Holobionts are cumulative biological components of a host and all of its associated microbial life. This is inclusive symbiotic microbes that affect the holobiont’s phenotype, and have most likely coevolved with the host (denoted as blue microbes in figure). Some might affect the holobiont’s phenotype but have not coevolved with that specific host (denoted as red microbes in figure) but rather acquired laterally sometime in it’s evolutionary history. Some microbial components might not affect the holobiont’s phenotype at all (denoted as gray microbes in figure). The collection of genomes of all (host and it’s microbes) constitute the hologenomes. This is an umbrella term that might sometimes denote microbial components at a given stage, or time, or season, or combination of all.  

(figure from Theis et al 2016)


Microbial transmissions might be vertical or lateral. Most lateral could be of historical biogeographical importance, having been acquired at some point by an ancestor, or through an holobiont host that shares it ecological space. In the accompanying image from Moran and Sloan et al (2015), the left panel shows individual symbiont lineages that have been retained along with the host’s evolution and thus following host lineages. These organisms are co-inherited with both gains and losses of symbiont lineages through their phylogenetic lineage. In cases represented in the right panel, the hosts evolve to shift their selectivity of microbes from around their environment. In theory, closer the phylogenetic distance between hosts, similar should be the microbiome.


Plants pose distinct microbial niches in the flower (anthosphere), surface of leaves (phylloplane), fruits (carposphere), stem (caulosphere), root surfaces (rhizoplane) and soil under the influence of roots (rhizosphere). These microbiomes could be acquired through different mechanisms. For instance, different species of trees and grasses could influence each other’s microbial holobiontic components.

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