Black soldier fly larvae (Hermetia illucens) (BSFL) are insect larvae with significant ecological and economic value. This study aims to investigate whether swill and manure had any effects on the transcriptome and metabolome of BSFL. Through high-throughput transcriptome sequencing, we found that larvae fed with swill exhibited higher levels of gene expression, especially with the upregulation of genes related to energy metabolism, amino acid metabolism, and redox reactions. Metabolomics analysis showed a significant increase in energy metabolism-related metabolites, such as organic acids and amino acids, in the swill-fed larvae. In contrast, gene expression and metabolic characteristics in the pig manure-fed group indicated a higher stress response, with relevant genes and metabolites (such as short-chain fatty acids and antioxidants) showing significant upregulation. GO and KEGG enrichment analyses further supported these results, suggesting that swill promotes larval growth and metabolism, whereas pig manure induces the activation of stress response mechanisms. These findings offer clear molecular and physiological insights into the optimization of substrate selection for enhancing the performance of BSFL in waste management.

Black soldier flies (Hermetia illucens) are widely used in organic waste bioconversion, and their adaptive capacity to region-specific food waste is critical for efficient application. This study aimed to explore the molecular mechanisms underlying the adaptation of black soldier fly larvae to long-term domestication on regional food waste from Kunming and Qujing. Integrated transcriptomic and metabolomic analyses were performed to identify differences in gene expression and metabolite profiles between the two groups of larvae. The results showed significant divergence in gene expression networks, with key differences in cytochrome P450 detoxification pathways, TOR nutrient-sensing pathways, and zf-C2H2 zinc finger transcription factor families. Metabolomic analysis revealed region-specific metabolic reprogramming, including enhanced branched-chain amino acid degradation in one group and activated sphingolipid signaling pathways with accumulated indole derivatives in the other. Additionally, 13.86% of unannotated metabolites in the metabolome exhibited high connectivity in metabolic networks, suggesting potential roles as “bridge metabolites” in adaptation. These findings demonstrate that long-term domestication on regional food waste drives adaptive differentiation in black soldier fly larvae through regulatory network remodeling, metabolic reprogramming, and activation of hidden metabolic reserves. The study provides a theoretical basis for optimizing the application of black soldier flies in waste treatment and strain breeding and establishes a “substrate-gene-metabolism” multi-omics framework for understanding insect adaptive evolution.