A holobiont is a multi-species assemblage consisting of a host organism and its associated communities of microorganisms — bacteria, archaea, fungi, viruses. The term, introduced by Lynn Margulis and popularized in the context of coral biology by Forest Rohwer, designates not just the host but the entire consortium of organisms that function as an integrated biological unit.
The human holobiont includes roughly as many microbial cells as human cells. The gut microbiome participates in digestion, synthesizes essential vitamins, trains the immune system, influences neurological function through the gut-brain axis, and mediates susceptibility to disease. These are not peripheral additions to human physiology; they are constitutive components of it. A germ-free mouse — raised without microbiome — has an underdeveloped immune system, altered brain chemistry, and abnormal gut morphology. The “individual” organism, stripped of its microbial partners, is not the same organism functioning in isolation. It is a different organism.
Fungal associations push the holobiont concept further. Lichens are composite organisms — a fungus, a photosynthetic alga or cyanobacterium, and often additional microbial communities — whose body emerges entirely from the association. No single partner generates the lichen structure; it is produced by the relation itself. Mycorrhizal networks extend the holobiont principle to the landscape scale: fungal hyphae connect the roots of multiple plants, often of different species, into shared nutrient economies. The boundaries of the holobiont become not just negotiable at the individual level but dissolved into a network that encompasses entire plant communities and their fungal partners.
The holobiont concept raises a fundamental question about biological individuality. If the functional unit is the multi-species assemblage rather than the genetically defined organism, then what counts as an individual? The boundary between self and non-self becomes a product of immunological and metabolic negotiation rather than a given. The immune system does not simply reject foreign organisms; it manages a community, tolerating beneficial symbionts and policing the boundary between mutualism and pathogenesis. Individuality is maintained not by exclusion but by relational management.
For the vault’s relational framework, the holobiont is a concrete case study in relational individuality. The holobiont is not an entity that enters into relations with its microbiome; it is constituted by those relations. Remove the relations — eliminate the microbiome — and what remains is not the “real” individual minus accessories. What remains is a biologically impoverished system that can barely function. The holobiont demonstrates at the biological level what relationality argues at the ontological level: individuals are constituted by their relations, not prior to them.
Related
- Symbiosis — the relational foundation of holobiont organization
- Autopoiesis — self-production at the holobiont level involves multi-species coordination
- Homeostasis — maintained across species boundaries within the holobiont
- Niche Construction — holobionts as niche constructors at micro and macro scales
- Fungal Symbiosis — lichens and mycorrhizae as holobionts that challenge individuality
- Mycelial Networks — network-scale holobionts connecting entire plant communities