Biologists and philosophers of biology are increasingly focusing on the ecological and evolutionary dynamics of host-microbial organization, interaction, and function. They are pursuing questions about organismality, individuality, levels of selection, fidelity of microbiome transmission and/or transgenerational association among hosts, the scope of host-microbiota cooperation and conflict, and the scales at which ecology and evolution feed into each other in the context of host-microbial symbioses. The hologenome concept of evolution is one contemporary framework for engaging these questions. Its tenets are that hosts ubiquitously associate with symbiotic (i.e. resident) microbes, that these associations can affect the fitness of holobionts, that variation among hologenomes can arise via changes in host or symbiotic microbial genomes, and that specific microbial alleles can be reliably associated with host genomes across generations. The hologenome concept is a fundamental reconception of that which constitutes an individual animal or plant, in that it emphasizes that the phenotype of an individual host is necessarily a product of interactions among the host’s genome, its microbiome, and the environment. The value of the hologenome concept is then proportional to the fitness consequences of those interactions within holobiont populations and the extent to which those interkingdom allelic interactions transgenerationally occur.
A principal aim of ecology is to develop sufficient understanding of a system such that it can ultimately be managed. In addition to providing a vocabulary and framework for contemporary dialogue on hosts in light of their ubiquitous and intricate interactions with microbiomes, foundational theses such as the hologenome concept of evolution have theoretical and practical ramifications for the study of animal ecology, including medical microbiology. We are at a pivotal point in medical microbiology wherein researchers are shifting focus to studying microbiota in the context of individual hosts (i.e. holobionts) and utilizing systems-level approaches to investigate interactions between host genomes, microbiomes and environments (i.e. hologenomes). This shift in focus has promise for pursuing both understanding and management of complex medical syndromes of great health and economic consequence. A hologenomic perspective can be beneficially employed in the burgeoning subdisciplines of evolutionary and precision medicine, and can be directly applied to elucidating and managing holobiotic etiologies of metabolic and obstetric syndromes, such as obesity, type 2 diabetes, and preterm birth.