Holobionts

A holobiont is a host organism together with its associated microorganisms, including bacteria, archaea, fungi, viruses, and their genetic material. The holobiont view treats the host and its microbiota as an integrated ecological and evolutionary unit, in which metabolic exchange and immune interactions shape physiology and development. The collective genome of the holobiont—host plus microbiome—is referred to as the hologenome.

Originating from the work of Lynn Margulis and later developed in symbiosis research, the holobiont concept emphasizes that many traits of an organism are influenced by microbial partners. The hologenome theory of evolution posits that natural selection can act on this combined genome, not solely on the host’s genome. However, this view is debated, because microbiome composition can change with environment and over time, and not all associations are strictly heritable. Holobionts can be maintained through vertical transmission of microbes, horizontal acquisition, or mixed modes, leading to varying degrees of genetic cohesion.

Examples include humans and their gut, oral, and skin microbiota; ruminant animals with specialized gut communities; corals with algal endosymbionts; and plants harboring endophytes. In research and medicine, holobiont concepts guide studies of health and disease, nutrition, and ecology, as well as agricultural and conservation strategies that consider microbiomes. Critics caution that the term is a useful descriptor rather than a universally applicable unit of selection, and that defining boundaries and heritability in complex microbiomes remains challenging.