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

Area of Science:

• Entomology
• Microbiology
• Animal Science

Background:

• Coprophagous flies convert livestock manure into valuable protein biomass for animal feed.
• Manure-based fly rearing presents biosafety challenges due to microbial contamination.

Purpose of the Study:

• Characterize internal bacterial communities in Aldrichina grahami and Boettcherisca peregrina during development.
• Identify fly developmental stages with reduced microbial hazard for safer animal feed production.

Main Methods:

• 16S rRNA gene amplicon sequencing of internal bacterial communities.
• Analysis across multiple developmental stages: third-instar larvae, dispersing larvae, pupae, and adults.
• Comparison of bacterial composition and richness between species and developmental stages.

Main Results:

• Developmental stage significantly structured bacterial communities in both fly species.
• Bacterial communities were dominated by Bacillota and Pseudomonadota, reflecting swine manure origin.
• Dispersing larvae exhibited a lower microbial-hazard indicator profile compared to later stages, suggesting developmental filtering.

Conclusions:

• The dispersing larval stage presents a pragmatic harvest window for manure-reared flies, offering a lower initial microbial hazard.
• Selecting this stage is an effective upstream control to mitigate biosafety concerns in animal feed production.
• Downstream processing further reduces microbial risks, making stage selection a key biosecurity measure.