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

Abstract

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 identifies mechanisms that underpin observed patterns of temperate phage-bacteria co-existence and bacterial resistance in this clinically relevant microbiome. Specifically, we show that limited phage infectivity observed against sympatric and allopatric hosts can be explained by the prevalence of spontaneous prophage induction (SPI) bacterial phenotypes and ecological shifts and turnover in focal host populations at multiple taxonomic levels. 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.