There is an increasing interest in the use of spore-forming Bacillus spp. as probiotic ingredients on the market. However, probiotics Bacillus species are insufficient, and more safe Bacillus species were required. In the study, traditional fermented foods and soil samples were collected from all over the country in China, and 506 Bacillus were selected from 109 samples. Using the optimized procedure, we screened 9 strains, which successfully passed the acid, alkali, bile salt and trypsin resistance test. Drug sensitivity test results showed that three Bacillus out of the 9 isolates exhibited antibiotic sensitivity to more than 29 antibiotics. The 3 strains sensitive to antibiotics were identified by 16S ribosomal RNA analysis, two isolates (38327 and 38328) belong to the specie Lysinibacillus macrolides and one isolate (37326) belong to Bacillus halotolerans. Moreover, the 3 strains were confirmed safe through animal experiments. Finally, L. macrolides 38327 and 38328 showed the protection in Salmonella infection mouse model, which manifested in slowing down weight loss, reducing bacterial load, improving antioxidant capacity. Altogether, our data demonstrate selected L. macrolides strains can be used novel probiotics for intestinal health.