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As alternatives to antibiotics in feed, probiotic  Bacillus  carries multiple advantages in animal production. Spores undergo strain-related germination in the gastrointestinal tract, but it is still unknown whether the probiotic function of the  Bacillus  depends on the germination of spores  in vivo . In this study, based on 14 potential probiotic  Bacillus  strains from fermented food and feed, we detected the germination response of these  Bacillus  spores in relation to different germinating agents. The results showed the germination response was strain-specific and germinant-related, and nutrient germinant L-alanine significantly promoted the growth of strains with germination potential. Two strains of  Bacillus subtilis , S-2 and 312, with or without a high spore germination response to L-alanine, were selected to study their morphological and genic differences induced by L-alanine through transmission electron microscopy and comparative transcriptomics analysis. Consequently, after L-alanine treatment, the gray phase was largely increased under microscopy, and the expression of the germination response genes was significantly up-regulated in the  B. subtilis  S-2 spores compared to the  B. subtilis  312 spores ( p  &amp;lt; 0.05). The protective effect of L-alanine-induced spore germination of the two strains was comparatively investigated both in the IPEC-J2 cell model and a Sprague–Dawley (SD) rat model challenged by enterotoxigenic  Escherichia coli  K99. The result indicated that L-alanine helped  B. subtilis  S-2 spores, but not 312 spores, to decrease inflammatory factors (IL-6, IL-8, IL-1 β, TNF-α;  p  &amp;lt; 0.05) and promote the expression of occludin in IPEC-J2 cells. Besides, supplement with L-alanine-treated  B. subtilis  S-2 spores significantly improved the growth of the SD rats, alleviated histopathological GIT lesions, and improved the ratio of jejunal villus length to crypt depth in comparison to the  B. subtilis  S-2 spores alone ( p  &amp;lt; 0.05). Improved species diversity and abundance of fecal microbiota were only observed in the group with L-alanine-treated S-2 spores ( p  &amp;lt; 0.05). The study demonstrates L-alanine works well as a probiotic  Bacillus  adjuvant in improving intestinal health, and it also provides a solution for the practical and accurate regulation of their use as antibiotic alternatives in animal production.

Nutrient L-Alanine-Induced Germination of Bacillus Improves Proliferation of Spores and Exerts Probiotic Effects in vitro and in vivo