Phage and their bacterial hosts are the most abundant and genetically diverse group of organisms on the planet. Given their dominance, it is no wonder that many recent studies have found that phage-bacteria interactions strongly influence global biogeochemical cycles, incidence of human diseases, productivity of industrial microbial commodities, and patterns of microbial genome diversity. Unfortunately, given the extreme diversity and complexity of microbial communities, traditional analyses fail to characterize interaction patterns and underlying processes.
Despite increasing recognition that phages play a significant role in shaping microbial ecosystems, fundamental questions remain unanswered. Quantifying who infects whom is essential to understand how infections at the cellular level (such as changes to metabolic rates, gene transfer, and the fate of cells) scale-up to influence ecosystem function in complex environments. This paper reviews systems approaches that combine empirical data with rigorous theoretical analysis to study phage-bacterial interactions as networks rather than as coupled interactions in isolation, and highlights the ways in which a better understanding of phage–bacteria infection networks will aid predictive models of viral effects on microbial communities, from microbiomes to the whole Earth.