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Multi-omics comparison of two emerging storage pests (Necrobia rufipes and Tribolium castaneum) of dried black soldier fly larvae product

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Abstract

The black soldier fly (BSF) larvae is a rich and promising source of alternative protein that continues to increasingly gain global traction as a functional ingredient for sustainable livestock and fish production. The key setback to postharvest processing of stored BSF larvae (BSFL) products is the significant damage caused by two notable storage pests (Tribolium castaneum and Necrobia rufipes). Here, we present a comparative analysis of the complete mitochondrial genomes and gut microbiome profiles of T. castaneum and N. rufipes. The study mitogenomes were similar in size and structure to other coleopteran mitogenomes. The gut microbiome profiles of the two pests showed a high abundance of bacteria in the Proteobacteria and Firmicutes phyla. However, T. castaneum had 78% more phyla represented within its microbiome than N. rufipes. The most abundant genera in T. castaneum were Staphylococcus and Streptococcus, while in N. rufipes, the dominant genera were Klebsiella and Synechococcus. We also identified the presence of potentially clinically harmful microbial genera (Stenotrophomonas maltophilia) in the gut of T. castaneum and N. rufipes in relatively high abundance. These results provide insight into potential harmful associations in the gut of the storage pest, picked from contaminated, poorly processed BSFL products.

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Data availability

All sequences generated in this study were deposited in the GenBank database ( [www.ncbi.nlm.nih.gov/genbank](http:/www.ncbi.nlm.nih.gov/genbank) ) under the BioProject number: PRJNA995429 and accession number: OR450807.1.

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Acknowledgements

The authors gratefully acknowledge the financial support for this research by the following organizations and agencies: Australian Centre for International Agricultural Research (ACIAR) (ProteinAfrica: LS/2020/154), Rockefeller Foundation (WAVE-IN: 2021 FOD 030); IKEA Foundation (G-2204-02144); European Commission (NESTLER Project: 101060762 and INNOECOFOOD project: 101136739), the Curt Bergfors Foundation Food Planet Prize Award; the Swedish International Development Cooperation Agency (Sida); the Swiss Agency for Development and Cooperation (SDC); the Australian Centre for International Agricultural Research (ACIAR); the Government of Norway; the German Federal Ministry for Economic Cooperation and Development (BMZ); and the Government of the Republic of Kenya. The views expressed herein do not necessarily reflect the official opinion of the donors. We thank Mr Fidelis Levi Ombura, Ms Maureen Adhiambo, and Mr Eric Rachami for their technical assistance.

Funding

This research was funded by the following organizations and agencies: Australian Centre for International Agricultural Research (ACIAR) (ProteinAfrica: LS/2020/154), Rockefeller Foundation (WAVE-IN: 2021 FOD 030); IKEA Foundation (G-2204-02144); European Commission (NESTLER Project: 101060762 and INNOECOFOOD project: 101136739), the Curt Bergfors Foundation Food Planet Prize Award.

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Authors and Affiliations

  1. International Centre of Insect Physiology and Ecology, Nairobi, Kenya

    Inusa Jacob Ajene, Chrysantus M. Tanga, Komivi S. Akutse, Samantha W. Karanu & Fathiya M. Khamis

  2. College of Tropical Agriculture and Human Resilience, Komohana Research and Extension Center, University of Hawaii at Manoa, Hilo, Hawai’i, 96720, USA

    Inusa Jacob Ajene

  3. Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2520, South Africa

    Komivi S. Akutse

  4. Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa

    Fathiya M. Khamis

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  1. Inusa Jacob Ajene
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  2. Chrysantus M. Tanga
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  3. Komivi S. Akutse
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  4. Samantha W. Karanu
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  5. Fathiya M. Khamis
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IJA: Conceptualization; data curation; investigation; formal analysis; methodology; validation; visualization; writing—original draft; writing— review and editing. CMT: Conceptualization; funding acquisition; resources; project administration; supervision; writing—original draft; writing—review and editing. KSA: Data curation; resources; validation; writing—review and editing. SWK: Data curation; investigation; formal analysis; methodology; writing—review and editing. FMK: Conceptualization; methodology; resources; supervision; validation; writing—review and editing. All authors have read and approved the manuscript.

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Inusa Jacob Ajene or Fathiya M. Khamis.

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Ajene, I.J., Tanga, C.M., Akutse, K.S. et al. Multi-omics comparison of two emerging storage pests (Necrobia rufipes and Tribolium castaneum) of dried black soldier fly larvae product.
Sci Rep (2026). https://doi.org/10.1038/s41598-025-34902-7

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Keywords

  • Gut microbiome
  • Mitogenome
  • Postharvest storage pest
  • Red flour beetle
  • Red-legged ham beetle

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