Cultivating the uncultured

TLDR

Molecular phylogeny of environmental samples has revealed abundant unique microorganisms, most of which remain uncultured. We aim to provide a universal method that unlocks this vast reservoir of untapped microbial diversity. The method encapsulates cells in gel microdroplets for massively parallel cultivation under low nutrient flux, then uses flow cytometry to detect microcolonies. This technology enables growth and study of previously uncultured organisms, enhancing understanding of microbial physiology and metabolism, offering new microbial metabolites, and works on seawater and soil samples.

Abstract

The recent application of molecular phylogeny to environmental samples has resulted in the discovery of an abundance of unique and previously unrecognized microorganisms. The vast majority of this microbial diversity has proved refractory to cultivation. Here, we describe a universal method that provides access to this immense reservoir of untapped microbial diversity. This technique combines encapsulation of cells in gel microdroplets for massively parallel microbial cultivation under low nutrient flux conditions, followed by flow cytometry to detect microdroplets containing microcolonies. The ability to grow and study previously uncultured organisms in pure culture will enhance our understanding of microbial physiology and metabolic adaptation and will provide new sources of microbial metabolites. We show that this technology can be applied to samples from several different environments, including seawater and soil.