metaorganism

A metaorganism is the integrated unit formed by a host organism and its associated microbial communities, including bacteria, archaea, fungi, and viruses. The concept emphasizes that the physiology, development, and health of the host are closely shaped by these microorganisms, which can act as a functional extension of the organism.

The term is used across plants and animals, including humans, to describe how the host and its microbiota operate together as a system. The boundary between host and microbiota is context-dependent and can shift with health, diet, environment, and life stage. Related ideas include the holobiont and the hologenome theory of evolution, which propose that hosts and their microbial partners form co-evolving units.

Within a metaorganism, interactions among residents influence metabolism, immune function, development, and defense against pathogens. Microbiota can provide nutrients, synthesize essential compounds, modulate immune responses, and help defend against invaders, while the host offers habitat, resources, and selective pressures that shape microbial communities. Both mutualistic and commensal relationships are common, with pathogenic microbes representing a potential, though typically conditional, component of the system.

Research approaches include metagenomics, metatranscriptomics, metabolomics, and gnotobiotic models to dissect the contributions of microbial partners. Clinically and environmentally, the metaorganism concept informs therapies such as probiotics, prebiotics, diet modification, and microbiota transplants, with implications for health, disease, agriculture, and ecology.

Despite its utility, the concept faces debates about boundaries and levels of selection, and about how best to define a unit of analysis given the fluid and context-dependent nature of host–microbiota associations.