(1) The files in data fold are input for the script in script folder.

(2)The description and the output for each script. 1_preterm_ARGs_profile_host.R This script is used to analyze the composition and host of ARGs in preterm infants, including Figure 1b, Figure 1c, Figure 1d, Figure 4d, Supplementary Figure 1a, Supplementary Figure 1b, Supplementary Figure 1c, Supplementary Figure 1d, Supplementary Figure 1e, Supplementary Figure 1f, Supplementary Figure 1g, Supplementary Figure 2a, Supplementary Figure 2b, Supplementary Figure 3a, Supplementary Figure 3b, Supplementary Figure 3c, Supplementary Figure 3d, Supplementary Figure 7, Supplementary Figure 8a.

2_term_ARGs_profile_host_comparisonWithpreterm.R This script is used to analyze the composition and host of ARGs in full-term infants, and also the comparisons between preterm and full-term infants, including Figure 2a, Figure 2b, Figure 2c, Figure 2d, Figure 2e, Figure 2f, Figure 2g, Figure 3, Supplementary Figure 4a, Supplementary Figure 4b, Supplementary Figure 4c, Supplementary Figure 4d, Supplementary Figure 4e, Supplementary Figure 5a, Supplementary Figure 5b, Supplementary Figure 5c, Supplementary Figure 5d, Supplementary Figure 5e, Supplementary Figure 5f, Supplementary Figure 6a, Supplementary Figure 6b.

3_preterm_ARGs_dynamics_covariate_maaslin2.R This script is used to analyze the dynamics and covariates of ARGs in preterm infants, including Figure 4a, Figure 4b, Figure 4c, Figure 4e, Figure 4f, Supplementary Figure 8b, Supplementary Figure 8c, Supplementary Figure 8d, Supplementary Figure 9a, Supplementary Figure 9b.

4_nec_diversity_signatures.R This script is used to analyze differences between cases and controls, including Figure 5a, Figure 5b, Figure 5c, Supplementary Figure 10a, Supplementary Figure 10b, Supplementary Figure 10c.

5_nec_rf.R This script is used to analyze the predictive performance from public cohorts and validation cohort, including Figure 5d, Figure 5e, Figure 5f.