First Evidence of Past and Present Interactions between Viruses and the Black Soldier Fly, Hermetia illucens

detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data

Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.

Novel RNA viruses in a commercial colony of Tenebrio molitor

Insect mass rearing for food and feed purposes is rapidly expanding in response to the current increase in protein demand. The mass reared insect strains are characterized by interactions with microorganisms, including viruses, that can be either beneficial or pathogenic and might lead to improved or decreased host health. The yellow mealworm, Tenebrio molitor, is a coleopteran species mainly reared for food and feed purposes showing high susceptibility to the Tenebrio molitor densovirus (TmDNV), which can lead to the loss of the entire population in a few days. The potential effect of viruses on mass-reared yellow mealworm highlights the need to screen for additional insect viruses associated with this insect species. In this study, we described and characterized five novel viruses associated with a European commercial T. molitor strain: Tenebrio molitor virga-like virus 1 (TmViLV1), Tenebrio molitor virga-like virus 2 (TmViLV2), Tenebrio molitor iflavirus 1 (TmIV1), Tenebrio molitor tombusvirus 1 (with two segments) (TmToV1), and Tenebrio molitor associated narnavirus 1 (TmAsNaV1). Then, we assessed the prevalence of these viruses in T. molitor samples derived from T. molitor rearings located worldwide. Assessing host-virus interactions aids in unravelling the effect of viruses on insect development, giving insights into possible implications for mass-rearing facilities.

High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens)

Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.

Review: A journey into the black soldier fly digestive system: From current knowledge to applied perspectives

Recent literature on the black soldier fly (BSF) confirms the deep interest in this species for the bioconversion of organic waste, including challenging substrates that contain recalcitrant macromolecules, and highlights the growing trend in new applications for this insect. While protein meal remains the most prominent use of BSF larvae, emerging research is increasingly exploring alternative applications of biomolecules derived from these larvae, including proteins, lipids, chitin, and antimicrobial peptides. Moreover, the high feeding versatility of this insect is being recognised in fields beyond animal feed, such as bioremediation, where its potential ability to degrade contaminants can present significant ecological benefits. Although there is now widespread agreement that a thorough understanding of BSF biology is essential to enlarge the range of applications in which this insect may offer new sustainable solutions, studies on the digestive system are still limited and we are far from having a whole comprehension of the functional features of this complex structure. In fact, the gut is not only the core of the bioconversion process but also represents the first defence barrier against ingested pathogens, and due to the presence of a highly versatile gut microbiota, it may be a potential source of novel microbes and enzymes that could find application in various biotechnological sectors. This review aims to provide a comprehensive overview of the current knowledge on the BSF midgut -the central region of the gut responsible for nutrient digestion and absorption- in both larvae and adults, together with information about mouthparts and the organisation of the alimentary canal. Moreover, starting from the most recent studies on the midgut and its microbiota, we discuss implications for improving larval production, exploiting challenging substrates, and mitigating pollutants in contaminated biomasses.

Use of a Novel Feeding System to Assess the Survival of a Very Stable Mammalian Virus, Porcine Parvovirus, Within Black Soldier Fly (Hermetia illucens) Larvae: A Comparison with Mealworm (Tenebrio molitor) Larvae

Insect larvae production offers the potential for large-scale synthesis of high-quality protein that can be used as feed or food. However, currently, there are limitations on the source of substrates for the insect larvae to use. One concern is the potential survival of animal pathogens within insect larvae if their feed is contaminated. In this study, the survival of a very stable virus, porcine parvovirus (PPV), within mealworm (Tenebrio molitor) and black soldier fly (BSF) (Hermetia illucens) larvae has been analyzed after oral ingestion of the virus. PPV genomic DNA could be readily detected by PCR in both species of larvae up until 9 days post ingestion (DPI), the end of the study period. Furthermore, infection of susceptible PK15 cells by PPV from homogenized mealworm larvae could be detected until at least 3 DPI, using an immunoperoxidase staining method and, up until 9 DPI, with a more sensitive real time PCR assay. Thus, PPV can remain infectious within mealworm larvae during their main growth phase through to their harvesting. However, it may be considered that PPV is exceptional in this respect since it displays unusual stability, e.g., to heat.

Endogenous viral elements: insights into data availability and accessibility

Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.

Detection of Known and Novel Virus Sequences in the Black Soldier Fly and Expression of Host Antiviral Pathways

