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Holobionts are assemblages of different species that form ecological units. Lynn Margulis proposed that any physical association between individuals of different species for significant portions of their life history is a symbiosis. All participants in the symbiosis are bionts, and therefore the resulting assemblage was first coined a holobiont by Lynn Margulis in 1991 in the book Symbiosis as a Source of Evolutionary Innovation. Holo is derived from the Ancient Greek word ὅλος (hólos) for “whole”. The entire assemblage of genomes in the holobiont is termed a hologenome.
In 1992, David Mindell subsequently used the word holobiont in a BioSystems article in general reference to host-microbe symbioses. This was followed in 1993 by its use in another BioSystems article by R. Jorgensen. The word rested dormant for about a decade. Forest Rohwer, Victor Seguritan, Farooq Azam, and Nancy Knowlton adopted the term in a figure legend to describe the complex relationships between various microbes and coral in 2002. In this system, the zooxanthellae determine the light level required by the coral holobiont and a complicated web involving the Bacteria, Archaea and fungi recycles its nitrogen. The word holobiont has been increasingly used since then, with its next appearance in 2005. It has been popularized by the hologenome concept. All macrobes, animals and plants, are today deemed holobionts consisting of the host plus its entire microbial community, and these associations can be transient or stable.Recently the concept of Holobiont has been extended to consider niche construction, given place to a new proposal of evolutionary ontology the "Ecobiont" which states that socio-cultural context may modulates evolutionary process, and so it must be taken into account. Consider the classic example of Kwa-speaking yam cultivators in West Africa. These people increased the frequency of a gene for sickle-cell anemia in their own population as a result of the indirect effects of a socio-cultural process: the yam cultivation. By making clearings in the rainforest for the yam cultivation, they created more standing water and increasing the breeding grounds for malaria-carrying mosquitoes. This, in turn, intensifies selection for the sickle-cell allele because of the protection offered by this allele against malaria in the heterozygotic condition. 
Relationship to viromes and microbiomes
Holobionts are traditionally divided into three major divisions: 1) viruses, 2) unicellular microbes and 3) the macrobial host. Collectively, the viruses make up the virome and microbes make up the microbiome. There is no specific terminology for other multicellular organisms associated with the holobiont other than symbiont. The collective genomic DNA and RNA of a holobiont is called a hologenome.
Holobionts are considered multipartite ecological entities, whereas hologenomes are multigenomic entities that encode holobiont phenotypes. Here, the word hologenome follows a conceptual continuum from words such as chromosome and genome. The terms are therefore structural definitions relating to host-microbial assemblages and their genomes.
Superorganisms are organisms consisting of many individuals and was first applied to the eusocial insects (Wheeler 1928). An ant colony is a superorganism. Holobionts are assemblages of many different species. Each ant is an individual holobiont consisting of the ant, fungi, bacteria, etc. However, ″superorganism″ has also been used as a synonym for ″Holobiont″.
Some authors reject the concept since they consider is far from encompassing most of host-symbiont relationships to make it justifiable. They would also argue that symbionts do not necessarily co-evolve with the host.
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