Transgenerational dynamics of gut microbiota in black soldier fly larvae ( <i>Hermetia illucens</i> ) reared on a novel substrate

, increased in abundance. These trends indicate a shift from growth-promoting to digestion- and resilience-oriented microbial strategies under prolonged dietary stress. The stochastic emergence of distinct microbial patterns across sub-lines underscores the plastic and adaptable nature of BSFL gut microbiota. Recognizing this plasticity emphasizes the need to maintain large, genetically and microbially diverse BSF populations, which is critical for preserving functional stability and supporting long-term adaptation when utilizing novel or suboptimal substrates in industrial production.IMPORTANCEThe black soldier fly is rapidly gaining recognition globally as a key agent in circular bioeconomy for its ability to convert diverse organic waste into high-value products. However, the long-term stability and resilience of its gut microbiota on novel, low-cost diets remain poorly understood. This study addressed that knowledge gap by tracking transgenerational changes in larval gut microbial communities over four generations, using a single population reared on a novel diet, both with and without selection for larval size. Despite a shared genetic background, different sub-lines developed distinct microbiota and growth patterns, with early developmental stages showing the greatest sensitivity to generational microbial shifts. Initial increases in certain bacterial groups were followed by community restructuring by the fourth generation, indicating a dynamic but unstable microbial response to prolonged dietary stress. These findings highlight the importance of preserving microbial and genetic diversity when breeding black soldier flies for industrial use. Understanding how host-microbiota responses shift across generations is essential for sustaining performance and ensuring resilience in large-scale black soldier fly production systems.