Assessment of Microbiota Modulation in Poultry to Combat Infectious Diseases

SIMPLE SUMMARY: This research was designed to evaluate the differences in caecal microbiota in broilers reared under two different farm conditions (commercial vs. optimal) during the growing period, using 16 rRNA sequencing analysis. Microbiota composition is affected by stress; for this reason, it could be considered a biomarker of poultry welfare and health. The main results demonstrated that no statistically significant differences were found between groups on microbiota composition from the beginning to the mid-period. However, significant differences were found at the end of growing, when a higher level of microbiota diversity was observed in the optimal farm conditions group. In conclusion, microbiota composition could be an interesting tool to evaluate new management conditions at field level, and could be developed to improve animal welfare during the growing period. ABSTRACT: Poultry is one of the main agricultural sub-sectors worldwide. However, public concern regarding animal welfare and antimicrobial resistance has risen in recent years. Due to the influence of management practices on microbiota, it might be considered to evaluate poultry welfare and health. Therefore, the objective of this research was to analyse the influence on microbiota balance of broilers under commercial and optimal farm conditions, using 16S rRNA sequencing analysis. The research was performed in two identical poultry houses (commercial vs. optimal). Results showed a higher level of microbiota complexity in the group reared under optimal farm conditions at the end of rearing. Regarding microbiota composition, Firmicutes was the dominant phylum during the entire growing period. However, the second most prevalent phylum was Proteobacteria at the arrival day, and Bacteroidetes from the mid-period onward in both groups. Moreover, the most predominant genera identified were Oscillospira, Ruminococcus, Bacteroides, and Coprococcus. In conclusion, it is necessary to optimize farm management as much as possible. Using gut microbiota diversity and composition as biomarkers of animal health could be an important tool for infectious disease control, with the aim of reducing the administration of antibiotics at field level.