Opportunities and Challenges in Applying Defined Co-cultures for Microbial Biotechnology

Abstract

The natural world is shaped by ecological networks. In all geographical contexts, species coexist and interact with other species, in often complex synergistic or antagonistic ways. This interplay is also apparent at the microbial scale. In the human gut microbiome, for example, dozens of species carve out any available niche to access nutrients, allowing them to persist. To do this, they can form mutualistic alliances with other species, feed on their metabolic products or exploit alliances between other species by intercepting their exchanged nutrients. Such complex networks confer stability by reducing the possibility of opportunistic species taking over, enable formation of new products, and make near-complete use of all available nutrients. Microbial co-cultures exhibiting these advantages are ubiquitous in food fermentation processes, where they have for millennia been used to ferment bread, beer, tea leaves, and milk. In modern food fermentation processes, co-cultures often comprise a defined selection of species and strains, optimized for the intended application....