Microbiota in children after amoxicillin-clavulanic acid use
120 gut metagenome samples, 40 from Italy (rest unspecified), from a case-control study comparing children treated with amoxicillin-clavulanic acid to untreated children. machine-written summary
120 samples · 120 runs · IT · Age unknown · 2021 · 28.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 300 sample values (antibiotic exposure, collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked · PMC8091617 |
| – 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 · share metadata |
| – 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 observational_with_procedure · population healthy_control · Amoxicillin-clavulanic acid therapy in children, gut microbiota compared
“23 children that had undergone AMC antibiotic therapy” — abstract:33483308 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
2 of 2 people sampled more than once (80 samples; median 40, up to 40 per person).
Genera, mean relative abundance over 1 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 | 0 | 0% | ||||
| country | 40 | 33% | 40 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 80 | 67% | 80 | |||
| timepoint_label | 80 | 67% | 80 | |||
| antibiotic_exposure | 60 | 50% | 60 | |||
| collection_date | 40 | 33% | 40 |
- Amoxicillin-Clavulanic Acid Resistance in the Genus Bifidobacterium. 2021 PMID 33483308 PMC8091617 own_data
Archive description
Unveiling the bifidobacterial resistance mechanism against amoxicillin-clavulanic acid: genetic and ecological insights
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16178950 | antibiotic_exposure | yes | R1 | 0.70 | sample.name_rule:alias | FecalSample-1898B-AMC-12h |
| SAMN16178945 | collection_date | 2020-06-04 | R1 | 0.90 | biosample.attribute:collection_date | 2020-06-04 |
| SAMN16178945 | country | IT | R1 | 0.90 | sample.attr.geo_loc_name | Italy |
| SAMN17309608 | subject_id | F2 | R1 | 0.70 | sample.name_rule:alias | F2-12 |
| SAMN17309608 | timepoint_label | 12 | R1 | 0.70 | sample.name_rule:alias | F2-12 |
Sequencing
120 runs over 120 samples · mean 33.1 Mbp per run (median 28.6 Mbp, total 3.97 Gbp; 120 runs with a base count) · layout PAIRED 120 · platform ILLUMINA 120 · models NextSeq 550 (72), Illumina MiSeq (48) · 1% of runs with a Sandpiper profile · first public 2021-01-12 – 2021-01-15
Authors (12)
Mancabelli L first · Mancino W · Lugli GA · Argentini C · Longhi G · Milani C · Viappiani A · Anzalone R · Bernasconi S · van Sinderen D · Ventura M · Turroni F last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJNA663786.csv.gz (3.3 KB) · parquet (73.4 KB) — all 120 samples, every field with route and confidence · PRJNA663786_determinations.csv.gz (3.3 KB) — 300 evidence rows