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Background Rearing systems can affect livestock production directly, but whether they have effects on intestinal growth states and ceca microorganisms in ducks is largely unclear. The current study used Nonghua ducks to estimate the effects of rearing systems on the intestines by evaluating differences in intestinal growth indices and cecal microorganisms between ducks in the floor-rearing system (FRS) and net-rearing system (NRS). Results The values of relative weight (RW), relative length (RL) and RW/RL of the duodenum, jejunum, ileum and ceca in the FRS were significantly higher than those in the NRS during weeks 4, 8 and 13 ( p  &lt; 0.05). A total of 157 genera were identified from ducks under the two systems, and the dominant microorganisms in both treatments were Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria at the phylum level. The distribution of microorganisms in the ceca of the two treatments showed significant separation during the three time periods, and the value of the Simpson index in the FRS was significantly higher than that in the NRS at 13 weeks ( p  &lt; 0.05). Five differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 4, seven differential microorganisms and 25 differential metabolic pathways were found in the ceca at week 8, and four differential microorganisms and two differential metabolic pathways were found in the ceca at week 13. Conclusions The rearing system influences duck intestinal development and microorganisms. The FRS group had higher intestinal RL, RW and RW/RL and obviously separated ceca microorganisms compared to those of the NRS group. The differential metabolic pathways of cecal microorganisms decreased with increasing age, and the abundance of translation pathways was higher in the NRS group at week 13, while cofactor and vitamin metabolism were more abundant in the FRS group.

Effects of floor- and net-rearing systems on intestinal growth and microbial diversity in the ceca of ducks