Abstract/Summary

Advances in genetic selection and intensification of management systems has led to the production of highly efficient broiler chickens. Attention is being turned to the role of gut microbes to further growth efficiency and improve animal health, particularly with the rise of antimicrobial resistance and the need to consider animal welfare and food safety. The microbiome is sensitive to management strategies, which may affect the growth and metabolism of the bird. Here, four studies are presented which explore the effects of antibiotic treatment with Linco-spectin and the subsequent use of Aviguard®, a mixed probiotic, diet in terms of protein source and the use of wheat or maize as a cereal base, and the supplementation of bedding with excreta from mature birds on the caecal microbiome and hepatic metabolome of broilers through population profiling metabolomic approaches. A final analysis of all datasets highlights consistent trends that appeared irrespective of treatment. Alpha diversity increased between days 4 and 9 (P<0.001) and 15 and 22 (P=0.001) and was affected by all treatments but differences dissipated with age. Beta diversity also changed with age, but again differences were reduced by around two weeks of age, suggesting that diversity naturally reaches a plateau, irrespective of perturbations in early life. Age-related shifts in bacterial populations were observed in all studies with a reciprocal relationship between phyla Firmicutes and Tenericutes (P<0.001). The microbiome was consistently affected by management strategy, with evidence that different taxa are affected by diet, bedding and antibiotic/probiotic treatment. Energyrelated metabolites were affected by treatment, but birds appeared to grow equally as well suggesting isofunctionality of the hepatic metabolome. Concentrations of short chain fatty acids (SCFA) increased between days 4 and 15 (P<0.001) and were affected by diet alone. Concentrations of all SCFA exhibited both positive and negative relationships with bacterial taxa. Despite the plethora of treatment-associated differences in the microbiome, no single group of birds performed worse than another with a lack of a significant relationships between differences in the caecal bacterial populations and differences in feed conversion ratio (r=0.386; P=0.270). It is hypothesised that the ability of a bird to thrive and grow is independent of the profile of its microbiome, so long as key metabolic activities are performed. This thesis is an overview that will provide a base to be utilised in exploring more specific relationships in depth in future work with methods and understanding of metagenomic-metabolomic relationships improved by the findings herein.