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Facultative endosymbionts, such as Wolbachia, perpetuate by vertical transmission mostly through colonization of the germline during embryogenesis. The remaining Wolbachia inside the embryo are internalized in progenitor cells of the somatic tissue. This perpetuation strategy triggers a cyclic bacterial bottleneck across host generations. However, throughout the host's life history (Drosophila, for example), some somatic tissues such as the Malpighian tubules (MTs) show large numbers of Wolbachia. It is assumed that Wolbachia present in the progenitor cells of the MTs are confined to this somatic tissue, implicitly considering MTs as an evolutionary dead-end for these bacteria. Nevertheless, the fact that bacteria can survive and proliferate inside MTs suggests a different fate as they may access the host's reproductive system and persist in the host population through vertical transmission. Indeed, based on the particular physiological and developmental characteristics of MT, as well as of Wolbachia, we argue the bacteria present in the MTs may constitute a secondary pool of vertically transmitted bacteria. Moreover, somatic pools of Wolbachia capable of reaching the gonads and insure vertical transmission may also provide an interesting element to the elucidation of horizontal transmission mechanisms. Finally, we also speculate that somatic pools of Wolbachia may play an important role in host fitness, namely during viral infections. In brief, we argue that the somatic pools of Wolbachia, with special emphasis on the MT subset, deserve experimental attention as putative players in the physiology and evolution of both bacteria and hosts., (Copyright © 2013 Wiley Periodicals, Inc.)