Bacterial resistance and co-existence with temperate bacteriophages in the human gut

Our understanding of the eco-evolutionary dynamics and consequences of bacteria-phage interactions in nature is limited. By combining longitudinal sampling and analysis of Enterobacterales and associated phages isolated from the human gut with experimental evolution, our work highlights the constraints phage lifestyle can impose on cycles of co-evolution and identifies mechanisms that underpin observed patterns of temperate phage-bacteria co-existence in this clinically relevant microbiome. Specifically, we show that patterns of phage infectivity and temperate phage persistence in natura can be explained by ecological shifts in the relative abundance of susceptible hosts across taxonomic scales and the prevalence of spontaneous prophage induction (SPI) bacterial phenotypes, rather than rapid antagonistic co-evolution within bacterial and phage populations. Despite the ubiquity of temperate phages in the human gut these findings challenge the assumption that they are major drivers of within-host bacterial evolution and diversification over short-time scales in this natural ecosystem.