The importance of the gut microbiome has become increasingly evident with an explosion of research linking its activity to a range of disorders and diseases from gut disease and autoimmune disease to brain function. Early colonisation in the infant is key to the establishment of a health microbiome. Breastfeeding is the major determinant of appropriate colonisation. Breastmilk contains many nutritional and functional components that promote colonisation by mainly bifidobacteria spp and fewer bacteroides and clostridia. These factors include human milk oligosaccharides, low iron and lactoferrin. Human breastmilk also has its own microbiome which may aid the colonisation process.