Eugen Pfeifer, Jorge Moura de Sousa, Marie Touchon, Eduardo P. C. Rocha

Studies of viral adaptation have focused on the selective pressures imposed by hosts. However, there is increasing evidence that interactions between viruses, cells, and other mobile genetic elements (MGEs) are determinant to the success of infections. These interactions are often associated with antagonism and competition, but sometimes involve cooperation or parasitism. They involve mechanism of defense or genetic regulation that evolve by genetic exchanges followed by processes of co-option and diversification producing multi-layered networks of interactions. Gene exchanges thus facilitate the emergence of cross-talk between elements that co-inhabit the same bacterium. This creates opportunities for the exploitation of phages by other MGEs in the cell and for their manipulation by competing bacteria.