Fig. 3

Comparison of antimicrobial resistance classes between 25 and 240 days of age and between cecum lumen and feces samples. a Comparison of antimicrobial resistance classes between 25 and 240 days of age in pigs from the NC-F6 population. b Comparison of antimicrobial resistance classes between cecum lumen and feces samples in pigs from the NC-F6 population. The x-axis shows the sample IDs. W + numbers: feces samples at the age of 25 days, F + numbers: feces samples at the age of 240 days, and C + numbers: cecum samples at the age of 240 days. The same number represents the same pig. The antimicrobial resistance genes (ARGs) were classified into antimicrobial resistance classes according to antimicrobials that they show resistance for (the y-axis). The abundance of all ARGs belonging to a antimicrobial resistance class in a sample was summed together as the abundance of AMR class in that sample and was used for further comparisons. The full names of antimicrobials are presented in Additional file 4: Table S3. The comparisons were performed using the Wilcoxon test in the ggpubr package in R, and the P value corrected for multiple tests (FDR < 0.05) was treated as the significance threshold