The animal’s gut is a complex microbiological ecosystem playing key roles in shaping the host metabolism and maintaining the host health. It has been well understood that intestinal microflora is involved in nutrients metabolisms, such as carbohydrate metabolism, lipid metabolism, protein metabolism, and vitamin production. It also regulates immune responses and protects the host from pathogenic bacteria. In the past two decades, exogenous probiotics have been successfully developed and widely used to regulate micro-ecology in animals’ guts and replace antibiotics for sustainable farming.

With the rapid development of molecular biology and bioinformatics, animal intestinal metagenomic studies show that there exist great differences between the dominant flora of animal’s small and large intestine. The dominant flora of small intestine is lactic acid bacteria, while the dominant flora of large intestine is the symbiotic Clostridium. Therefore, the commercial probiotic products should consider the characteristics (composition, diversity, and function of the microbiota) of microflora in the different parts of animal intestine and the interaction with endogenous microorganisms, so as to build microbial protection barriers and realize the whole-intestinal health.