Mixed cultures as model communities : hunting for ubiquitous microorganisms, their partners, and interactions

Even though thousands of microbial strains have now been successfully cultivated and described, these only represent a small fraction of global microbial diversity. Moreover, many of the ubiquitous and abundant environmental microorganisms still defy axenic cultivation. Here, I present mixed cultures as a powerful tool to cultivate and study ubiquitous but hard-to-cultivate microorganisms. A mixed culture is a subsample from a complex natural community that contains 2 or more microbial strains. When cultivated together with their metabolic partners, these ubiquitous microorganisms can mutually satisfy metabolic dependencies just as they do in the environment. By reducing the complexity while keeping some diversity, mixed cultures can then be used as model communities. Furthermore, by combining the relative simplicity of these model communities with molecular and bioinformatics tools, the complex natural interactions could be deciphered one model community at a time. Ultimately, mixed cultures can be used to generate a working hypothesis to explore the microbial ecology and genetic population structures of the unseen vast majority of microorganisms