holobiont

Holobiont is the term used to describe a host organism and all of its associated microorganisms, including bacteria, archaea, fungi, protists, and viruses, along with the collective genome of these partners. The concept, popularized by Lynn Margulis, emphasizes that the host and its microbiota form a single ecological unit whose interactions influence development, physiology, and ecology. The term is closely linked to the hologenome concept, which regards the combined genetic material of the host and its microbiota as the unit of natural selection.

Holobionts are characterized by a dynamic and context-dependent assemblage of microbial residents that are acquired from the environment or transmitted across generations. The microbiota can be mutualistic, commensal, or occasionally parasitic, and it can contribute to digestion, immune function, nutrient acquisition, and protection against pathogens. The composition of a holobiont is influenced by host genotype, diet, health, age, and environmental conditions, leading to a core microbiome in some taxa and highly variable communities in others.

In research, holobionts are studied across plants, animals, and other life forms to understand how host–microbe interactions shape development, metabolism, and adaptation. Examples include plant–rhizosphere communities that aid nutrient uptake, and human-associated microbiomes that influence digestion and immunity.

Debates surround whether holobionts act as cohesive units of selection or whether they are transient associations. Critics argue that not all members are reliably transmitted or integrated, challenging the view of holobionts as strict evolutionary units. Nonetheless, the concept provides a framework for examining the integrated biology of hosts and their microbial partners.

Methods such as metagenomics, metatranscriptomics, and 16S rRNA sequencing are used to characterize holobionts, revealing patterns of diversity, function, and dynamics within these complex assemblages.