hologenome

Definition: The hologenome is the sum of the genetic material of a host and its associated microbial communities, including bacteria, archaea, fungi, viruses, and other microorganisms. The hologenome concept treats the host and its microbiome as an integrated unit of biology, sometimes referred to as a holobiont, in which the genomes of host and microbes interact to influence development, physiology, and adaptation.

Origins and scope: The term and its formalization as a theory were proposed by Eugene Rosenberg and colleagues in the late 2000s. They argued that natural selection can act on the hologenome as a unit, rather than on the host genome alone, owing to tight functional relationships with microbial partners.

Components and dynamics: The hologenome includes the host genome plus microbial genomes that persistently associate with the host. Microbial communities can be inherited vertically or acquired anew (horizontally). Microbial genes contribute functions such as digestion, immunity, metabolism, and resistance to stress; the host genome, immune system, and environment shape microbiome composition and activity.

Implications and methods: Research spans humans, animals, plants, and invertebrates. Metagenomics, metatranscriptomics, and metabolomics reveal the functional potential of the hologenome and how microbial activities affect host fitness and adaptation.

Criticism and debates: The concept is contested. Critics argue that selection largely acts on the host and microbes separately, that holobiont boundaries are fluid, and that defining fitness at the hologenome level is challenging. Proponents emphasize contextual utility for understanding host-microbe interactions.

See also: Holobiont, microbiome.