Internal Microbiota Guided Stage Selection in Two Swine-Manure Bioconversion Flies for Feed-Protein Harvest
Henan Key Laboratory of Insect Biology, Henan Province Engineering Research Center of Insect Bioreactor, China-UK International Joint Laboratory for Insect Biology of Henan Province, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China
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Insects 2026, 17(4), 353; https://doi.org/10.3390/insects17040353
Submission received: 30 January 2026
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Revised: 9 March 2026
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Accepted: 18 March 2026
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Published: 24 March 2026
(This article belongs to the Topic Sustainable Utilization of Insect Biodiversity in Agriculture Forestry and Food Systems Resource Utilization, Food Security and Policy Integration)
Simple Summary
Manure-rearing insects offer a sustainable protein source for feed, but managing microbial risks is crucial. To identify an optimal harvest stage balancing yield and safety, we tracked internal bacterial communities in two fly species across development. Bacterial communities shifted significantly, with specific taxa dominating later pupal and adult stages. In contrast, dispersing-stage larvae—which stop feeding and leave the manure—maintained a more stable bacterial profile and were easier to collect. Harvesting at this dispersing stage therefore provides a practical balance between biomass production and microbial safety, supporting the design of safer manure-to-feed systems.
Abstract
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.
Keywords:
Diptera; Calliphoridae; Sarcophagidae; biosafety risk; 16S rRNA
