Fig. 3

Regional taxonomic differences of GIT microbiota of sika deer from birth to postweaning. PCoA of GIT taxonomic community composition at phylum (a), family (b), and genus levels (c, d) based on Bray-Curtis dissimilarity. The microbial samples from GIT regions were indicated as different shapes (rumen: circle, jejunum: triangle, ileum: inverted triangle, cecum: rhombus, and colon: square), and different time points were indicated by filling color (day 1: gray, day 42: blue, day 70: red) in a, b, and c. ANOSIM analysis was used for statistical testing of group similarities. The proportion of variation explained for each axis is given after colon. e Bar plot revealing the Shannon diversity index among the three age groups. The diversity index was calculated using the taxonomic composition at genus level. Bar and whiskers represent the mean ± s.d. f Relative abundances of bacteria, archaea, eukaryotes, and virus, as averaged over all samples (n = 5) in each GIT regions for each time points, are given as percentages (× 100). Prevalence heat map indicates the proportion of any specific taxonomy observed in all samples. D, day. *** indicates the Benjamini-Hochberg-adjusted P-value < 0.001