Gut microbiome-metabolome and bone density, China
496 samples from pe machine-written summary
496 samples · 497 runs · CN · Adult · 2022 · 7.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,968 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,488 sample values (antibiotic exposure, location site, subject id) · PMC8966780, PMC9425034 |
| ○ 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 449 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 | 496 | 100% | ||||
| country | 496 | 100% | 496 | |||
| health_condition | 496 | 100% | 496 | |||
| subject_id | 496 | 100% | 496 | |||
| antibiotic_exposure | 496 | 100% | 496 | |||
| collection_date | 496 | 100% | 496 | |||
| detailed_location | 496 | 100% | ||||
| health_condition_detail | 496 | 100% | 496 | |||
| latitude | 496 | 100% | 496 | |||
| location_region | 496 | 100% | 496 | |||
| location_site | 496 | 100% | 496 | |||
| longitude | 496 | 100% | 496 | |||
| sex | 496 | 100% | 496 |
- Integration of the Human Gut Microbiome and Serum Metabolome Reveals Novel Biological Factors Involved in the Regulation of Bone Mineral Density. 2022 PMID 35372129 PMC8966780 own_data
- Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women. 2022 PMID 36051762 PMC9425034 own_data
Archive description
While the gut microbiome has been reported to play a role in bone metabolism, the individual species and underlying functional mechanisms have not yet been characterized. We conducted a systematic multi-omics analysis using paired metagenomic and untargeted serum metabolomic profiles from a large sample of 499 peri- and early post-menopausal women to identify the potential crosstalk between these biological factors which may be involved in the regulation of bone mineral density (BMD). Single omics association analyses identified 22 bacteria species and 17 serum metabolites for putative association with BMD. Among the identified bacteria, Bacteroidetes and Fusobacteria were negatively associated, while Firmicutes were positively associated. Several of the identified serum metabolites including 3-phenylpropanoic acid, mainly derived from dietary polyphenols, and glycolithocholic acid, a secondary bile acid, are metabolic byproducts of the microbiota. We further conducted a supervised integrative feature selection with respect to BMD and constructed the inter-omics partial correlation network. Although still requiring replication and validation in future studies, the findings from this exploratory analysis provide novel insights into the interrelationships between the gut microbiome and serum metabolome that may potentially play a role in skeletal remodeling processes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “paired metagenomic and untargeted serum metabolomic profiles”
- life stage study.description · “peri- and early post-menopausal women”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12907953 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | taken antibiotics or estrogens within three months of enrollment |
| SAMEA12907953 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA12907953 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA12907953 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | gut metagenome from healthy menopausal Chinese woman |
| SAMEA12907953 | health_condition_detail | gut metagenome from healthy menopausal Chinese woman | R1 | 0.85 | biosample.attribute:DESCRIPTION | gut metagenome from healthy menopausal Chinese woman |
| SAMEA12907953 | latitude | 23.1291 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 23.1291 113.2644 |
| SAMEA12907953 | location_region | Guangdong | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 23.1291 113.2644 |
| SAMEA12907953 | location_site | Third Affiliated Hospital of Southern Medical University | R3 | 0.70 | paper.fulltext.methods | Third Affiliated Hospital of Southern Medical University |
| SAMEA12907953 | longitude | 113.2644 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 23.1291 113.2644 |
| SAMEA12907953 | sex | female | R1 | 0.85 | biosample.attribute:DESCRIPTION | gut metagenome from healthy menopausal Chinese woman |
| SAMEA12907953 | subject_id | SAMEA12907953 | R3 | 0.75 | design.one_sample_per_subject:fulltext | Each subject provided stool and blood samples for metagenomic and metabolomics analyses, respectively. |
Sequencing
497 runs over 496 samples · mean 7.36 Gbp per run (median 7.02 Gbp, total 3,656.32 Gbp; 497 runs with a base count) · layout PAIRED 497 · platform ILLUMINA 497 · models Illumina HiSeq 4000 (497) · 91% of runs with a Sandpiper profile · first public 2022-03-03
Authors (21)
Greenbaum J first · Lin X · Su KJ · Gong R · Shen H · Shen J · Xiao HM · Deng HW last · Tian B first · Yao JH · Lv WQ · Jiang LD · Wang ZQ · Xu H · Xu LL · Cheng X · Qiu C · Luo Z · Zhao LJ · Yan Q · Zhang LS last
Downloads
PRJEB50761.csv.gz (14.0 KB) · parquet (92.0 KB) — all 496 samples, every field with route and confidence · PRJEB50761_determinations.csv.gz (31.9 KB) — 5,456 evidence rows