Nanopore- and AI-empowered metagenomic viability inference

The ability to differentiate between viable and dead microorganisms in metagenomic samples is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens. While established viability-resolved metagenomic approaches are labor-intensive as well as biased and lacking in sensitivity, we here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting. The application of explainable AI tools then allows us to robustly pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as efficient explainable AI-based rules, we show that our framework can be leveraged in a real-world application to estimate the viability of pathogenic Chlamydia, where traditional culture-based methods suffer from inherently high false negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can in principle be utilized to predict viability across taxonomic boundaries and indendent of the killing method used to induce bacterial cell death. While the generalizability of our computational framework needs to be assessed in more detail, we here demonstrate for the first time the potential of analyzing freely available nanopore signal data to infer the viability of microorganisms, with many applications in environmental, veterinary, and clinical settings.Competing Interest StatementThe authors have declared no competing interest.