[Objective] Koumiss had beneficial therapeutic effects on cardiovascular disease, digestion disease, tuberculosis, diabetes and diarrhea, especially Kluyveromyces marxianus had antibacterial effect on Listeria monocytogenes. There was limited knowledge about antimicrobial compounds of K. marxianus in Koumiss, so, we evaluated the effect of antimicrobial compounds of K. marxianus in Koumiss on immune function and caecal microflora in mice challenged with pathogenic Escherichia coli O8. [Methods] Kunming strain mice (128 heads, 20±2 g) were divided into 4 groups, the control group, the challenged control group，K2 group, and K8 group. Mice in the challenged control group were oral administrated sterile PBS by gavage for 7 d, then were administered intraperitoneally E. coli O8 at 4 d. Mice in K2 group were oral administrated K. marxianus pH 2.0 and K8 group were oral administrated K. marxianus pH 8.0, then were administered intraperitoneally E. coli O8. The pathological section of small intestine of mice were observed by HE staining at 0, 4, 7 d. The thymus index and spleen index were weighed and calculated. Immunoglobulins in serum were monitored by enzyme-linked immunosorbent assay (ELISA). T subsets were analyzed by ?ow cytometry. The caecal microflora was calculated by the spread plate method. [Results] Mice in the challenged control group appeared clinical symptoms and pathological changes of small intestine after they were challenged with E. coli O8 at 4 d. Mice in K2 and K8 groups had better mental state, and less died mice than the challenged control group, K2 and K8 could improve pathological changes of small intestine after mice were challenged with E. coli O8. Compared with the control group, the thymus index was decreased at 7 d by the challenged control group, while the spleen index was increased at 4 d and 7 d by K2 and K8 groups (P<0.05). Compared with the control group, IgA was decreased at 7 d by the challenged control group, while IgA and IgG were increased at 4 d, IgG and IgM were increased at 7 d by K2 group, IgM was increased at 7 d by K8 group (P<0.05). Compared with the control group, CD8+ was decreased and CD4+/CD8+ was increased at 4 d and 7 d by K2 group, CD8+ was decreased at 4 d by K8 group, CD8+ was decreased and CD4+/CD8+ was increased at 7 d by K8 group (P<0.05). Compared with the control group, E. coli was increased and Bifidobacterium was decreased at 7 d by the challenged control group (P<0.05), while E. coli was decreased, Enterococcus was decreased, and Lactobacillus was increased at 7 d by K2 group (P<0.05), Enterococcus was decreased, Lactobacillus was increased at 7 d by K8 group (P<0.05). [Conclusion] These results suggested that antimicrobial compounds of K. marxianus in Koumiss named K2 and K8 could ease clinical symptoms after mice were challenged with pathogenic E. coli O8, enhance their immune function, influence their caecal microflora as Bifidobacterium and Lactobacillus increased, E. coli and Enterococcus decreased.