Drug metabolism in 28 healthy US gut communities
28 gut microbiome samples from healthy adults in the USA, cross-sectionally tested for in vitro metabolism of four drugs (dexamethasone, diltiazem, famciclovir, norethindrone acetate) using metagenomic sequencing of community composition. machine-written summary
28 samples · 28 runs · US · Age unknown · 2019 · 7.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 112 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 28 sample values (health condition) |
| ✓ Full text | 56 sample values (location site, subject id) · PMC10289814, PMC12683948, PMC13092348, PMC6597290 |
| ✓ Supplementary tables | 56 sample values (age, sex) |
| – 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 not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population healthy_control · Ex vivo gut community incubation with dexamethasone, diltiazem, famciclovir, norethindrone acetate
“tested metabolism of four drugs” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 27 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 | 28 | 100% | ||||
| country | 28 | 100% | 28 | |||
| health_condition | 28 | 100% | 28 | |||
| subject_id | 28 | 100% | 28 | |||
| age_at_collection_days | 28 | 100% | 28 | |||
| collection_date | 28 | 100% | 28 | |||
| detailed_location | 28 | 100% | ||||
| latitude | 28 | 100% | 28 | |||
| location_site | 28 | 100% | 28 | |||
| longitude | 28 | 100% | 28 | |||
| sex | 28 | 100% | 28 |
- Mapping human microbiome drug metabolism by gut bacteria and their genes. 2019 PMID 31158845 PMC6597290 own_data
- Identification of medication-microbiome interactions that affect gut infection. 2025 PMID 40670788 PMC13092348 own_data
- SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations. 2023 PMID 37306300 PMC10289814 unsure
- Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria. 2025 PMID 40763732 PMC12683948 unsure
Archive description
In this study, we tested metabolism of four drugs (dexamethasone, diltiazem, famciclovir and norethindrone acetate) by 28 healthy human gut communities. Community composition was determined with metagenomic sequencing. Analysis schemes, code and data of this study are available on GitHub (https://github.com/mszimmermann/drug-bacteria-gene_mapping)
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “human gut communities”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5537482 | age_at_collection_days | 10592 | R2 | 0.85 | paper.supp.NIHMS1530152-supplement-Supplementary_Tables_1-21.xlsx[Supplementary Table 9!Donor age (years)] | 29 |
| SAMEA5537482 | collection_date | 2011 | R1 | 0.90 | biosample.attribute:collection_date | 2011 |
| SAMEA5537482 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA5537482 | health_condition | healthy_control | R4 | 0.50 | study.description | 28 healthy human gut communities |
| SAMEA5537482 | latitude | 39.3800 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.38 -97.92 |
| SAMEA5537482 | location_site | Yale University School of Medicine | R3 | 0.70 | paper.fulltext.methods | Yale University Human Investigation Committee protocol number 1106008725 at Yale University School |
| SAMEA5537482 | longitude | -97.9200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39.38 -97.92 |
| SAMEA5537482 | sex | female | R2 | 0.85 | paper.supp.NIHMS1530152-supplement-Supplementary_Tables_1-21.xlsx[Supplementary Table 9!Donor Sex (m/f)] | f |
| SAMEA5537482 | subject_id | SAMEA5537482 | R3 | 0.70 | design.one_sample_per_subject:fulltext | We measured ex vivo diltiazem deacetylation kinetics of fecal samples collected from 28 unrelated human donors. |
Sequencing
28 runs over 28 samples · mean 8.77 Gbp per run (median 7.29 Gbp, total 245.64 Gbp; 28 runs with a base count) · layout PAIRED 28 · platform ILLUMINA 28 · models Illumina NovaSeq 6000 (28) · 96% of runs with a Sandpiper profile · first public 2019-04-09
Authors (21)
Zimmermann M first · Zimmermann-Kogadeeva M · Wegmann R · Goodman AL last · Bustion AE first · Nayak RR · Agrawal A · Turnbaugh PJ · Pollard KS last · Kumar A first · Sun R · Habib B · Deng T · Bencivenga-Barry NA · Palm NW · Ivanov II · Tamblyn R · Zhou Z first · Jiang A · Jiang X · Hatzios SK last
Downloads
PRJEB31790.csv.gz (1.8 KB) · parquet (71.6 KB) — all 28 samples, every field with route and confidence · PRJEB31790_determinations.csv.gz (2.8 KB) — 252 evidence rows