In the last decade, biology has made revolutionary advances from century-old debates about the relative importance of non-pathogenic bacteria. Today we know that individuals are not solitary, homogenous entities but consist of complex communities of many species that likely evolved during a billion years of coexistence. Holobionts (hosts and their microbes) and hologenomes (all genomes of the holobiont) are multipartite entities that result from ecological, evolutionary and genetic processes. I propose, therefore, that the health of animals, including humans, is fundamental multi-organismal; that any disturbance within the complex community of host and microbial cells has drastic consequences for the wellbeing of the individual member of this association; and that the microbiome should be viewed as an organ of the host. This newfound awareness of the dependency of phenotypes on other species and environmental conditions presents additional layers of complexity for the life sciences including medicine and evolutionary theory; and raises many questions that are being addressed by new research programmes.