Fig. 1

Dynamics of fecal microbiome in a cohort of pigs (2 days of age to market age). A The number of pigs, housing, and sampling of feces of pigs for microbiome and resistome analyses. B, C Longitudinal development of Alpha diversity (at the genus level) measured by richness and Shannon diversity. D Non-metric multidimensional scaling (NMDS) ordinating plot based on Bray–Curtis distances illustrate the variation in microbial community structures (i.e. beta diversity; R² represents the amount of variability explained by age and associated P values based on PERMANOVA analysis), ellipses represent 95% confidence intervals for each age point. E Fecal microbiome community dissimilarity (Bray–Curtis dissimilarity index value) among age-points. F Stacked bar representing relative abundance of phyla over time; phyla with relative abundances less than 3% were grouped into “Others < 3%”