The results of this study suggest that FLE and Rickettsia endosymbionts partially exclude each other in co-infections of the same D. occidentalis tick. Although interference between Rickettsia co-infections has been known for many years, this is the first study that suggests possible exclusion between different endosymbiont genera in ticks. Whether FLEs can be shown to inhibit Rickettsia co-infection in the laboratory, the mechanisms for their interaction and whether they could be propagated through a tick population as a means to render ticks unable to vector pathogenic Rickettsia are intriguing prospects that warrant further investigation. In addition to more mechanistic investigations, future research should also apply approaches such as shotgun metagenomics that can be used to assemble long sequence reads and even complete genomes from whole microbiome samples for more accurate species and strain identification.