Gut microbiome response to amoxicillin/azithromycin, USA
Shotgun metagenomic sequencing of 281 fecal samples from 60 US adults (24 households given amoxicillin, azithromycin, or placebo, plus 12 unrelated controls) collected over 6 months. machine-written summary
281 samples · 281 runs · US · Adult · 2022 · 6.57 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 971 sample values (antibiotic exposure, intervention, subject id, timepoint) |
| ✓ Abstract / description | 281 sample values (location site) |
| ✓ Full text | 281 sample values (country) · PMC10394940 |
| ○ 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 |
intervention · arms resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population healthy_control · Amoxicillin or azithromycin vs placebo (vitamin C), 3 or 7 days
“received treatment with an antibiotic, either amoxicillin” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalhouseholds — not resolved
60 of 60 people sampled more than once (281 samples; median 5, up to 5 per person) · follow-up median 56 d (max 56 d) · median interval between samples 4 d (time from timepoint labels). Schedule stated by the source: “Fecal samples collected day 0, day 3, day 7, week 8, and month 6 per subject” (time origin: intervention_start); stated follow-up 6 mo.
Each row is one person (13 shown of 60); dots are samples at days since that person's first sample.
24 two-person cohabitant households (one antibiotic, one placebo) + 8 no-housemate controls; household pairing not given per sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 281 | 100% | ||||
| country | 281 | 100% | 281 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 281 | 100% | 281 | |||
| detailed_location | 281 | 100% | ||||
| intervention | 281 | 100% | 281 | |||
| location_site | 281 | 100% | 281 | |||
| timepoint_label | 234 | 83% | 234 | |||
| antibiotic_exposure | 175 | 62% | 175 |
- Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household 2023 PMID 37528343 PMC10394940 own_data
Archive description
We recruited 60 subjects over a 6-month period from the University of California San Diego undergraduate campus. Within this group of subjects were 24 separate households consisting of 2 individuals. We also enrolled 12 separate control subjects not enrolled with a housemate. In each household, 1 individual received treatment with an antibiotic, either amoxicillin (n=12) or azithromycin (n=12), and the other individual received treatment with a placebo (vitamin C, n=24). Antibiotic/placebo were given once per day with half the participants receiving therapy for 3 days and the other half for 7 days. The additional 12 subjects who were not enrolled with a housemate and did not receive either antibiotic or placebo (e.g., non-household controls). Fecal samples were collected on day 0 (day prior to antibiotics), day 3 (on the third day of antibiotics), day 7, week 8, and at 6 months.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by curator_audit with confidence 0.80. Assay shotgun_dna.
- host runs.scientific_name · “human gut metagenome (281)”
- host runs.isolation_source · “feces (281)”
- body site runs.scientific_name · “human gut metagenome (281)”
- body site runs.isolation_source · “feces (281)”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN21216447 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:TITLE+source_material_id | Amox_7d CA05aGut_Amox_7d |
| SAMN21216447 | country | US | R3 | 0.70 | paper.body.PMC10394940 | University of California San Diego undergraduate campus |
| SAMN21216447 | intervention | antibiotic | R1 | 0.70 | sample.name_rule:TITLE | Amox_7d |
| SAMN21216447 | location_site | University of California San Diego undergraduate campus | R4 | 0.45 | ena.study_description | University of California San Diego undergraduate campus |
| SAMN21216447 | subject_id | CA05 | R1 | 0.70 | sample.name_rule:library_names | SampleID-CA05aGut |
| SAMN21216447 | timepoint_label | day 0 | R1 | 0.70 | sample.name_rule:library_names | SampleID-CA05aGut |
Sequencing
281 runs over 281 samples · mean 6.49 Gbp per run (median 6.57 Gbp, total 1,822.71 Gbp; 281 runs with a base count) · layout PAIRED 281 · platform ILLUMINA 281 · models Illumina HiSeq 1500 (281) · 92% of runs with a Sandpiper profile · first public 2022-05-02 – 2023-04-02
Authors (0)
No author record.
Downloads
PRJNA715245.csv.gz (8.2 KB) · parquet (79.8 KB) — all 281 samples, every field with route and confidence · PRJNA715245_determinations.csv.gz (14.2 KB) — 1,533 evidence rows