Cultivating the uncultured: limits, advances and future challenges
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Since the invention of the Petri dish, there have been continuous efforts to improve efficiency in microbial cultivation. These efforts were devoted to the attainment for diverse growth conditions, simulation of in situ conditions and achievement of high-throughput rates. As a result, prokaryotes catalysing novel redox reactions as well as representatives of abundant, but not-yet cultured taxa, were isolated. Significant insights into microbial physiology have been made by studying the small number of prokaryotes already cultured. However, despite these numerous breakthroughs, microbial cultivation is still a low-throughput process. The main hindrance to cultivation is likely due to the prevailing lack of knowledge on targeted species. In this review, we focus on the limiting factors surrounding cultivation. We discuss several cultivation obstacles, including the loss of microbial cell–cell communication following species isolation. Future research directions, including the refinement of culture media, strategies based on cell–cell communication and high-throughput innovations, are reviewed. We further propose that a combination of these approaches is urgently required to promote cultivation of uncultured species, thereby dawning a new era in the field.
KeywordsCulture Isolation Metabolism Microbial community Cell–cell communication High-throughput cultivation
This work was funded by the Région Bretagne for the CPER Souchothèque and the joint research unit UMR6197, linking the Université de Bretagne Occidentale, the Ifremer and the Centre National de la Recherche Scientifique. We thank Stéphane L’Haridon for constructive discussions and critical reading of this manuscript.
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