Bao, N., Qin, G., Zhang, P., Zhao, Y., Sun, Z. and Pan, L. 2014. Strain screening for lowering immune activity of β-conglycinin in defatted whole soybean flour through fermentation. Can. J. Anim. Sci. 94: 427-436. β-conglycinin is one of the major allergenic soybean proteins that can lead to hypersensitivity in newly weaned pigs or calves. The goal of this study was to evaluate the activities of various microorganisms on the immunogenicity of β-conglycinin in newly weaned pigs following fermentation. Defatted whole soybean flour (SBM) was separately fermented in a 5-L fermenter with one of 10 microorganisms (Bacillus subtilis subsp. spizizenii, Bacillus licheniformis, Bifidobacterium breve, Bifidobacterium animalis, Bifidobacterium longum, Aspergillus oryzae, Aspergillus niger, Lactobacillus fermentum, Saccharomyces cerevisae and S-8) for 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, or 48 h. The molecular weight and the reactogenicity of β-conglycinin (intact β-conglycinin and/or its degradation product) in the SBM before and after fermentation were measured using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Western blot, and enzyme-linked immunosorbent assay (ELISA). After 12 h of fermentation with Bacillus licheniformis, S-8, Bacillus subtilis subsp. spizizenii, or Bifidobacterium longum, the reactogenicity was lowered to less than 40% and their inactivating immunogenicities were more effective than those of the other microorganisms (P≤0.01). The a and a' levels of β-conglycinin decreased significantly in the samples (P<0.05) fermented for 48 h with Bacillus subtilis subsp. spizizenii, Bacillus licheniformis, Bifidobacterium breve, Bifidobacterium animalis, or Bifidobacterium longum. The level of β-conglycinin in the SBM fermented with S-8 was decreased by 44.73% after 8 h (P<0.01) and completely hydrolysed to small (<20 kDa) peptides after 24 h. These data demonstrated that S-8 was the most effective microorganism for inactivating the allergenicity of β-conglycinin in SBM. This study may directly benefit the production of low soybean allergen food for animals.