | ||||
| health_condition_detail | 57 | 100% | 57 | |||
| location_locality | 57 | 100% | 57 | |||
| location_region | 57 | 100% | 57 | |||
| location_site | 57 | 100% | 57 | |||
| sex | 57 | 100% | 57 |
- Gut Microbiome Signature Are Correlated With Bone Mineral Density Alterations in the Chinese Elders. 2022 PMID 35433497 PMC9008261 own_data
Archive description
Intestinal flora metagenomics in older female (normal BMD group, osteopenia group and osteoporosis group) and male (normal BMD group, osteopenia group and osteoporosis group)
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 · “fecal sample Raw sequence”
- body site study.description · “Intestinal flora metagenomics in”
- 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 |
|---|---|---|---|---|---|---|
| SAMN12751402 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | none of the participants had a history of fractures |
| SAMN12751402 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Shaanxi |
| SAMN12751402 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:title | gut microbiota metagenome from normal BMD female |
| SAMN12751402 | health_condition_detail | gut microbiota metagenome from normal BMD female | R1 | 0.85 | biosample.attribute:title | gut microbiota metagenome from normal BMD female |
| SAMN12751402 | location_locality | Xi'an | R3 | 0.70 | paper.fulltext.methods | for residents near Xi’an (Xi’an, Shaanxi, China) |
| SAMN12751402 | location_region | Shaanxi | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Shaanxi |
| SAMN12751402 | location_site | Honghui Hospital, Xi'an Jiaotong University | R3 | 0.70 | paper.fulltext.methods | took place at Honghui Hospital, Xi’an Jiaotong University |
| SAMN12751402 | sex | female | R1 | 0.85 | biosample.attribute:title | gut microbiota metagenome from normal BMD female |
| SAMN12751402 | subject_id | SAMN12751402 | R3 | 0.70 | design.one_sample_per_subject:fulltext | 57 fecal samples (including 29 females and 28 males) from the previous 113 samples were |
Sequencing
57 runs over 57 samples · mean 6.64 Gbp per run (median 6.66 Gbp, total 378.67 Gbp; 57 runs with a base count) · layout PAIRED 57 · platform ILLUMINA 57 · models Illumina HiSeq 2500 (57) · 86% of runs with a Sandpiper profile · first public 2019-09-17
Authors (19)
Wang Y first · Gao X · Lv J · Zeng Y · Li Q · Wang L · Zhang Y · Gao W · Wang J last · Huang S first · Chaudhari DS · Shukla R · Kanani P · Zeidan RS · Lin Y · Burrow W · Mankowski RT · Jain S · Yadav H last
Downloads
PRJNA565546.csv.gz (2.5 KB) · parquet (72.8 KB) — all 57 samples, every field with route and confidence · PRJNA565546_determinations.csv.gz (4.0 KB) — 513 evidence rows