Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm

• Host genetics affects gut microbiomes in black soldier flies and yellow mealworms. • Gut microbiomes persist after generations of uniform insect rearing. • Shared core bacterial taxa exist but vary in abundance among populations. • Microbiome resilience challenges assumptions of environmental homogenization. • Breeding programs should integrate microbiome profiling for optimization. Production insects such as the black soldier fly ( BSF ) and yellow mealworm ( YM ) are increasingly recognized as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programs typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in 10 distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units ( zOTUs ) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.