A functional circadian clock regulates composition and daily bacterial load of the gut microbiome in Drosophila melanogaster

While Drosophila melanogaster serves as a crucial model for investigating both the circadian clock and gut microbiome, our understanding of their relationship in this organism is still limited. Recent analyses suggested that the Drosophila gut microbiome modulates the host circadian tran-scriptome to minimize rapid oscillations in response to changing environments. To delve deeper into the potential relationship between the gut microbiota and circadian clock in Drosophila , we examined the composition and abundance of the gut microbiota in wild-type and arrhythmic per ⁰¹ flies, under 12 h:12 h light: dark (12:12 LD) and constant darkness (DD) conditions. The gut microbiota of wild-type and per ⁰¹ flies showed differences in composition, suggesting that the D. melanogaster circadian clock has a role in shaping the gut microbiome. In 12:12 LD and DD conditions, per ⁰¹ mutants showed significant daily variations in gut bacterial quantity, unlike wild-type flies. This suggests that the circadian clock in D. melanogaster plays a role in maintaining daily stability in gut microbiome load. Finally, some gut bacteria exhibited significant 24 h fluctuations in their relative abundance, which appeared independent from the fly circadian clock, suggesting that certain gut commensal bacteria in Drosophila may possess a host-independent circadian clock.