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Prospecting the Chicken Microbiome for Anti-Infective Probiotics

2022 CPRF,Nutrition
The use of antibiotics in agriculture has significantly contributed to the expansion and global spread of antibiotic-resistant bacteria. In Canada, category I and II antibiotics are no longer used by poultry producers; however, poultry raised without in-feed antibiotics tend to have higher incidences of bacterial pathogens, posing a significant threat to both poultry health and food safety. Probiotics are an antibiotic alternative approved for use in chickens to reduce pathogen contamination. The most approved probiotic for chicken flocks are Gram-positive bacteria, while little is known about the probiotic potential of Gram-negative bacteria. Existing in 25% of Gram-negative bacteria, Type VI secretion systems (T6SSs) is a contractile protein nanomachine with the potential to increase their interspecies competitiveness and kill pathogens. Therefore, we hypothesize that certain Gram-negative bacteria with T6SSs from the chicken intestine have the potential to become effective probiotics for chickens. We will test this hypothesis in three ways: 1. Use a combined culture-dependent culturomics and culture-independent metagenomic approach to characterize and isolate a range of Gram-negative bacteria from the chicken intestine; 2. Test the anti-infective effect of isolates with novel T6SSs; 3. Whole-genome sequence strains with anti-infective activity. In the present work, we attempted to fill knowledge gaps regarding the diversity of domesticated poultry microbiome and establish a culture collection of commensal bacteria from healthy Canadian poultry. We have collected six chicken fecal samples from different farms and obtained 3898 unique bacterial isolates from 48 different genera. After the competition assay, some strains from Escherichia, Cronobacter and Citrobacter genus can decrease zoonotic pathogen colonization and show anti-infective ability. Future research will continue to identify the antagonistic activities of the Gram-negative bacteria isolates and sequence the whole genome for safety assessment.
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PhD Candidate

McGill University

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