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Many insects have evolved in beneficial associations with microorganisms, among which is the supplementation of nutrients. Some grain pest beetles have successfully adapted to dry conditions due to their thick cuticles, which is attributed to their ancient endosymbiont. Among the grain pest beetles with tyrosine supplementing symbionts, Prostephanus truncatus harbors the ancient symbiont, Shikimatogenerans bostrichidophilus, which diverged into three lineages with complementary gene repertoires. Symbiont genomic analyses revealed complementary gene distributions among the three strains, suggesting obligate metabolic exchange among the symbionts. Different Fluorescence in situ hybridization (FISH) techniques were used to localize bacterial lineage-specific DNA and RNA molecules. Macromolecular distribution and ultra-structure imaging demonstrated host-life-stage-dependent symbiont dynamics and presumable interactions among symbiont cells via connections and transport. Finally, experimental manipulation of symbionts resulted in thinner and brighter beetle cuticles, verifying the functional integrity of metabolically fragmented symbiont genomes. The results suggest that Prostephanus necessarily need to maintain and transmit three lineages of symbionts, which is widely considered to be non-adaptive. Applying different imaging techniques, we present potential mechanisms of interactions among the interdependent bacteria and illustrate the context- dependent FISH results in endosymbiont research.