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Background  Some  Bacillus  strains have recently been identified for potential use as probiotics and food additives. The present study evaluated the antimicrobial effects of  Bacillus subtilis  ATCC 6633 and its metabolite on the enterotoxin and vegetative cells, spore and germinated spore of  Clostridium perfringens  type A in Caco-2 cells.    Results  We used flow cytometry and MTT assays to evaluate the cytotoxicity effect of treatments. According to the results, the most cell survival was found in the 4% crude antimicrobial substance (CAS) with the vegetative form of  C. perfringens  among co-cultured groups. Furthermore, the apoptosis and necrosis in co-cultured groups were significantly decreased ( P  < 0.05).    Conclusion  The present results suggested the crucial role of the current probiotic in the control of various forms of  C. perfringens  type A which was investigated for the first time. Also, the majority of treatments showed higher cell viability in flow cytometry compared to the MTT assay.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-1051-1) contains supplementary material, which is available to authorized users.

The effects of probiotic Bacillus subtilis on the cytotoxicity of Clostridium perfringens type a in Caco-2 cell culture