Tsetse flies have a highly regulated and defined microbial fauna made of 3 bacterial symbionts (obligate Wigglesworthia glossinidia, commensal Sodalis glossinidius and parasitic Wolbachia pipientis) in addition to a DNA virus (. Glossina pallidipes Salivary gland Hypertrophy Virus, GpSGHV). It has been possible to rear flies in the absence of either Wigglesworthia or in totally aposymbiotic state by dietary supplementation of tsetse's bloodmeal. In the absence of Wigglesworthia, tsetse females are sterile, and adult progeny are immune compromised. The functional contributions for Sodalist are less known, while Wolbachia cause reproductive manupulations known as cytoplasmic incompatibility (CI). High GpSGHV virus titers result in reduced fecundity and lifespan, and have compromised efforts to colonize flies in the insectary for large rearing purposes. Here we investigated the within community effects on the density regulation of the individual microbiome partners in tsetse lines with different symbiotic compositions. We show that absence of Wigglesworthia results in loss of Sodalis in subsequent generations possibly due to nutritional dependancies between the symbiotic partners. While an initial decrease in Wolbachia and GpSGHV levels are also noted in the absence of Wigglesworthia, these infections eventually reach homeostatic levels indicating adaptations to the new host immune environment or nutritional ecology. Absence of all bacterial symbionts also results in an initial reduction of viral titers, which recover in the second generation. Our findings suggest that in addition to the host immune system, interdependencies between symbiotic partners result in a highly tuned density regulation for tsetse's microbiome.