Antibiotic exposure and gut microbiome in US infants
Longitudinal cohort study of 669 stool samples from healthy term African American infants in the USA, comparing antibiotic-exposed and unexposed groups to assess gut microbiome perturbations via shotgun metagenomics. machine-written summary
669 samples · 669 runs · US · Infant / toddler · 2024 · 2.13 Gbp / sample · cohort Benitez 2025 USA
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,961 sample values (age, antibiotic exposure, collection date, country, delivery mode, feeding mode, gestational age weeks, maternal antibiotics) |
| ✓ Abstract / description | 669 sample values (health condition) |
| ✓ Full text | 802 sample values (age, location site, preterm status) · PMC11558993, PMC11761179 |
| ○ 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 design observational_with_procedure · population healthy_control · Observed antibiotic exposure (predominantly amoxicillin) in infants, not trial-assigned
“antibiotic-exposed (n = 170) and unexposed (n = 153) participants” — abstract:39856742 (study level; per-sample arms are in the intervention column below)
longitudinal
208 of 223 people sampled more than once (654 samples; median 3, up to 7 per person) · follow-up median 20 mo (max 22 mo) · median interval between samples 8 mo (time from age at collection). Schedule stated by the source: “Stool samples at ages 4, 12, and 24 months; short-term substudy at first antibiotic exposure and weekly for 3 weeks after” (time origin: birth); stated follow-up 24 mo.
Each row is one person (36 shown of 208); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 603 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 | 669 | 100% | ||||
| country | 669 | 100% | 669 | |||
| health_condition | 669 | 100% | 669 | |||
| subject_id | 669 | 100% | 669 | |||
| age_at_collection_days | 669 | 100% | 664 | 5 | ||
| collection_date | 669 | 100% | 669 | |||
| delivery_mode | 669 | 100% | 669 | |||
| detailed_location | 669 | 100% | ||||
| gestational_age_weeks | 669 | 100% | 669 | |||
| location_site | 669 | 100% | 669 | |||
| preterm_status | 669 | 100% | 541 | 128 | ||
| timepoint_label | 669 | 100% | 669 | |||
| maternal_antibiotics | 666 | 100% | 666 | |||
| antibiotic_exposure | 542 | 81% | 542 | |||
| feeding_mode | 534 | 80% | 534 |
- Metal availability shapes early life microbial ecology and community succession. PMID 39440978 PMC11558993 curated
- Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants. PMID 39856742 PMC11761179 curated
- Amino acid competition shapes Acinetobacter baumannii gut carriage. PMID 40763731 PMC12375414 curated
Archive description
This is a prospective longitudinal birth cohort of n=323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid pofiles through liquid chromatography-mass spectrometry. Stool samples were collected at ages 4, 12, and 24 months for antibiotic exposed (n=170) and unexposed (n=153) participants. A short-term substudy (n=39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “associated with minimal gut microbiome perturbations in”
- body site study.description · “exposure and the gut microbiome through shotgun”
- body site study.description · “as well as bile acid pofiles through”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “in healthy term infants”
- life stage study.description · “term African American children to determine the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN41143468 | age_at_collection_days | 729 | R1 | 0.60 | biosample_attr | 23.9507179260254 |
| SAMN41143599 | age_at_collection_days | 730 | R3 | 0.40 | paper.fulltext.abstract | collected at ages 4, 12, and 24 months |
| SAMN41143468 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | False |
| SAMN41143468 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | 2016 |
| SAMN41143468 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN41143468 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | SVD |
| SAMN41143468 | feeding_mode | formula | R1 | 0.85 | biosample_attr | other milk |
| SAMN41143468 | gestational_age_weeks | 40.0 | R1 | 0.90 | biosample_attr | 280 |
| SAMN41143468 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy term African American children |
| SAMN41143468 | location_site | Children's Hospital of Philadelphia | R3 | 0.60 | paper.fulltext.results | conducted at the Children's Hospital of Philadelphia |
| SAMN41143468 | maternal_antibiotics | no | R1 | 0.85 | biosample_attr | No |
| SAMN41143468 | preterm_status | term | R1 | 0.85 | biosample_attr | 280 |
| SAMN41143712 | preterm_status | term | R3 | 0.80 | paper.fulltext.abstract | n = 323 healthy term African American children |
| SAMN41143468 | subject_id | s100 | R1 | 0.85 | biosample_attr | s100 |
| SAMN41143468 | timepoint_label | 24M | R1 | 0.80 | biosample_attr | 24M |
Sequencing
669 runs over 669 samples · mean 2.10 Gbp per run (median 2.13 Gbp, total 1,404.64 Gbp; 669 runs with a base count) · layout PAIRED 669 · platform ILLUMINA 669 · models Illumina HiSeq 2500 (669) · 90% of runs with a Sandpiper profile · first public 2024-05-12
Authors (33)
Soto Ocaña J first · Friedman ES · Keenan O · Bayard NU · Ford E · Tanes C · Munneke MJ · Beavers WN · Skaar EP · Bittinger K · Zemel BS · Wu GD · Zackular JP last · Benitez AJ first · Gerber JS · DeRusso PA · Kelly A · Li H · Elovitz MA · Zemel B · Ren X first · Clark RM · Bansah DA · Varner EN · Tiffany CR · Jaswal K · Geary JH · Todd OA · Winkelman JD · Jarrett RN · DePas WH · Behnsen J · Palmer LD last
Downloads
PRJNA1106565.csv.gz (24.7 KB) · parquet (102.7 KB) — all 669 samples, every field with route and confidence · PRJNA1106565_determinations.csv.gz (53.5 KB) — 8,432 evidence rows