Overdue community effort on getting the hologenome concept right

More and more, it is becoming clear that the population biology processes affecting animal and plant phenotypes interface with ecosystems science and the ecology of host-associated microbiomes. Indeed, the so-called individual animal or plant is increasingly appreciated as a "holobiont" comprised of the host plus all of its associated microbes. Resultantly, all genomes of the holobiont have been termed the “hologenome”. These terms and associated concepts are relatively new and liable to misinterpretation. Our new preprint at bioRxiv / manuscript published at mSystems is a community effort to pull various biologists and philosophers together around a definitive set of arguments that accurately reflect the original literature. As the largest collection of authors to date in this area, spanning fifteen junior and senior investigators in the life sciences and philosophy, we think this article will encourage productive discussion to stimulate new ideas and understanding on holobionts and hologenomes that consider the link between phenotype and genotype. I hope you check out the short piece. Feedback is most welcome!

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes

Kevin R Theis, Nolwenn M. Dheilly, Jonathan L. Klassen, Robert M. Brucker, John F. Baines, Thomas C.G.Bosch, John F. Cryan, Scott F. Gilbert, Charles J. Goodnight, Elisabeth A. Lloyd, Jan Sapp, PhilippeVandenkoornhuyse, Ilana Zilber-Rosenberg, Eugene Rosenberg, Seth R. Bordenstein

doi: http://dx.doi.org/10.1101/038596 

Given the recently appreciated complexity of symbioses among hosts and their microbes, significant rethinking in biology is occurring today. Scientists and philosophers are asking questions at new biological levels of hierarchical organization - What is a holobiont and hologenome? When should this vocabulary and associated concepts apply? Are these points of view a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Legitimate questions, advancements and revisions are warranted at this nascent stage of the field. However, a productive and meaningful discourse can only commence when skeptics and proponents alike use the same definitions and constructs. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not necessarily the primary unit of selection is not synonymous with arguing that it is not a unit of selection in general. Here, we succinctly deconstruct and clarify these recent misconceptions. Holobionts (hosts and their microbes) and hologenomes (all genomes of the holobiont) are multipartite entities that result from ecological, evolutionary and genetic processes. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome. We invite the community to consider these new perspectives in biology.