Cultivation in a bottom-up manner: a new way to explore environmental microbiome

Abstract

As the most diverse form of life on Earth, environmental microorganisms represent a vast treasure trove for resource exploitation and environmental applications. Nonetheless, currently, over 90% of microorganisms remain uncultured, which is mainly due to the inherent limitations of the widely employed top-down cultivation methods. Therefore, in this review, we first comprehensively reviewed the progress in microbial cultivation technologies and methods, summarized the major obstacles existing in microbial cultivation, and then proposed a bottom-up cultivation strategy and associated roadmap to complement current top-down cultivation methods. The core of the bottom-up cultivation strategy is the establishment of a standardized, open-ended, and scalable “CPR Module Bank—comprising Core, Population-specific, and Redundant function modules” that can be continuously expanded, refined, and improved by pulling together ideas and efforts of the worldwide microbial cultivation society. Further integration of top-down and bottom-up cultivation strategies may facilitate the comprehensive cultivation of all microorganisms in the future and advance the field of environmental microbiology.

Graphical abstract

Keywords

Microbial cultivation / Uncultured microorganisms / Environmental microbiome / Cultivation methods

Highlight

	● Breakthroughs in cultivation of environmental microbiomes were reviewed.
	● Barriers to current microbial cultivation were summarized and discussed.
	● Bottom-up cultivation complementing current top-down cultivation was proposed.
	● CPR Module Bank for cultivation was proposed for the bottom-up cultivation.

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