Antimicrobial compounds from Bacillus subtilis for use against animal and human pathogens. A novel strain of Bacillus subtilis was isolated from the gastrointestinal tract of poultry and was found to produce a factor or factors that have excellent inhibitory effects on Clostridium perfringens, Clostridium difficile, Campylobacter jejuni, Campylobacter coli, and Streptococcus pneumoniae. The factor(s) retain full viability and antimicrobial activity after heat treatment. The invention provides a method of treatment of pathogenic microorganisms including C. perfringens.