Gut microbiome in healthy US adults given antibiotics
26 stool samples from healthy adult volunteers in the USA, studying gut microbiome changes before, during, and after antibiotic exposure, in an intervention study design. machine-written summary
26 samples · 26 runs · US · Age unknown · 2022 · 1.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 130 sample values (age, collection date, country, latitude, longitude) |
| ✓ Abstract / description | 52 sample values (antibiotic exposure, health condition) |
| – Full text | no open-access full text linked |
| – 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 not resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · 4 commonly used antibiotic regimens given to healthy volunteers
“exposure to 4 commonly used antibiotic regimens” — abstract:35417701 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 23 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 | 26 | 100% | ||||
| country | 26 | 100% | 26 | |||
| health_condition | 26 | 100% | 26 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 26 | 100% | 26 | |||
| antibiotic_exposure | 26 | 100% | 26 | |||
| collection_date | 26 | 100% | 26 | |||
| latitude | 26 | 100% | 26 | |||
| longitude | 26 | 100% | 26 |
- Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. 2022 PMID 35417701 PMC9066705 unsure
Archive description
Metagenomics of Stool from ICU Patients
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Stool from ICU Patients”
- body site study.title · “Metagenomics of Stool”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18006444 | age_at_collection_days | 21915.00 | R1 | 0.85 | sample.name_rule:isolation_source | M_60 |
| SAMN18006444 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | exposure to 4 commonly used antibiotic regimens |
| SAMN18006444 | collection_date | 2016-01/2017-01 | R1 | 0.90 | biosample.attribute:collection_date | 2016-01/2017-01 |
| SAMN18006444 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN18006444 | health_condition | healthy_control | R4 | 0.30 | paper.abstract | healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months |
| SAMN18006444 | latitude | 36.6270 | R1 | 0.90 | biosample.attribute:lat_lon | 36.627 N 90.1994 W |
| SAMN18006444 | longitude | -90.1994 | R1 | 0.90 | biosample.attribute:lat_lon | 36.627 N 90.1994 W |
Sequencing
26 runs over 26 samples · mean 1.47 Gbp per run (median 1.51 Gbp, total 38.19 Gbp; 26 runs with a base count) · layout PAIRED 26 · platform ILLUMINA 26 · models NextSeq 500 (26) · 88% of runs with a Sandpiper profile · first public 2022-03-03
Authors (13)
Anthony WE first · Wang B · Sukhum KV · D'Souza AW · Hink T · Cass C · Seiler S · Reske KA · Coon C · Dubberke ER · Burnham CD · Dantas G · Kwon JH last
Downloads
PRJNA703034.csv.gz (1.6 KB) · parquet (70.6 KB) — all 26 samples, every field with route and confidence · PRJNA703034_determinations.csv.gz (2.1 KB) — 182 evidence rows