Antibiotic resistance may have the potential to spread from animals to humans through the food chain. It has been observed that prebiotics such as mannan rich fraction (MRF) improve broiler growth and performance in a similar manner to antibiotic growth promotors. They have also been linked to a reduction in antibiotic resistance gene numbers. It was hypothesised that MRF has the ability to decrease resistance by reducing the variety or transfer of plasmids. The most effective and efficient method to extract plasmids from the complex broiler caecum was investigated, and determined to be the exogenous plasmid isolation method. Analysis into the plasmids present in the broiler caecum was performed for a greater understanding of the genetic basis of this resistance. Plasmids were identified that matched to previously isolated plasmids from animal and human samples from locations worldwide. The microbiome and mobile resistome was assessed over time. A more stabilised microbiota was found to develop as the birds age, which may be better established to harbour the increased number of resistance plasmids identified in the older birds. The effect of MRF on the metagenome of broilers was examined. No significant changes were observed in the microbiome, which we attributed to the already resident community of beneficial bacteria. Changes in the abundance of the resistome was observed at day 27, which may be the result of MRF, but high levels of variability were noted within the sampled groups. A study incorporating both metagenomic and plasmid based analysis concluded that MRF may have the ability to restore the microbiome of broilers after antibiotic treatment. A lower percentage of multi-drug resistance plasmids and a reduced profile of resistance was observed in birds that had received MRF. Mannan rich fraction may have the ability to decrease the conjugative capability of the plasmids, and thus reduce the spread of antibiotic resistance.