A Bacillus -based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella -infected pigs

Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus -based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella -infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella -only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella -only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health. IMPORTANCE Antibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus , as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella -infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus -based DFM could improve outcomes along the gut–lung axis under realistic co-infection conditions.