Many multicellular organisms are closely associated with a specific bacterial community and therefore considered metaorganisms. Controlling the bacterial community composition is essential for the stability and function of metaorganisms, but the factors contributing to the maintenance of host specific bacterial colonization are poorly understood. Here we demonstrate that in Hydra the most dominant bacterial colonizer Curvibacter sp. is associated with an intact prophage which can be induced by different environmental stressors both in vitro and in vivo. Differences in the induction capacity of Curvibacter phage TJ1 in culture (in vitro) and on Hydra (in vivo) imply that the habitat of the prokaryotic host and/or bacterial frequency dependent factors influence phage inducibility. Moreover, we show that phage TJ1 features a broad host range against other bacterial colonizer and is directly capable to affect bacterial colonization on Hydra. From these results we conclude that prophages are hidden part of the microbiome interfering with bacteria-bacteria interactions and have the potential to influence the composition of host associated bacterial communities.

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