Probiotics or direct-fed microbials (DFM) are alternatives to antibiotic growth promoters (AGP) in poultry production. However, there is limited information on their role in birds subjected to an enteric pathogen challenge. Herein are the investigations of Bacillus subtilis (BS-9) DFM on the growth performance and intestinal histomorphology (Chapter 3; Experiment 1) and on cecal microflora activity (Chapter 4; Experiment 1 & 2) in Ross x Ross 708 broiler chickens subjected to an Eimeria challenge. The DFM improved body weight, weight gain, and intestinal surface area but not feed conversion ratio (FCR). However, DFM birds had similar FCR to non-challenge control due to increased feed intake (FI), reduced members of Clostridiales, and altered SCFA production. The DFM effect on members of Firmicutes, particularly from order Clostridiales, was interactive, with the largest reduction in challenged DFM birds. Overall, DFM mitigated the adverse effects of an Eimeria challenge, suggesting potential for modulating the gut microbiota.