Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds enormous potential to understand common mechanisms and concepts underlying microbiome assembly and microbial processes that sustain life of Eukaryotes. The gut and plant rhizosphere are both open systems with large surface areas overpopulated with microbes. Despite distinct differences in microbiome composition, these two ecosystems share striking similarities in microbiome functions related to nutrient acquisition, immune system modulation and protection against infections. We also discuss how humans and plants exchange microbes, for better or for worse. We propose that adopting ecological theory, combined with modeling and synthetic microbial ecosystems, provides a promising strategy to identify host traits and cues involved in microbiome assembly on and in Eukaryotes.

A staggering number of microbes lives on and in cell tissues of eukaryotic organisms, thereby influencing the functioning and evolution of their host. The microbiome concept, that is, the collective communities of microorganisms, their genomes and interactions, was first used in the context of microorganisms that inhabit the human body. Since then, numerous studies have adopted this term to describe microbial communities associated with other mammals, insects, fish or plants. For humans, the microbiome significantly contributes to metabolism and provides functions that humans did not need to evolve on their own (Gill et al., 2006). Hence, the genes present in the human microbiome are considered the secondary genome. Plants also rely on their microbiome for specific traits and functions, including nutrient acquisition and tolerance to (a)biotic stress factors (Mendes et al., 2013). In the human microbiome, the highest density of microbes is found in the gastrointestinal tract, where ‘they synthesize essential amino acids and vitamins, and process components of otherwise indigestible contributions to our diet such as plant polysaccharides’ (Backhed et al., 2005). Similarly, microbes overpopulate the plant rhizosphere, that is, the narrow zone of soil surrounding and influenced by plant roots via the exudation of nutrients and other chemically diverse compounds. In this context, the rhizosphere can be seen as ‘the gut inside out’ (Ramírez-Puebla et al., 2013).

Log in or create a free account to read this content

Gain free access to this article, as well as selected content from this journal and more on nature.com

Access through your institution

or

Sign in or create an account
Continue with Google
Continue with ORCiD