Antibiotic impact on gut microbiome, Oxfordshire, UK
Shotgun metagenomic sequencing of 452 stool samples from 232 adults (inpatients, outpatients, and healthy volunteers) in Oxfordshire, UK, assessing how antimicrobial exposure affects gut microbiome diversity and resistance genes. machine-written summary
452 samples · 452 runs · GB · Adult · 2025 · 3.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,712 sample values (collection date, country, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 904 sample values (location region, location site) · PMC12695023 |
| ✓ Supplementary tables | 812 sample values (antibiotic exposure, 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 |
longitudinal — not resolved
83 of 232 people sampled more than once (303 samples; median 4, up to 7 per person). Schedule stated by the source: “stool sample every other day until discharge (HCT patients)”.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 452 | 100% | ||||
| country | 452 | 100% | 452 | |||
| health_condition | 452 | 100% | 452 | |||
| subject_id | 452 | 100% | 452 | |||
| collection_date | 452 | 100% | 452 | |||
| detailed_location | 452 | 100% | ||||
| health_condition_detail | 452 | 100% | 452 | |||
| location_region | 452 | 100% | 452 | |||
| location_site | 452 | 100% | 452 | |||
| timepoint_label | 452 | 100% | 452 | |||
| sex | 443 | 98% | 443 | |||
| antibiotic_exposure | 369 | 82% | 369 |
- The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study. 2025 PMID 41370178 PMC12695023 own_data
Archive description
The Antibiotic Resistance in the Microbiome – Oxford (ARMORD) study recruited inpatients, outpatients and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by curator_audit with confidence 0.57. Assay shotgun_dna.
- host description · “who provided stool samples for metagenomic sequencing”
- host runs.scientific_name · “human gut metagenome (452)”
- body site description · “who provided stool samples for metagenomic sequencing”
- body site runs.scientific_name · “human gut metagenome (452)”
- life stage study.description · “recruited inpatients, outpatients and healthy volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120505903 | antibiotic_exposure | yes | R2 | 0.80 | paper.supp.elife-97751-code1.zip/Source Code 1/ARMORD R project/armord_data/study_data/Antimicrobial_exposures.csv[drug;firstdose/lastdose_days_after_first_sample] | C001_1: clarithromycin, co_amoxiclav dose within 7 d before sample |
| SAMEA120505903 | collection_date | 2015 | R1 | 0.85 | biosample.attribute:collection date | collection date: 2015 |
| SAMEA120505903 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA120505903 | health_condition | other_disease | R1 | 0.70 | biosample.attribute:host health state | host health state: diseased |
| SAMEA120505903 | health_condition_detail | diseased (hospital patient; general medical or HCT, per paper) | R1 | 0.70 | biosample.attribute:host health state | host health state: diseased |
| SAMEA120505903 | location_region | Oxfordshire | R3 | 0.70 | paper.body.methods_results | recruited healthy individuals living in Oxfordshire, and patients at the Oxford University Hospitals NHS Foundation Trust |
| SAMEA120505903 | location_site | Oxford University Hospitals NHS Foundation Trust | R3 | 0.70 | paper.body.methods_results | patients at the Oxford University Hospitals NHS Foundation Trust (OUH) |
| SAMEA120505903 | sex | male | R2 | 0.80 | paper.supp.elife-97751-code1.zip/Source Code 1/ARMORD R project/armord_data/study_data/Patients.csv[sex] | pid 1; sex male |
| SAMEA120505903 | subject_id | C001 | R1 | 0.70 | sample.name_rule:alias | C001_1 |
| SAMEA120505903 | timepoint_label | sample 1 | R1 | 0.70 | sample.name_rule:alias | C001_1 |
Sequencing
452 runs over 452 samples · mean 3.85 Gbp per run (median 3.40 Gbp, total 1,742.45 Gbp; 452 runs with a base count) · layout SINGLE 452 · platform ILLUMINA 452 · models Illumina HiSeq 4000 (452) · 94% of runs with a Sandpiper profile · first public 2025-11-07 – 2025-11-10
Authors (0)
No author record.
Downloads
PRJEB86785.csv.gz (12.6 KB) · parquet (88.4 KB) — all 452 samples, every field with route and confidence · PRJEB86785_determinations.csv.gz (39.8 KB) — 4,428 evidence rows