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Mass rearing the black soldier fly, Hermetia illucens, for waste bioremediation and valorisation is gaining traction on a global scale. While the health and productivity of this species are underpinned by associations with microbial taxa, little is known about the factors that govern gut microbiome assembly, function, and contributions towards host phenotypic development in actively feeding larvae. In the present study, a 16S rDNA gene sequencing approach applied to a study system incorporating both feed substrate and genetic variation is used to address this knowledge gap. It is determined that the alpha diversity of larval gut bacterial communities is driven primarily by features of the larval feed substrate, including the diversity of exogenous bacterial populations. Microbiome beta diversity, however, demonstrated patterns of differentiation consistent with an influence of diet, larval genetic background, and a potential interaction between these factors. Moreover, evidence for an association between microbiome structure and the rate of larval fat accumulation was uncovered. Taxonomic enrichment analysis and clustering of putative functional gut profiles further suggested that feed-dependent turnover in microbiome communities is most likely to impact larval characteristics. Taken together, these findings indicate that host–microbiome interactions in this species are complex yet relevant to larval trait emergence.

The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect farming industry with favourable characteristics for both bioremediation and production of animal delivered nutritive and industrial compounds. The genetic management of commercial colonies will become increasingly important for the sustainability of the industry. However, r-selected life history traits of insects pose challenges to conventional animal husbandry and breeding approaches. In this study, the long-term genetic effects of mass-rearing were evaluated as well as mating systems in the species to establish factors that might influence genetic diversity, and by implication fitness and productivity in commercial colonies. Population genetic parameters, based on microsatellite markers, were estimated and compared amongst two temporal wild sampling populations and four generations (F28, F48, F52, and F62) of a mass-reared colony. Furthermore, genetic relationships amongst mate pairs were evaluated and parentage analysis was performed to determine the oc-currence of preferential mate choice and multiple paternity. The mass-reared colony showed a reduction in genetic diversity and evidence for inbreeding with significant successive generational genetic differentiation from the wild progenitor population. Population-level analysis also gave the first tentative evidence of positive assortative mating and genetic polyandry in BSF. The homoge-neity of the mass-reared colony seems to result from a dual action caused by small effective popu-lation size and increased homozygosity due to positive assortative mating. However, the high ge-netic diversity in the wild and a polyandrous mating system might suggest the possible restoration of diversity in mass-reared colonies through augmentation with the wild population.