Symbiotic microbial relationships shape developmental biology and recently are being shown to influence immunity and disease susceptibility. These interactions are complex to say the least, involving the host and its mechanisms, and the vast composition of the micfloral environment and each of its individual dynamics. This system is in a constant state a flux, with the host growing and changing and the microbiota doing the same to meet its own needs. Little is known about the changes that occur throughout the midgut micobiome proliferation in vectors. This system becomes even more complex when involving vectors of tropical diseases. In this case, the host and microbiome not only interact with each other, they also interact with an invading pathogen. There is also little understood concerning how this affects the host development and molecular mechanisms. Through our work, we were able to address all of these topics for a more holistic approach of microbiome research. We showed that fitness characteristics of the dengue vector, Aedes aegypti, vary largely between strains, including varying response to microflora presence or absence, but did not vary in response to dengue virus infection We were able to elucidate the microbiome composition of Ae. aegypti throughout the life cycle of a susceptible and resistant strain, documenting differences between the two strains. We also observed the ability for individuals grown under the same conditions to harbor diverse microbiomes. Finally, we investigated how the presence of the microbiome influence microRNA expression of Ae. aegypti strains that are susceptible or resistant to dengue virus and found that in the resistant strain, microbiome absence dramatically decreases microRNA expression. This shows that symbiotic relationship between the midgut microbiota and the host can extends to molecular mechanisms and to the cellular processes of the host. These studies allow researchers to observe the different facets of microbial interactions that occur within vectors and open up new opportunities for vector control strategies including selecting paratransgenesis candidates.