Bacillus species, particularly Bacillus subtilis, are used as probiotics, and research suggests they play a crucial role in the development of a strong gut-associated lymphoid system (GALT). In this study, various gut isolates of Bacillus, including B. subtilis, Bacillus licheniformis, and Bacillus flexus, were used to investigate their interaction with the GALT. Mice orally administered with Bacillus spores showed evidence of cell proliferation in the germinal centers of Peyer’s patches. The spores enhanced stimulation of antigen-presenting cells and T lymphocytes, leading to the induction of cytokines, including proinflammatory cytokines like tumor necrosis factor-alpha and IL-6 in the spleens and mesenteric lymph nodes of the mice. Additionally, the study found that vegetative cells of B. subtilis stimulated the expression of toll-like receptor (TLR) genes TLR2 and TLR4, but spores interacted with another TLR, promoting the activation of innate immunity.