Gut microbiome in children receiving antibiotics
132 stool metagenome samples from children, studied in an intervention design examining the effect of antibiotic treatment on gut microbiome, resistome, and colonization resistance. machine-written summary
132 samples · 132 runs · Child · 2023 · 9.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 393 sample values (collection date, subject id, timepoint) |
| ✓ Abstract / description | 396 sample values (antibiotic exposure, health condition, health condition detail) |
| – 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 |
longitudinal
62 of 69 people sampled more than once (124 samples; median 2, up to 2 per person) · follow-up median 10 d (max 4.0 y) · median interval between samples 10 d (time from collection dates). Schedule stated by the source: “Two timepoints per subject labeled A and B (pre/post antibiotic treatment), subject sampled twice” (time origin: intervention_start).
Each row is one person (36 shown of 62); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 117 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 | 132 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 132 | 100% | 132 | |||
| subject_id | 131 | 99% | 131 | |||
| antibiotic_exposure | 132 | 100% | 132 | |||
| health_condition_detail | 132 | 100% | 132 | |||
| collection_date | 131 | 99% | 131 | |||
| timepoint_label | 131 | 99% | 131 |
- Antibiotic courses for acute otitis media alter human gut microbiome resistome and colonization resistance against antimicrobial resistant species in children 2022 own_data
Archive description
Metagenomic study on the effect of antibiotic treatments on children's gut microbiome, resistome and colonization resistance
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_rule with confidence 0.90. Assay shotgun_dna.
- host run.host_tax_id · “host_tax_id 9606”
- body site study.title · “reads from human stool microbiome from children”
- body site study.description · “treatments on children's gut microbiome, resistome and”
- life stage study.title · “stool microbiome from children receiving antibiotics”
- life stage study.description · “antibiotic treatments on children 's gut microbiome,”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25247813 | antibiotic_exposure | yes | R4 | 0.50 | study.title | children receiving antibiotics |
| SAMN25247813 | collection_date | 2020-12-13 | R1 | 0.90 | biosample.attribute:collection_date | 2020-12-13 |
| SAMN25247813 | health_condition | other_infection | R4 | 0.50 | paper.abstract | treatment for acute otitis media in a randomized clinical trial |
| SAMN25247813 | health_condition_detail | acute otitis media | R4 | 0.50 | paper.abstract | treatment for acute otitis media in a randomized clinical trial |
| SAMN25247813 | subject_id | 101 | R1 | 0.85 | sample.attr.subject | 101 |
| SAMN25247813 | timepoint_label | A | R1 | 0.85 | sample.attr.time | A |
Sequencing
132 runs over 132 samples · mean 9.18 Gbp per run (median 9.24 Gbp, total 1,211.90 Gbp; 132 runs with a base count) · layout PAIRED 132 · platform ILLUMINA 132 · models Illumina NovaSeq 6000 (132) · 89% of runs with a Sandpiper profile · first public 2023-02-02
Authors (0)
No author record.
Downloads
PRJNA800433.csv.gz (4.9 KB) · parquet (75.6 KB) — all 132 samples, every field with route and confidence · PRJNA800433_determinations.csv.gz (5.5 KB) — 789 evidence rows