Infant fecal metagenomes before/after antibiotics and FMT, USA
12 fecal samples from infants in the USA, studying antibiotic treatment with or without fecal microbiota transplant (FMT) restoration, as a case series. machine-written summary
12 samples · 12 runs · US · Infant / toddler · 2024 · 35.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 24 sample values (collection date, country) |
| ✓ Abstract / description | 12 sample values (antibiotic exposure) |
| ○ Full text | read; no usable statement or table · PMC13343926 |
| ○ 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 not resolved
Antibiotic given as the study intervention (incl. eradication therapy Faecal microbiota transplantation design single_arm_before_after · population preterm_nicu · Autologous FMT after amoxicillin treatment in infant
“before and after antibiotic treatment w/ or w/o afmt restoration” — bioproject.description (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 11 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 | 12 | 100% | 12 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 |
- Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report. PMID 42214386 PMC13343926 curated
Archive description
Baby feces before and after antibiotic treatment w/ or w/o afmt restoration.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “Baby feces before and after”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “Baby feces before and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA116106061 | antibiotic_exposure | yes | R4 | 0.50 | study.description | Baby feces before and after antibiotic treatment |
| SAMEA116106061 | collection_date | 2023-04-13 | R1 | 0.85 | biosample.attribute:collection_date | 2023-04-13 |
| SAMEA116106061 | country | US | R1 | 0.90 | biosample_attr | USA |
Sequencing
12 runs over 12 samples · mean 35.97 Gbp per run (median 35.15 Gbp, total 431.59 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 2000 (12) · 92% of runs with a Sandpiper profile · first public 2024-10-10 – 2025-01-22
Authors (23)
Sun H first · Dulencin A · Kirn TJ · Vo J · Liachko I · Rao D · Manzano-Santana J · Patel E · Looi C · Horton DB · Barrett E · Weidner M · Bachmann G · Panettieri RA · Connor BA · Rogova M · Nagy-Szakal D · Couto-Rodriguez M · Kotwal S · Wu Q · Simon J · Blaser MJ · Dominguez Bello MG last
Downloads
PRJEB80456.csv.gz (1.2 KB) · parquet (69.3 KB) — all 12 samples, every field with route and confidence · PRJEB80456_determinations.csv.gz (715 B) — 36 evidence rows