How many phage species remain undiscovered? Species sampling approaches to inform phage discovery

The emergence of antimicrobial resistant bacteria has been identified as one of the most serious public health and development threats for the near future. The use of bacteriophages (phages) is a promising solution for the sustainable control of these pathogens. Phages are natural viral predators of bacterial pathogens. However, due to the variability and adaptability of bacteria, developing effective and sustainable phage treatments requires drawing from a wide variety of different phage species. This study applies specialised mathematical and computational estimation approaches to the problem of sampling and discovering species of phages in microbiological communities. We show that classical non-parametric estimator techniques lead to robust results and outperformed, for existing data settings in phages, model-based approaches. We then show how efficient the continuation of current phage collection and isolation effort is expected to be for discovering new phage species in various relevant bacterial host genera, a prerequisite for phage applications to provide sustainable control of pathogens in human and environmental settings. Our results have the potential to inform and optimise the hunt for and isolation of novel of phages from the the natural environment.