OCA Effects on Human Gut Microbiome, USA Intervention Study
64 samples from healthy US participants in an intervention study examining how the FXR agonist obeticholic acid (OCA), via bile acid suppression, affects gut microbiome composition. machine-written summary
64 samples · 64 runs · US · Age unknown · 2018 · 8.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 384 sample values (collection date, country, intervention, intervention detail, subject id, timepoint) |
| ✓ Abstract / description | 128 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC6279623 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention · arms resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population healthy_control · Obeticholic acid (FXR agonist) treatment, before/after
“Suppression of endogenous bile acid synthesis by OCA treatment” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
22 of 24 people sampled more than once (62 samples; median 3, up to 3 per person). Schedule stated by the source: “stool at baseline (day 0), day 17 (end of dosing), day 37 (end of study)” (time origin: treatment_start); stated follow-up 37 d.
Genera, mean relative abundance over 58 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 | 64 | 100% | ||||
| country | 64 | 100% | 64 | |||
| health_condition | 64 | 100% | 64 | |||
| subject_id | 64 | 100% | 64 | |||
| collection_date | 64 | 100% | 64 | |||
| health_condition_detail | 64 | 100% | 64 | |||
| intervention | 64 | 100% | 64 | |||
| intervention_detail | 64 | 100% | 64 | |||
| timepoint_label | 64 | 100% | 64 |
- FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid. 2018 PMID 30144429 PMC6279623 own_data
Archive description
Bile acids play a role in regulating the gut microbiome by inhibiting bacterial growth. Using the FXR agonist obeticholic acid (OCA), we investigated the impact of modulating bile acid synthesis on the human gut microbiome. Suppression of endogenous bile acid synthesis by OCA treatment led to a reversible induction of Gram-positive bacterial taxa that are consumed in the diet, found in the small intestine, and sensitive to growth inhibition by bile acids in vitro. OCA treatment enhanced the representation of genomic pathways involved in DNA synthesis and amino acid metabolism, suggesting greater growth of these bacterial taxa. Indeed, mice fed OCA had reduced endogenous bile acid levels and an increased proportion of Firmicutes, specifically in the small intestine. These results demonstrate the dynamic interplay between bile acids and the human small intestinal microbiome, and suggest opportunities for microbiome biomarker discovery as well as novel modalities to engineer the human microbiome via FXR activation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08475326 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN08475326 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN08475326 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | We performed a phase I study in 24 healthy volunteers given OCA (5, 10, or 25 mg/d for 17 days). |
| SAMN08475326 | health_condition_detail | healthy volunteers | R4 | 0.50 | paper.abstract | We performed a phase I study in 24 healthy volunteers given OCA (5, 10, or 25 mg/d for 17 days). |
| SAMN08475326 | intervention | drug_therapy | R1 | 0.80 | biosample.attribute:study_group | study_group: 10 |
| SAMN08475326 | intervention_detail | obeticholic acid 10 mg dose group | R1 | 0.80 | biosample.attribute:study_group | study_group: 10 |
| SAMN08475326 | subject_id | 7563 | R1 | 0.85 | sample.attr.sid | 7563 |
| SAMN08475326 | timepoint_label | 44 | R1 | 0.85 | sample.attr.day | 44 |
Sequencing
64 runs over 64 samples · mean 8.49 Gbp per run (median 8.47 Gbp, total 543.60 Gbp; 64 runs with a base count) · layout PAIRED 64 · platform ILLUMINA 64 · models Illumina HiSeq 2500 (64) · 91% of runs with a Sandpiper profile · first public 2018-02-08
Authors (0)
No author record.
Downloads
PRJNA432958.csv.gz (2.6 KB) · parquet (72.7 KB) — all 64 samples, every field with route and confidence · PRJNA432958_determinations.csv.gz (3.8 KB) — 512 evidence rows