Role of Early-Life Microbiome Colonization in Physiological Development of Drosophila melanogaster

The influences of the gut microbiome on animal physiology are well-documented, yet the developmental timing of microbial colonization and its long-term consequences remain poorly understood. In this study, we investigated how the timing of bacterial colonization during development affects transcriptional programming and phenotypic outcomes in adult Drosophila melanogaster reared on a common, rich diet. Using RNA-seq analysis on whole flies colonized either as newly hatched larvae or as newly eclosed adults, we observed minor but distinct transcriptional responses dependent on when flies were colonized. Both embryonic and adult colonization were associated with ∼ 25 to ∼ 200 differentially expressed genes compared to axenic controls, with the majority upregulated and enriched for immune-response genes, suggesting that colonization establishes a broader immune competence. However, only 10 genes showed persistent differential expression that was not normalized by introducing bacteria to adult axenic flies, including mitochondrial genes, the adipokinetic hormone ( Adh ), and a putative secreted neuropeptide. Overall, these findings suggest that Drosophila development on a rich diet is largely robust to the timing of bacterial colonization but that certain metabolic effects may occur.