Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry

Abstract

Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming <i>Bacillus</i> spp. offer advantages over traditional probiotic strains as <i>Bacillus</i> spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal's gastrointestinal tract. Despite numerous reports on the use of <i>Bacillus</i> spores as feed additives, detailed characterizations of <i>Bacillus</i> probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of <i>Bacillus</i> spp. for use in broiler chickens. Host-derived <i>Bacillus</i> strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two <i>Bacillus amyloliquefaciens</i> (<i>Ba</i> ATCC PTA126784 and ATCC PTA126785), and a <i>Bacillus subtilis</i> (<i>Bs</i> ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of <i>Ba</i> ATCC PTA12684 (<i>Ba</i>-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from <i>Ba PTA</i>84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.