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 Bacillus spp. offer advantages over traditional probiotic strains as Bacillus 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 Bacillus spores as feed additives, detailed characterizations of Bacillus 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 Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-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 Ba PTA84-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.

In silico, in vitro and in vivo characterization of host-associated Latilactobacillus curvatus strains for potential probiotic applications in farmed Atlantic salmon (Salmo salar)

“…Lactic acid bacteria were passaged under both aerobic and microaerophilic conditions at 15 °C and 23 °C. Three of the candidates used in salmon studies were Bacillus isolated in the same way from chicken cecum and swine intestine described previously 40 , 41 .…”

“…Candidates were sent to Microbial Research Inc (Fort Collins, CO) for antimicrobial susceptibility analysis, performed as previously described 40 , 41 for Bacillus. Latilactobacillus strains were also analyzed at Microbial Research Inc using broth microdilution method in laked horse blood (LHB) medium [Mueller Hinton broth (BD) containing 5% horse blood] following Clinical and Laboratory Standards Institute (CLSI) guidelines.…”

Identification and characterization of the causative agents of Focal Ulcerative Dermatitis in commercial laying hens

“…Bacilli are endospore-forming bacteria widely used in DFM preparations due to their ability to survive high temperatures, acidic environments, and desiccation, thus increasing their viability during manufacturing and pelleting processes and enhancing their stability in the host' GIT ( 54 , 55 ). They are known to promote gut health by the production of enzymes, antimicrobial peptides, and other metabolites that inhibit/reduce the growth of bacterial pathogens ( 56 ).…”

Screening and characterization of Bacillus velezensis LB-Y-1 toward selection as a potential probiotic for poultry with multi-enzyme production property

“…Bacillus spp. was isolated according to the method described as previously, with minor modification ( Susanti et al, 2021 ; Liu et al, 2022 ). Heat the intestinal contents at 95°C for 5 min in order to separate out the Bacillus spores, followed by a 10-fold series dilution with sterile normal saline to ensure recovery of individual colonies on agar plates.…”