The temporal and spatial dynamic characterization of intestinal microbiota in Taihe Silky Fowl

Abstract Background Through large-scale sampling and 16S sequencing at 8 timepoints and 3 intestinal regions (288 samples), this study aimed to systematically elucidated the dynamic characterization in intestinal microbiota and core microbiota of Taihe Silky Fowl, providing a theoretical basis for precise regulation of native microbiota in this precious Chinese local breed through nutritional means. Results The results showed that the alpha and beta diversity of intestinal microbiota changed significantly with the different age and intestinal regions. In alpha diversity, Ace index and Shannon index: cecum > rectum > duodenum; Simpson index: cecum > rectum and duodenum. In beta diversity, compared to the duodenum and rectum, cecum samples were more concentrated. The core phylum (top 5) of Taihe Silky Fowl was Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Cyanobacteria. The core genus (top 10) was Lactobacillus, Bacillus, Escherichia-Shigella, Alistipes, norank_o__Clostridia_UCG-014, Bacteroides, Faecalibacterium, norank_f__Ruminococcaceae, Enterococcus and Streptococcus. As age increased, the cecal microbiota degree centrality rapidly increased from 0 to 1 weeks old, then rapidly decreased from 1 to 2 weeks old and remained relatively stable from 2 to 21 weeks old, while the betweenness centrality was opposite. Closeness centrality decreased continuously with increasing age. The cecal microbiota function varied at different age, the central functions were nucleic acid metabolism and protein synthesis in 0 weeks old, carbohydrate metabolism and quorum sensing in 9 weeks old. Conclusions In conclusion, the structure, composition, and function of intestinal microbiota in Taihe Silky Fowl dynamically changed with age and intestinal regions.