Scientists from the Institut Pasteur have identified the original strategy used by bacteriophages, the most abundant viruses in human-associated microbiota, to persist in the gut of mammals. Results demonstrate that bacteriophages take advantage of the diversity of bacteria residing in the intestines to modify their host range in order to withstand in this environment. The role for intestinal bacteriophages as sentinels maintaining or restoring a healthy microbial equilibrium is supported by these results as well as a novel role for the microbiota to facilitate viral persistence.
High throughput sequencing projects of human microbiomes have confirmed that beside many bacteria they also contain an abundant and diverse population of bacteriophages, viruses infecting bacteria. Recently, the scientific community has established that half of the human healthy population share some of their bacteriophages. Studies have also shown that intestinal bacteriophage composition is affected during some diseases, such as Crohn’s disease. However, the role of these bacterial viruses in the equilibrium of the gut microbiota and the mechanisms by which they can withstand in such competitive environment remain elusive.
To identify such mechanisms, researchers from Institut Pasteur have compared the behaviour of one bacterial virus in presence of two bacterial hosts, in both defined and complex ecosystems. By monitoring over time the ability of this bacteriophage to modify its infectivity, they found that only the presence of the gut microbiota was promoting infection of new bacteria. As explained by Luisa De Sordi, first author of the study, “It is known that “opportunity makes the thief” and this study shows how the microbiota provides bacteriophages with tools to break into diverse bacterial cells and specifically lower outgrowing bacterial populations”.
Using population genomics and molecular biology techniques, researchers have elucidated the mechanism involved in the host adaptation of this virus (host-jump). They also identified a homologous intragenomic recombination event never reported in bacteriophage genomes, which demonstrates that these viruses possess their own genomic resources to favour host jumps. According to Laurent Debarbieux, coordinator of the study, “By keeping in their genomes the information required to adapt their infectivity to their environment, these viruses display an unanticipated resource to evolve and survive in the gut”.
Overall, beyond the identification of a novel mechanism of evolution of bacterial viruses, these results attribute a new function to the gut microbiota that provides the resources required for such evolution allowing viruses to persist by continuously shaping the gut bacterial composition.
The gut microbiota facilitates drifts in the genetic diversity and infectivity of bacterial viruses, Cell Host and Microbe, November 22, 2017.
Luisa De Sordi1, Varun Khanna2, Laurent Debarbieux1
1 Department of Microbiology, Institut Pasteur, Paris F-75015 France.
2 Hub Bioinformatique et Biostatistique, Institut Pasteur – C3BI, USR 3756 IP CNRS, Paris F-75015, France.