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The mammalian gut microbiome participates in almost all life processes in the host. In addition to diet, the breed is the main factor affecting changes in the swine gut microbiota. The composition of the gut microbiota changes significantly during different growth stages. Research on developmental changes in the gut microbiota of indigenous Chinese pig breeds is limited. In this study, the fecal microbiota of Wuzhishan pigs (a Chinese indigenous miniature pig) at different growth stages was investigated using high-throughput 16S rRNA sequencing.  Firmicutes  and  Bacteroidetes  were the two dominant phyla, accounting for more than 80% of all sequences. With increasing age, the fecal microbial diversity increased, and the proportion of  Firmicutes  increased, whereas the proportion of  Bacteroidetes  decreased. A total of 49 biomarkers with statistical differences were detected in the four growth stages. The different microbiota among groups enhanced the ability to degrade fiber, carbohydrates, and other substances during the growth stages. The endocrine system was different in multiple growth stage paired comparisons, which was attributed to the different body statuses in the growth stages. This study revealed developmental changes in the structure and function of gut microbes in local pigs.   Supplementary Information  The online version contains supplementary material available at 10.1186/s13568-021-01249-x.

Fecal microbial composition and functional diversity of Wuzhishan pigs at different growth stages