Fig. 2
Longitudinal and gut spatial characterization of the gut microbiota. A: Principal coordinates analysis (PCoA) of the fecal microflora based on the weighted UniFrac distance in the litter and cage groups at different days of age. R,2 which is calculated from PERMANOVA, indicates the variation in distances explained by the grouping. B: Abundant phyla in litter and cage groups at different days of age. The average abundance for each of the phyla from samples at the corresponding days of age in each group was used to plot the alluvial diagram. C: Abundant phyla in the litter and cage groups at different gut sites. The average abundance of each of the phyla from samples at the corresponding days of age in each group was used to plot the alluvial diagram. D: Differential abundances of genera between the litter and cage groups at different days of age. E: Differential abundances of genera between the litter and cage groups at different gut sites. The nonparametric factorial Kruskal-Wallis (KW) sum-rank test was performed to detect significantly differential genera between the litter and cage groups at different days of age or at different gut sites. Linear discriminant analysis (LDA) scores were calculated for significantly different genera and then the scores were transformed by logarithm. Only genera with LDA scores over 3.5 are shown