The gut is home to an astonishingly diverse, dynamic, and populous ecosystem. This complex microbial community, termed the microbiota, is critical for host wellbeing. Disturbances in our microbiota, such as via caesarian sections and antibiotic exposure, can lead to increased susceptibility to pathogens, as well as atopic, and chronic inflammatory diseases. Bifidobacteria constitute a substantial proportion of the gut microbiota, particularly during early life and high-levels are associated with the development of mucosal defence. Currently there are many bifidobacterial species and strains with claimed health promoting or ‘probiotic’ attributes, however the mechanisms through which these strains reside within their host and exert benefits is far from complete. In this talk I will discuss the role of the gut microbiota with the host, focusing on the example of bifidobacteria in host colonisation, epithelial cell cross-talk, pathogen protection, and how probiotics represent a powerful opportunity for strategically manipulating the early life microbiota when bacterial assembly is disturbed within the context of preterm birth.