The mass rearing of animals in close quarters can be highly conducive to microbe transmission, including pathogens. This has been shown multiple times in the case of important industrial insects such as crickets, silkworms, and honeybees. One industrial insect of increasing importance is the black soldier fly (Diptera: Hermetia illucens), as it can convert organic waste into high-quality protein and fatty acids. Along with this, they take up far less space than traditional protein sources, as millions of black soldier flies can be reared in a relatively small facility. Because of this, there is a growing interest in the pathogens that could impact black soldier fly-rearing efforts. So far, only three black soldier fly-associated viruses have been identified. We used metatranscriptomic sequencing to survey black soldier fly guts, frass, and diet for viruses. We detected sequences from two novel viruses. One, which we name Hermetia illucens sigma-like virus 1, is phylogenetically related to viruses of the genus Sigmavirus, which have been highly studied in Drosophila. The other novel virus, which we name Hermetia illucens inse-like virus 1, is the second double-stranded RNA virus of the order Ghabrivirales described in the black soldier fly, and groups within a new family of insect viruses called the Inseviridae. We also detected two black soldier fly-associated viruses previously identified by our group: BSF nairo-like virus 1 and BSF uncharacterized bunyavirus-like 1. Consistent with our previous study, these two viruses are found primarily in frass samples and occur together more often than expected at random. When analyzing host transcription, we found significant differences in gene expression for eight candidate antiviral genes in the black soldier fly when comparing samples with and without viral sequences. Our results suggest that black soldier fly-virus interactions are ongoing, and they could be of interest to black soldier fly producers.

Effect of entomopathogenic fungus Beauveria bassiana on the growth characteristics and metabolism of black soldier fly larvae

Beauveria bassiana is an entomopathogenic fungus widely used in agriculture to reduce populations of various pests. However, when agricultural waste is utilized for organic recycling, B. bassiana has the potential to impact recycling performance, by affecting the survival, and body mass of decomposing organisms (such as insect's larvae). Additionally, in natural conditions where decayed organic matter contains a high load of different entomopathogenic organisms, larval growth may be affected when consumed or in contact. In a laboratory study, we aimed to comprehend the effects of B. bassiana on the growth characteristics and larval metabolism of the black soldier fly larvae, which is a known decomposing insect. The experiments used both feeding (mixing the spores with the diet, hereafter BF) and contact treatments (by dipping the larva in the spores solution, hereafter BD), and were compared to a water-treated control group. The BF treatment significantly reduced larval body weight, adult emergence, and adult weight compared to both the control and the BD treatment. Furthermore, an analysis of hemolymph metabolites, categorized by class, indicated a higher accumulation of metabolites belonging to the purine and purine derivative classes, as well as carboxylic acids and their derivatives, including peptides and oligopeptides, indicating potential disruption of protein synthesis or degradation caused by the BF treatment. Pathway enrichment analysis showed significant alterations in purine metabolism and D-Arginine and D-ornithine metabolism compared to the control. Taurine and hypotaurine metabolism were significantly altered in the BD treatment compared to the control but not significantly enriched in the BF treatment. Our results suggest that the BF treatment impairs protein synthesis or degradation, affecting larval growth characteristics. Future studies should explore innate immunity-related gene expression and antimicrobial peptide production in BSF larvae to understand their immunity to pathogens.

Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges

Bioconversion using insects is a promising strategy to convert organic waste (catering leftovers, harvest waste, food processing byproducts, etc.) into biomass that can be used for multiple applications, turned into high added-value products, and address environmental, societal and economic concerns. Due to its ability to feed on a tremendous variety of organic wastes, the black soldier fly (Hermetia illucens) has recently emerged as a promising insect for bioconversion of organic wastes on an industrial scale. A growing number of studies have highlighted the pivotal role of the gut microbiota in the performance and health of this insect species. This review aims to provide a critical overview of current knowledge regarding the functional diversity of the gut microbiota of H. illucens, highlighting its importance for bioconversion, food safety and the development of new biotechnological tools. After providing an overview of the different strategies that have been used to outline the microbial communities of H. illucens, we discuss the diversity of these gut microbes and the beneficial services they can provide to their insect host. Emphasis is placed on technical strategies and aspects of host biology that require special attention in the near future of research. We also argue that the singular digestive capabilities and complex gut microbiota of H. illucens make this insect species a valuable model for addressing fundamental questions regarding the interactions that insects have evolved with microorganisms. By proposing new avenues of research, this review aims to stimulate research on the microbiota of a promising insect to address the challenges of bioconversion, but also fundamental questions regarding bacterial symbiosis in insects.

Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly

The black soldier fly (Hermetia illucens, BSF) has emerged as an industrial insect of high promise because of its ability to convert organic waste into nutritious feedstock, making it an environmentally sustainable alternative protein source. As global interest rises, rearing efforts have also been upscaled, which is highly conducive to pathogen transmission. Viral epidemics have stifled mass-rearing efforts of other insects of economic importance, such as crickets, silkworms, and honeybees, but little is known about the viruses that associate with BSF. Although BSFs are thought to be unusually resistant to pathogens because of their expansive antimicrobial gene repertoire, surveillance techniques could be useful in identifying emerging pathogens and common BSF microbes. In this study, we used high-throughput sequencing data to survey BSF larvae and frass samples, and we identified two novel bunyavirus-like sequences. Our phylogenetic analysis grouped one in the family Nairoviridae and the other with two unclassified bunyaviruses. We describe these putative novel viruses as BSF Nairovirus-like 1 and BSF uncharacterized bunyavirus-like 1. We identified candidate segments for the full BSF Nairovirus-like 1 genome using a technique based on transcript co-occurrence and only a partial genome for BSF uncharacterized bunyavirus-like 1. These results emphasize the value of routine BSF colony surveillance and add to the number of viruses associated with BSF.