Mining traits for the enrichment and isolation of not-yet-cultured populations

Abstract

Background: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. Results: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. Conclusion: Our method could shed light to the exploration into the bacterial dark matter in the environments.