The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition
2019
Despite an overall stability in time of the human gut microbiota at the phylum level, strong temporal variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous
prophages, or dormant viruses. A breakdown of
prophagedormancy can evolve through the selection of ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the gut microbiota has been largely unexplored. Here we studied temperate phage-bacteria
coevolutionin gnotoxenic mice colonised with Escherichia coli and
Roseburia intestinalis, a dominant symbiont of the human gut microbiota. We show that R. intestinalis harbors two active
prophages, Jekyll and Shimadzu, and observed the systematic evolution of ultravirulent Shimadzu phage mutants, leading to a collapse of R. intestinalis population. In a second step, phage infection drove the fast evolution of host phage-resistance mainly through phage-derived spacer acquisition in a Clustered Regularly Interspaced Short
PalindromicRepeats (CRISPR) array. Alternatively, phage resistance was conferred by a
prophageoriginating from an ultravirulent phage with a restored ability to
lysogenize. Our results demonstrate that
prophagesare the potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that
prophagescan play important roles in the short-term temporal variations observed in the composition of the gut microbiota.
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