The hologenome theory of evolution proposes that an organism is simply not an individual but the totality of numerous microbial symbionts to the host. In fact, the evidence of biochemical and physiological associations between the symbionts and the host has been growing fast in all major taxa. The Vollenhovia emeryi ant is tiny and found nationwide in Korea. The ant can be further categorized by its wing morphology, eg. long-winged and short-winged. Our initial screening process showed that the microbial reproductive manipulator, the Wolbachia bacterium, only infected the long-winged morph. This gave us a good opportunity to investigate the effect of the Wolbachia infection on the bacterial community diversity using the next generation sequencing technique. We find that there are about 180 bacterial symbionts in the short-winged morph. On the other hand, the long-winged morph has only about 20 bacterial symbionts. This implies that the bacterial community diversity may be subject to the existence of Wolbachia. Furthermore, the Wolbachia strain diversity is unexpectedly high. In addition, the bacterial structure difference among castes indicates that there may be labour division even between queens. The results and future research direction will be discussed from the hologenome theory perspective.