Bacterial community and metabolome shifts in the cecum and colon of captive sika deer (Cervus nippon) from birth to post weaning

Ruminant productivity is associated with the gastrointestinal tract bacterial community, which matures progressively with animal growth. However, knowledge of the bacteriome and metabolome dynamics in cecum and colon during the early lives of neonatal ruminants is limited. Thus, we examined the bacteriome and metabolomes of the cecum and colon in neonatal sika deer at days 1, 42 and 70. The bacterial diversity and richness in the cecum and colon increased with age, and the bacterial community significantly changed across three time points. For cecum and colon, the proportions of Bacteroides spp., Escherichia-Shigella, Clostridium sensu stricto 1, Lachnoclostridium spp. and Lactobacillus spp. were predominated at day 1 and decreased with age, while the proportions of Ruminococcaceae UCG 005, Ruminococcaceae UCG 010, Rikenellaceae RC9 and Prevotellaceae UCG 003 were predominated at days 42 and 70 and increased with age. The concentrations of creatine and serine were significantly decreased, whereas the concentrations of total short-chain volatile fatty acids, pelargonic acid and leucine were increased in both the cecum and colon during development. These data document the development of the bacterial community and the metabolites in the cecum and colon of sika deer, and suggest a possible importance of ecology niche on gut development.