Culturing the uncultured anaerobes from the perspective of microbial growth curves.

Abstract

Anaerobic microorganisms inhabit diverse anoxic environments and play a fundamental role in global biogeochemical cycles. Expanding our knowledge of these organisms offers the potential to transform our understanding of ecological and evolutionary processes and to uncover new biotechnological applications. Recent advances in DNA sequencing have revealed a striking gap between the vast microbial diversity found in anoxic environments and the small number of anaerobes - fewer than 0.1% of the estimated millions of anaerobic species in nature - that have been cultivated in the laboratory. This challenge reflects the 'great plate count anomaly', in which most microorganisms observed in nature fail to grow in laboratory conditions, and aligns with the 'scout' model, which suggests that only a few opportunistic species thrive under standard cultivation approaches. Overcoming these limitations requires a shift in cultivation strategies. Here, we review recent advances in the cultivation and isolation of novel anaerobes. Specifically, we introduce a growth-curve-guided strategy that uses real-time monitoring of microbial growth (primarily at the species level) to inform approaches that leverage relative growth advantages and improve the recovery of target microorganisms. By prioritizing growth performance over abundance and selectively removing non-target microbes, this approach offers a more predictable and adaptable framework for isolating anaerobes from complex communities.