Genome-Resolved Metagenomic Analysis of the Gut Mocrobiome in Reared House Fly Larvae (Musca domestica)

During the last decades there has been an increasing focus on utilizing insects for food and feed.
Especially black soldier fly and housefly larvae are interesting organisms due to their potential in
converting low value biomaterial into protein. One central question is what role the microbiome
plays on insect performance and how the microbiome can be utilized to improve insect health and
performance. In this study larvae of the housefly (Musca domestica) were reared on three substrates,
their growth performance measured, and their microbiome sequenced. A catalogue of
metagenome assembled genomes (MAGs) was constructed with hybrid assembling using both
Illumina and Oxford Nanopore reads. The MAG catalogue was used to study the effect of
substrate on microbiome composition and metabolic capacity as well as correlations between larval
growth performance and microbial dynamic, including taxonomy and functionality. Results clearly
reveal effect on the microbial dynamics by diet mediums. Our investigations reveal MAGs, which
are highly related to the intestinal environment and that these MAGs affect the growth phenotypes
of the house fly larvae, including survival and feed conversion. Subsequent investigations on the
metabolic capacity indicate a lack of correlation between taxonomy and functionality - a result that
should cause reflection given the widespread use of amplicon-based methods in insect rearing
research.