Improving the odds: Artificial intelligence and the great plate count anomaly

Next-generation DNA sequencing has shown that the great plate count anomaly, that is, the difference between bacteria present in the environment and those that can be obtained in culture from that environment, is even greater and more persisting than initially thought. This hampers fundamental understanding of bacterial physiology and biotechnological application of the unculture majority. With big sequence data as foundation, artificial intelligence (AI) may be a game changer in bacterial isolation efforts and provide directions for the cultivation media and conditions that are most promising and as such be used to canalize limited human and financial resources. This opinion paper discusses how AI is or can be used to improve the success of bacterial isolation. Artificial intelligence can provide new hypotheses to isolate currently uncultivable bacteria beyond individual researcher's imagination. It has applications in (1) identifying growth on plates before the human eye can, (2) taxonomically identifying bacterial colonies and (3) predicting metabolic properties and propose cultivation media and conditions to isolate currently uncultivable bacteria.image