We are surrounded by microbes, mostly bacteria and their viruses or phages, on 
the inside and outside of our bodies. These bacteria in constant interactions 
with phages are regulating multiple functions critical to our health. Luckily, 
they are amenable, but we need precise tools for their safe manipulation and 
improving human health. Here, we argue that recent advances in single-cell 
technologies, culturomics and synthetic biology offer exciting opportunities to 
create these tools as well as revealing specific phages-bacteria interactions in 
the body.