Research is being conducted on the dynamics between phages and bacteria in the gut microbiome, particularly in early life. Studies using long-read metagenomics and other methods are shedding light on these interactions, including the role of horizontal gene transfer and the composition of the neonatal microbiome. The findings have implications for understanding the development and function of the human gut microbiome, although some ideas about the determinants of microbiota composition may not be supported by the evidence.