On 2016 Sep 11, Seth Bordenstei commented:

The authors write that the hologenome concept is strictly based on a premise that the holobiont evolves as a "single cooperative unit". This central argument is unfortunately not accurate and misrepresents the framework. Holobionts and hologenomes are structural entities subject to ecological and evolutionary forces at varying levels. A clarification and review of the literature can be found here:

http://msystems.asm.org/content/1/2/e00028-16

Abstract: Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

On 2016 Sep 11, Seth Bordenstei commented:

The authors write that the hologenome concept is strictly based on a premise that the holobiont evolves as a "single cooperative unit". This central argument is unfortunately not accurate and misrepresents the framework. Holobionts and hologenomes are structural entities subject to ecological and evolutionary forces at varying levels. A clarification and review of the literature can be found here:

http://msystems.asm.org/content/1/2/e00028-16

Abstract: Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.