Although the environmental exposures are highly relevant and might at least partly transit to the body, microbes direct living on/in our body intuitively seem stronger involved in disease processes. This concerns different body sites. While the respiratory tract is the obvious target for respiratory diseases, the skin might be more relevant for atopic dermatitis, the gut for food allergy. Moreover the concept of a gut-lung or a gut-skin axis highlights the importance of the gut microbiome. We could show that the early maturation of the gut microbiome during the first year of life contributes to the protective effect of farming on childhood asthma. Also a higher cytokine activation by consumption of unprocessed cow’s milk was in part mediated by the gut microbiome. Looking at the upper respiratory tract, differences between asthmatics and healthy controls are more seen in the nose than in the throat. Now, there is ongoing work to further disentangle microorganisms or their interactions which are associated with allergic diseases.