Analysis of microbial diversity and composition in small intestine during different development times in ducks

We studied the microbial profiles of the duodenum, jejunum, and ileum during different developmental stages in the duck using high-throughput sequencing of the bacterial 16S rRNA gene. We also investigated the differences in the microbiota in the duodenum, jejunum, and ileum at different developmental times. A correlation analysis was performed between the most abundant bacterial genera and the development of the small intestine. An analysis of alpha diversity indicated different species richness and bacterial diversity in the different small intestinal segments and at different development times. A beta diversity analysis indicated differences in the bacterial community compositions across time. In a weighted UniFrac principal coordinates analysis, the samples clustered into two categories, 2 to 4 wk and 6 to 10 wk, in the duodenum, jejunum, and ileum. Our results show that the small intestine is predominantly populated by the phyla Firmicutes, Bacteroidetes, and Proteobacteria throughout the developmental stages of the duck. The duodenum, jejunum, and ileum shared most of the bacterial phyla and genera present, although they showed significant differences in their relative abundances in the intestinal segments and developmental stages. They shared different bacterial taxa during development times and among different segments when the intergroup differences were analyzed. The genera Bacillus, Corynebacterium 1, Lactococcus, Sphingomonas, and Haliangium correlated moderately positively with the increase in bodyweight and the lengths and weights of the duodenum, jejunum, and ileum, and these genera may be considered important markers when assessing the heath of the intestinal microbiota in ducks. This study provides a foundation upon which to extend our knowledge of the diversity and composition of the duck microbiota and a basis for further studies of the management of the small intestinal microbiota and improvements in the health and production of ducks.