Bile acid effects on gut bacteria, China, 28 samples
28 fecal samples from healthy adults in China, studied in vivo and in vitro for effects of bile acids (including deoxycholic acid) on gut bacterial composition, ribosomal transcription, and amino acid metabolism. machine-written summary
28 samples · 28 runs · CN · Age unknown · 2024 · 34.8 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 56 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 112 sample values (antibiotic exposure, health condition, health condition detail, sex) · PMC11496524 |
| ○ 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 |
Other administered intervention (see intervention_detail) · Bile acids (e.g., deoxycholic acid) administered in vivo/in vitro to gut bacteria
“investigated the effects of bile acids on the composition” — bioproject.description (study level; per-sample arms are in the intervention column below)
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 28 | 100% | ||||
| country | 28 | 100% | 28 | |||
| health_condition | 28 | 100% | 28 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 28 | 100% | 28 | |||
| collection_date | 28 | 100% | 28 | |||
| health_condition_detail | 28 | 100% | 28 | |||
| sex | 28 | 100% | 28 |
- Effects of bile acids on the growth, composition and metabolism of gut bacteria. 2024 PMID 39438471 PMC11496524 own_data
Archive description
As an endogenous substance in the human body, bile acids have been known to play an important role in the composition and growth of intestinal bacteria. However, there is still much to be discovered regarding which bacteria are affected by bile acids and the mechanisms of action involved. In this study, we have investigated the effects of bile acids on the composition of intestinal bacteria in both in vivo and in vitro settings, and have found that different bacterial strains display varying levels of sensitivity to bile acids. Moreover, we have determined that bacteria with a strong ability to accumulate bile acids are more susceptible to their effects. Using transcriptome sequencing, we have discovered that deoxycholic acid (DCA) can significantly alter ribosomal transcription and amino acid metabolism. This finding was further supported by targeted detection of amino acids, which demonstrated that bile acids have a significant impact on amino acid metabolism in both in vivo and in vitro settings. Our results provide new insights into the mechanisms by which bile acids can affect the growth and composition of different bacterial strains, and suggest that these effects are mediated through changes in ribosome and amino acid metabolism resulting from the accumulation of bile acids in intestinal bacteria. These findings are highly relevant to understanding the role of bile acids in maintaining the gut microbiota and could have important implications for the development of therapeutic strategies for various gut-related disorders.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.53. 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 |
|---|---|---|---|---|---|---|
| SAMN33549349 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not taken antibiotics or probiotics in the three months |
| SAMN33549349 | collection_date | 2022-05-19 | R1 | 0.90 | biosample.attribute:collection_date | 2022-05-19 |
| SAMN33549349 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN33549349 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 7 healthy male volunteers meeting specific inclusion criteria |
| SAMN33549349 | health_condition_detail | healthy male volunteers, no GI diseases | R3 | 0.70 | paper.fulltext.methods | 7 healthy male volunteers meeting specific inclusion criteria |
| SAMN33549349 | sex | male | R3 | 0.70 | paper.fulltext.methods | 7 healthy male volunteers meeting specific inclusion criteria |
Sequencing
28 runs over 28 samples · mean 34.3 Mbp per run (median 34.8 Mbp, total 0.96 Gbp; 28 runs with a base count) · layout SINGLE 28 · platform ILLUMINA 28 · models Illumina NovaSeq 6000 (28) · 0% of runs with a Sandpiper profile · first public 2024-12-01
Downloads
PRJNA939937.csv.gz (1.5 KB) · parquet (70.3 KB) — all 28 samples, every field with route and confidence · PRJNA939937_determinations.csv.gz (1.4 KB) — 168 evidence rows