Identification of microbiome tailored strategies to improve safety and sustainability of the poultry food system

This PhD study aimed to identify microbiome tailored strategies to improve safety and sustainability of poultry food system. Three methodological approaches were followed. Initially observational trial was conducted to identify microbiome population that consistently circulating in poultry house with better biosecurity infrastructures. Microbiome biomarkers were characterized by using 16S metagenomic sequencing and analysed with network analysis. Then, systematic literature review was conducted to identify nutritional strategy able to support microbiome markers identified in observational trial. Finally, intervention trial was conducted to test the efficacy of the identified supplement and re-check microbiome dynamics to validate the impact of the intervention on microbiome markers. Link between caeca microbial composition and microbiological safety of the meat was assessed. Observational trial identified Psychrobacter and Ruminiclostridium 9 for their positive actions whereas Bacteroides for negative action. The systematic review identified 91 nutritional interventions that can modulate gut microbiome of broilers and play role in improving performance and control of pathogens. Muramidase was found as the most suitable candidate to support target microbial communities identified in observational trial. Based on observational trial, systematic review, and discussion made with project partners, Muramidase was selected as feed supplement for the intervention trial. Genus level beta diversity showed Muramidase supplementation supported the modulation of caeca microbiome in the interventional trial versus the microbiome composition mapped in the chickens with better biosecurity infrastructures during the observation trial. This shift in the caecal microbiome did not result in better animal performances and blood biomarkers. The study provides insight on the contributions of factors that can possibly affect the microbial dynamics and jeopardize Muramidase supplementation. The findings highlighted the application of shotgun metagenomics sequencing technology for detection of foodborne pathogens. This study strongly encourages future studies on microbiome investigations in different components of broiler food system.