Summary Gut microbial diurnal oscillations are important diet-dependent drivers of host circadian rhythms and metabolism that ensure optimal energy balance. Yet, the interplay between diet, microbes, and host factors that sustain intestinal oscillations is complex and poorly understood. Here, we report the host C-type lectin antimicrobial peptide Reg3γ works with key ileal microbes to orchestrate these interactions in a bi-directional manner, independent from the intestinal core circadian clock. High fat diet diminishes physiologically relevant microbial oscillators essential for host metabolic homeostasis, resulting in arrhythmic host Reg3γ expression and increased abundance and oscillation of Reg3γ -independent gut microbes. This illustrates a transkingdom co-evolved biological rhythm involving reciprocating, sensor-effector signals between key host and microbial components that ultimately drive metabolism, but are also heavily influenced by diet. Restoring the gut microbiota’s capacity to sense and transduce dietary signals mediated by specific host factors such as Reg3γ could be harnessed to improve metabolic dysfunction.

High fat diet disrupts diurnal interactions between REG3γ and small intestinal gut microbes resulting in metabolic dysfunction