Microbiome in healthy adults before/after antibiotics
15 stool samples from healthy adults in Hong Kong, collected before and after antibiotic treatment (Augmentin, Azithromycin, Levofloxacin) in a prospective intervention study of temporal effects on gut microbiota. machine-written summary
15 samples · 15 runs · HK · Adult · 2020 · 5.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 135 sample values (antibiotic exposure, collection date, country, intervention, intervention detail, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 30 sample values (health condition, health condition detail) · PMC7488854 |
| ○ 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 single_arm_before_after · population healthy_control · Augmentin, Azithromycin, Levofloxacin given over 6 days
“treated with antibiotic drugs Augmentin, Azithromycin and Levofloxacin” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
4 of 4 people sampled more than once (15 samples; median 4, up to 4 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 25 d (time from collection dates). Schedule stated by the source: “Stool 1 week before antibiotic administration, then 4, 30, and 90 days afterwards” (time origin: intervention_start); stated follow-up 3 mo.
Each row is one person (4 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 14 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 | 15 | 100% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 15 | 100% | 15 | |||
| subject_id | 15 | 100% | 15 | |||
| antibiotic_exposure | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| detailed_location | 15 | 100% | ||||
| health_condition_detail | 15 | 100% | 15 | |||
| intervention | 15 | 100% | 15 | |||
| intervention_detail | 15 | 100% | 15 | |||
| latitude | 15 | 100% | 15 | |||
| location_region | 15 | 100% | 15 | |||
| longitude | 15 | 100% | 15 |
- Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria. 2020 PMID 32919472 PMC7488854 own_data
Archive description
Prospective study of four human subjects treated with antibiotic drugs Augmentin, Azithromycin and Levofloxacin. Sampling was performed 1 week before drug administration as well as 4 days, 30 days and 90 days afterwards. The goal was to study the temporal effects of antibiotic drugs on gut microbiota.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “shotgun sequencing of stool samples from human”
- body site study.description · “antibiotic drugs on gut microbiota.”
- 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 |
|---|---|---|---|---|---|---|
| SAMN12826447 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | Augmentin |
| SAMN12826447 | collection_date | 2017-03-08 | R1 | 0.90 | biosample.attribute:collection_date | 2017-03-08 |
| SAMN12826447 | country | HK | R1 | 0.90 | sample.attr.geo_loc_name | Hong Kong |
| SAMN12826447 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.abstract | 14 healthy human participants |
| SAMN12826447 | health_condition_detail | healthy human participants | R3 | 0.70 | paper.fulltext.abstract | 14 healthy human participants |
| SAMN12826447 | intervention | antibiotic | R1 | 0.90 | biosample.attribute:Antibiotic | Antibiotic: Augmentin |
| SAMN12826447 | intervention_detail | Augmentin (amoxicillin/clavulanate) | R1 | 0.90 | biosample.attribute:Antibiotic | Antibiotic: Augmentin |
| SAMN12826447 | latitude | 22.3340 | R1 | 0.90 | biosample.attribute:lat_lon | 22.334 N 114.1973 E |
| SAMN12826447 | location_region | Wong Tai Sin | R1 | 0.60 | biosample.attribute:lat_lon | 22.334 N 114.1973 E |
| SAMN12826447 | longitude | 114.1973 | R1 | 0.90 | biosample.attribute:lat_lon | 22.334 N 114.1973 E |
| SAMN12826447 | subject_id | 001 | R1 | 0.70 | sample.name_rule:library_names | A-001A |
Sequencing
15 runs over 15 samples · mean 5.34 Gbp per run (median 5.43 Gbp, total 80.08 Gbp; 15 runs with a base count) · layout PAIRED 15 · platform ILLUMINA 15 · models Illumina HiSeq 4000 (15) · 93% of runs with a Sandpiper profile · first public 2020-10-13
Authors (18)
Seelbinder B first · Chen J · Brunke S · Vazquez-Uribe R · Santhaman R · Meyer AC · de Oliveira Lino FS · Chan KF · Loos D · Imamovic L · Tsang CC · Lam RP · Sridhar S · Kang K · Hube B · Woo PC · Sommer MOA · Panagiotou G last
Downloads
PRJNA573821.csv.gz (1.4 KB) · parquet (71.3 KB) — all 15 samples, every field with route and confidence · PRJNA573821_determinations.csv.gz (2.1 KB) — 165 evidence rows