A Comparative Survey of Soldier Fly (Stratiomyidae) Larval Gut Microbiomes Across Five Subfamilies Reveals Novel Bacterial Diversity and a "Wild Core" in Hermetia illucens.

Soldier flies (Stratiomyidae) are a diverse group of over 3000 species with a global distribution. They include many species playing a significant ecological role as decomposers of decaying organic matter, including the industrially mass reared Black Soldier Fly (Hermetia illucens) used for organic waste recycling. Their gut microbiome likely contributes to their ability to digest organic matter. However, despite their ecological and industrial importance, microbiome studies have so far focused almost exclusively on captively reared H. illucens. We present the first comparative survey of the larval soldier fly gut microbiome sampling 5 subfamilies (Beridinae, Pachygastrinae, Chiromyzinae, Stratiomyinae, Hermetiinae). Full length 16S rRNA gene sequencing revealed distinct microbiomes for the different soldier fly species. However, some bacterial lineages were shared between multiple hosts including Dysgonomonas, Scrofimicrobium, Wohlfahrtiimonas, Enterococcaceae, Enterobacteriaceae and Lachnospiraceae. Dysgonomonas was present in all detritivorous species with high undescribed diversity. The root sap feeding larvae of Inopus sp. had a distinct, low diversity microbiome dominated by Paraburkholderia resembling the microbiota of plant sap-feeding true bugs (Heteroptera). Wild larvae of H. illucens and Exaireta spinigera had higher microbiome diversity compared to captively reared conspecifics. Moreover, wild H. illucens from three distant Australian sites shared a “wild core” of bacterial taxa including novel Orbaceae, Dysgonomonas, Scrofimicrobium, Enterococcaceae and Campylobacteraceae. These findings reveal both ecological specialization and conserved microbial associations, suggesting targets for functional studies and probiotic development to optimize industrial H. illucens rearing.