Internal Microbiota Guided Stage Selection in Two Swine-Manure Bioconversion Flies for Feed-Protein Harvest

Coprophagous flies can convert livestock manure into protein-rich larval biomass for animal feed, but manure-based rearing raises biosafety concerns. This study characterized the internal bacterial community dynamics across development in Aldrichina grahami and Boettcherisca peregrina reared on swine manure, aiming to identify developmental stages with a lower microbial hazard profile. Using 16S rRNA gene amplicon sequencing of pooled internal samples, we analyzed communities from third-instar larvae, dispersing-stage larvae, pupae at multiple time points, and newly emerged adults. Developmental stage strongly structured bacterial composition and altered richness in both species. Communities were dominated by Bacillota and Pseudomonadota, reflecting substrate origin, with pronounced turnover during metamorphosis and stage-specific dominance patterns, indicating developmental filtering rather than uniform microbial clearance. Crucially, dispersing larvae did not show the marked dominance signatures seen in later pupal or adult stages, supporting this stage as a pragmatic harvest window with a comparatively lower microbial-hazard indicator profile. Since downstream processing such as drying or heating will further reduce viable hazards, stage selection serves as an effective upstream control to lower the initial hazard burden entering production.