Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.

Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.