The current increase in human population and wealth is contributing to increased food demand and waste generation. With the effects of climate change weakening food security, this calls for new ways of securing food production.

Fly larvae is a potential solution to these problems as they are able to grow on a wealth of organic waste- and by-product and can be used as a nutritious feed for livestock. As fly larvae are still novel production animals, their production needs to be optimised to unfold their full potential and constitute a financially and environmentally competitive source of protein.

 Fly larvae interact with a wealth of microbes in their feed and in their guts, and these microbes are regarded important in shaping fly performance. Microbes therefore represent a way to improve the production traits of waste-converting fly larvae.

The aim of this thesis was to reveal host-microbiome interactions in fly larvae that could be of relevant use for microbiome manipulations in fly larvae rearing. In the conducted studies, the performance of larvae of the two fly species Musca domestica (house fly) and Hermetia illucens (black soldier fly) were tested on various waste- and by-product-based substrates and larval densities to assess how rearing conditions affect larval performance as well as to compare different species, which is rarely done.

Samples of house fly larvae were further investigated to understand the composition and functional potential of the house fly gut microbiome. Substrate and density were found to affect larval performance of both species in a similar manner but with the best performance for black soldier fly larvae in terms of mass gained and conversion efficiency. Substrate was also found to affect microbiome composition and function of house fly larvae, while the gut were enriched of certain functional groups of genes compared to the substrate.

Finally, larval traits survival and substrate conversion efficiency were found to correlate with metabolic functions of the microbiome and could indicate areas to further investigate to decipher the host-microbiome interactions in house fly larvae.

This thesis also contains a publication discussing the potential of understanding host-microbiome interactions in insects and how to analyse and manipulate these.