Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome

The importance of microorganisms in human biology is undeniable. The amount of research that supports that microbes have a fundamental role in animal and plant physiology is substantial and increasing every year. Even though we are only beginning to comprehend the broadness and complexity of microbial communities, evolutionary theories need to be recast in the light of such discoveries to fully understand and incorporate the role of microbes in our evolution. Fundamental evolutionary concepts such as diversity, heredity, selection, speciation, etc., which constitute the modern synthesis, are now being challenged, or at least expanded, by the emerging notion of the holobiont, which defines the genetic and metabolic networks of the host and its microbes as a single evolutionary unit. Several concepts originally developed to study ecosystems, can be used to understand the physiology and evolution of such complex systems that constitute “individuals.” In this review, we discuss these ecological concepts and also provide examples that range from squids, insects and koalas to other mammals and humans, suggesting that microorganisms have a fundamental role not only in physiology but also in evolution. Current evolutionary theories need to take into account the dynamics and interconnectedness of the host-microbiome network, as animals and plants not only owe their symbiogenetic origin to microbes, but also share a long evolutionary history together.