If a given holobiont is to be considered a unit of natural selection:

For those who accept the hologenome theory, the holobiont has become the principal unit of natural selection.

Consequently, the collective genomes of the holobiont form a "hologenome".

The partners are known as symbionts and the sum of the partnership as the holobiont.

By altering its composition, this "holobiont" can adapt to changing environmental conditions far more rapidly than by genetic mutation and selection alone.

As selection operates on phenotypes, classic individual selection is effectively selection on the holobiont.

The authors directly conclude: "Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution."

The lucinid-symbiont holobiont removes toxic sulfide from the sediment, and the seagrass roots provide oxygen to the bivalve-symbiont system.

It is thought that lichens may be even more complex symbiotic systems that include non-photosynthetic bacterial communities performing other functions as partners in a holobiont.

This hologenome...can change more rapidly than the host genome alone, thereby conferring greater adaptive potential to the combined holobiont evolution.

Each of these points taken together [led Rosenberg et al. to propose that] the holobiont with its hologenome should be considered as the unit of natural selection in evolution.

It is a chemosymbiotic holobiont hosting a thioautotrophic (i.e., sulfur-oxidising) gammaproteobacterial endosymbiont in a much enlarged oesophageal gland, and appear to rely on these for nutrition.

He contends that under environmental stress, the microbiome can change more rapidly and in response to more processes than the host organism alone and thus influences the evolution of the holobiont.

On the other hand, it has been stated that the holobiont is the result of other step of integration that it is also observed at the cell (symbiogenesis, endosymbiosis) and genomic levels.

The premise for his theory was that natural selection acts on the 'holobiont' comprising a 'scaffold genome' and myriad microbial constituents in diverse ecosystems, selecting for persistence of the set of genetically-encoded capabilities.

The hologenome theory of evolution proposes that evolutionary forces acting at the level of an individual organism (e.g., a single plant or animal) are instead acting on the "holobiont" - the inherent community of a host plus all of its symbiotic microbes.

Zilber-Rosenberg and Rosenberg (2008) have tabulated many of the ways in which symbionts are transmitted and their contributions to the fitness of the holobiont, beginning with mitochondria found in all eukaryotes, chloroplast in plants, and then various associations described in specific systems.

Recent perspectives on lichens include that they are relatively self-contained miniature ecosystems in and of themselves, possibly with more microorganisms living with the fungi, algae, and/or cyanobacteria, performing other functions as partners in a system that evolves as an even more complex composite organism (holobiont).

According to the hologenome concept microbial symbionts and the host interact in a cooperative way that affects the health of the holobiont within its environment, and the sum of these cooperative interactions characterizes the holobiont as a unique biological entity.

This groundbreaking concept posits that the holobiont (host plus all of its associated microorganisms) and its hologenome (sum of the genetic information of the host and its symbiotic microorganisms), function as a unique biological entity and therefore as a level of selection in evolution.

The ability to alter and modulate, amplify and suppress, disseminate and recruit new capabilities as microbially-encoded 'traits' means that sampling, sensing and responding to the environment become intrinsic features and emergent capabilities of the holobiont, with mechanisms that can provide rapid, sensitive, nuanced and persistent performance changes.

In 2015, Seth R. Bordenstein and Kevin R. Theis outlined additional history on the word holobiont and summarized a conceptual framework that aligns with pre-existing theories in biology and serves as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes.