RNA-Seq data that support the findings of this study have been deposited in ArrayExpress database (www.ebi.ac.uk/arrayexpress) with the accession code E-MTAB-6826 (www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6826). 16S rRNA data has been deposited in QIITA (https://qiita.ucsd.edu/) with the identifier 11242 (https://qiita.ucsd.edu/study/description/11242). Ileal NanoString data have been deposited in NCBI's Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number, GSE101721 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10171). Shotgun metagenomics data have been deposited in the European Nucleotide Archive (ENA) (www.ebi.ac.uk/metagenomics/) under the accession number, PRJEB26585 (www.ebi.ac.uk/ena/data/view/PRJEB26585). Metabolomics data have been deposited at the NIH Common Fund Metabolomics Workbench (www.metabolomicsworkbench.org; doi: 10.21228/M8C39R)
Ileal transcriptome profiles altered by early-life single pulse antibiotic exposurePublicly available at the Electron Microscopy Data Bank (accession no: E-MTAB-6826).
Intestinal microbiome altered by early-life pulse antibiotic exposurePublicly available at Qiita (identifier: 11242).
Intestinal immunity pathways altered by early-life single pulse antibiotic exposurePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE101721).
Intestinal metagenome and metabolic pathways altered by early-life single pulse antibiotic exposurePublicly available at the European Nucleotide Archive (accession no: PRJEB26585).
Metabolomics involved in early-life single pulse antibiotic exposurePublicly available at Metabolomics Workbench (10.21228/M8C39R).
Supplementary file 1
Supplementary file 2
Supplementary file 3
Supplementary file 4
Supplementary file 5
Supplementary file 6
Supplementary file 7
Transparent reporting form