Chicken meat is an important source of dietary protein in the global food chain. Although broiler chicken production is efficient compare to other sources of animal protein productivity will need to be increased through sustainable and ethical approaches to provide hygienically safe meat to meet the needs of a growing human population. Traditional methods of improving productivity have plateaued and new approaches are required to improve returns. Manipulation of the gut microbiota with antibiotic growth promotors has been a mainstay to improve growth performance, however this approach has fallen out of favour with regulators and consumers due to concerns about the spread of antimicrobial resistance. A potential alternative is the prebiotic galacto-oligosaccharide (GOS) - a by-product of the dairy industry that has been shown to affect human physiology. The articles presented here are the outputs of a systems biology approach to describing the effects of GOS on broiler chickens and upon colonization by the zoonotic pathogen Campylobacter jejuni. The focus of this thesis are findings generated by analysis of the gut microbiota using 16S rDNA cataloguing. The results show that the growth performance of fast-growing broiler chickens is improved by dietary GOS compared to birds sustained on an isocaloric control diet. Additionally, results presented here show how the dynamics of C. jejuni colonization are affected by the age of the bird at challenge alongside the accompanying changes to the gut microbiota and innate immunity. Finally, results demonstrate that phage therapy can reduce C. jejuni colonization of the gastrointestinal tract by >2 log10 CFU ml-1 without provoking dysbiosis of the gut microbiota. The novel findings presented here are of interest to the poultry industry and are the first step in determining a mode of action for GOS and potentially other prebiotic oligosaccharides. This work provides a foundation for future research with the goal of designing functional feed compositions to sustainably enhance chicken production whilst making the chicken gut less hospitable to pathogenic bacteria.