The invention relates to applications of Bacteroides fragilis in animal breeding, particularly to applications of Bacteroides fragilis in prevention and/or treatment of animal gastrointestinal diseases and in pharmaceutical compositions and feed additives, wherein the Bacteroides fragilis is ZY-312 and has the preservation number of CGMCC No.10685. According to the present invention, the Bacteroides fragilis ZY-312 does not contain the enterotoxin gene bft, has significant and high capabilities of cholate resistance and gastric acid resistance compared with the existing Bacteroides fragilis, can effectively prevent and/or treat animal gastrointestinal diseases, improves animal immunity and disease resistance, reduces animal prevalence, improves animal feed conversion rate, increases animal weight, promotes growth and development and production performance, can reduce the use of antibiotics, does not produce drug resistance, further has characteristics of safety and no toxicity, can improve the quality of products such as meat, eggs, milk and the like, can eliminate antibiotic drug residues, purify mew environment, and protects ecological environment.