Developmental Stage-Specific Microbiota Profile of a Polyphagous Fly

Gut bacteria play a key role in insect fitness, but the changes in gut microbiome profile across developmental stages of holometabolous insects remains little explored. Understanding changes in the microbiome across life stages is an important step toward understanding the associated shifts in functional relationships and trade-offs. Here, we characterised the microbiome of larvae, pupae, and adults of the highly polyphagous fruit fly Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) using next-generation sequencing. We sampled individuals from colonies that had been recently introduced to the laboratory environment from naturally infested fruits at generations one (‘G1’) and five (‘G5’). Alpha diversity increased across developmental stages at both G1 and G5, with maximum diversity in adults. Community composition changed across developmental stages and between generations. In G1, larval and pupal microbiomes were dominated by the genus Asaia whereas adult microbiomes were dominated by Enterobacter. In G5, larval and pupal microbiomes contained a high relative abundance of Asaia, but pupae also had a high relative abundance of Staphylococcus and Burkholderia, and there were no dominant patterns in adults. Our findings provide insights into the developmental stage-dependent microbiome associations of a polyphagous fly, and how host-symbiont interactions change at each life stage through the transition from nature to laboratory environments.