We commonly acknowledge that bacterial viruses (phages) shape the composition and evolution of microbial communities in nature and therefore play important roles in ecosystem functioning. This view stems from the 1990-2000s which revealed high viral abundance, diversity and virus-induced mortality in aquatic ecosystems as well as an association between collapses in bacterial density and peaks in phage abundance. The recent surge in metagenomics analyses has provided deeper insight into the abundance, genomic diversity and spatiotemporal dynamics of phages in a wide variety of ecosystems, ranging from deep oceans to soil and the mammalian digestive tract. However, the causes and consequences of variations in phage community compositions remain poorly understood. Here we review our current knowledge on the composition and evolution of phage communities, as well as their roles in controlling the population and evolutionary dynamics of microbial communities. We discuss the need for greater ecological realism in laboratory studies to capture the complexity of microbial communities that thrive in real environments.