The microbiome consists of the totality of all microbial species in a human host. It includes a combination of bacteria (bacteriome), viruses (virome) and fungi (fungome). Recent advancements in sequencing technologies and bioinformatics techniques have allowed for the large-scale characterisation of the microbiome in both healthy individuals and diseased patients. This research has shown that the microbiome (in particular the gut microbiome) plays in important role in the regulation of the host immune system, with a healthy microbiome being an essential element of good health. However, our understanding of the role of the microbiome in the context of patients with immune dysfunction is limited. It is particularly unclear how the microbiome influences the risk of downstream complications of therapies linked to immune dysfunction (e.g. stem cell transplant, steroids, antibiotics etc).