Gut microbiome and cholesterol metabolism, Boston, USA
Cross-sectional study of 8 gut metagenome samples from Boston, USA, examining uncultured bacteria whose ismA-encoded cholesterol dehydrogenases convert cholesterol to coprostanol, linked to lower fecal and serum cholesterol. machine-written summary
8 samples · 8 runs · US · Age unknown · 2020 · 0.72 Gbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16 sample values (country, location locality) |
| ✓ Abstract / description | 8 sample values (health condition detail) |
| ✓ Full text | 8 sample values (collection date) · PMC7435688 |
| ○ 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 7 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 | 0 | 0% | ||||
| country | 8 | 100% | 8 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 8 | 100% | 8 | |||
| detailed_location | 8 | 100% | ||||
| health_condition_detail | 8 | 100% | 8 | |||
| location_locality | 8 | 100% | 8 |
- Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. 2020 PMID 32544460 PMC7435688 own_data
Archive description
Efforts to investigate how gut microbes influence human metabolism are critical to understand how this microbial community impacts human health and disease. For example, while the metabolism of cholesterol to the poorly absorbed sterol coprostanol by the human gut microbiota is hypothesized to play a role in modulating human serum cholesterol concentrations, there is a gap in knowledge regarding which enzymes and microbes are responsible for this metabolism in the human gut. Here we identify a novel group of cholesterol oxidoreductase enzymes in the gut that are involved in the metabolism of cholesterol to cholestenone, an on-pathway intermediate to the final product coprostanol. These enzymes are prevalent in geographically diverse gut microbiota and are encoded by a clade of uncultured microorganisms. Individuals with coprostanol-forming microbes have significantly lower concentrations of fecal cholesterol and lower concentrations of serum total cholesterol (-0.14 mmol/L in TC 95% CI: -0.27, -0.02) and triglycerides. Thus, the metabolism of cholesterol by an uncultured clade of microorganisms may play an important role in modulating both intestinal and serum cholesterol concentrations, directly impacting human health.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14601846 | collection_date | 2016/2019 | R3 | 0.70 | paper.fulltext.methods | agreed to participate in the microbiome analysis at exam 3 (2016-2019) |
| SAMN14601846 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston |
| SAMN14601846 | health_condition_detail | mixed_case_control: Study compares individuals with coprostanol-forming microbes (cases) versus those without (controls) | R4 | 0.50 | study.description | Individuals with coprostanol-forming microbes have significantly lower |
| SAMN14601846 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston |
Sequencing
8 runs over 8 samples · mean 0.74 Gbp per run (median 0.72 Gbp, total 5.94 Gbp; 8 runs with a base count) · layout PAIRED 8 · platform ILLUMINA 8 · models Illumina HiSeq 2500 (8) · 88% of runs with a Sandpiper profile · first public 2020-06-18
Authors (11)
Kenny DJ first · Plichta DR · Shungin D · Koppel N · Hall AB · Fu B · Vasan RS · Shaw SY · Vlamakis H · Balskus EP · Xavier RJ last
Downloads
PRJNA559861.csv.gz (1.1 KB) · parquet (69.6 KB) — all 8 samples, every field with route and confidence · PRJNA559861_determinations.csv.gz (904 B) — 32 evidence rows