Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting

Potential of lavender essential oil to inhibit tetracycline resistance and modulate gut microbiota in black soldier fly larvae

The misuse of tetracycline in livestock farming leads to environmental residues that promote the proliferation of antibiotic resistance genes (ARGs), particularly tetracycline resistance (tet) genes. Black soldier fly (BSF) larvae, used for organic waste bioconversion, may carry tetracycline residues in their guts, raising concerns about ARG spread. To address this issue, plant-derived additives such as lavender essential oil (LEO) have been explored as alternative antibiotics. This study investigated the effects of LEO on tet gene suppression and gut microbiota modulation in BSF larvae. Results showed that oxytetracycline treatment increased tet gene relative abundance threefold compared to the control, reaching 1.13 ± 0.29 and enriched pathogens Klebsiella oxytoca and Enterobacter hormaechei. Conversely, LEO treatment (100 mg/kg) reduced tet gene abundance by 46.67 %, from 0.15 ± 0.02 to 0.08 ± 0.02, and enhanced beneficial microorganisms like Leuconostoc pseudomesenteroides. Furthermore, LEO reduced tet gene relative abundance in oxytetracycline-treated larvae from 1.13 ± 0.29 to 0.49 ± 0.19 and 0.70 ± 0.11 in separate treatments. LEO modified fungal composition and nutrient pathways. Network analysis revealed that LEO promoted a more integrated and modular gut microbiota, enhancing functional specialization and resilience. These findings suggest LEO can mitigate ARGs in BSF larvae, offering a sustainable approach for antibiotic resistance management in organic waste recycling and livestock farming.

Mitigating the transfer risk of antibiotic resistance genes from fertilized soil to cherry radish during the application of insect fertilizer

The transfer of antibiotic resistance genes (ARGs) from fertilized soil to vegetables, particularly those consumed raw, causes significant public health risks through the food chain. Black soldier fly larvae can efficiently convert animal manure into organic fertilizer with reduced antibiotic resistance. This study utilized metagenomic sequencing to investigate fields treated with control organic fertilizer (COF), black soldier fly organic fertilizer (BOF), and no fertilizer, with the aim of assessing the transfer risks of ARGs from soil to cherry radish. The results indicated that BOF significantly reduced the richness and abundance of ARGs in both soil and cherry radish compared to COF, reducing 13 ARG subtypes and a 27.6% decrease in ARG abundance in cherry radish. Moreover, a significant positive correlation was observed between mobile genetic elements (MGEs) and virulence factors (VFs) with ARGs, with BOF treatment resulting in a relative abundance reduction of 32.8% and 29.1%, respectively. The complexity of networks involving ARGs with MGEs, VFs, and microbial communities in the BOF treatment was 54.2%, 32.3%, and 32.8% lower, respectively, than the COF treatment. Further analysis of metagenomic-assembled genomes (MAGs) revealed the co-occurrence of ARGs, MGEs, and VFs in cherry radish, indicating the presence of potential pathogenic antibiotic-resistant bacteria (PARB). Notably, the abundance of these PARB in BOF radishes decreased by 45.6% compared to COF. These findings underscore the efficacy of insect fertilizer in mitigating the transfer risks of ARGs to radish, highlighting the significance of sustainable agricultural practices in managing the environmental and health risks associated with ARGs.

Mitigating the vertical migration and leaching risks of antibiotic resistance genes through insect fertilizer application

The leaching and vertical migration risks of antibiotic resistance genes (ARGs) from fertilized soil to groundwater poses a significant threat to ecological and public safety. Insect fertilizer, particularly black soldier fly organic fertilizer (BOF), renowned for its minimal antibiotic resistance, emerge as a promising alternative for sustainable agricultural fertilization. This study employs soil-column leaching experiments to evaluate the impact of BOF on the leaching behavior of ARGs. Our results reveal that BOF significantly reduces the leaching risks of ARGs by 22.1 %-49.3 % compared to control organic fertilizer (COF). Moreover, BOF promotes the leaching of beneficial Bacillus and, according to random forest analysis, is the most important factor in predicting ARG profiles (3.02 % increase in the MSE). Further network analysis and mantel tests suggest that enhanced nitrogen metabolism in BOF leachates could foster Bacillus biofilm formation, thereby countering antibiotic-resistant bacteria (ARB) and mitigating antibiotic resistance. In addition, linear regression analysis revealed that Bacillus biofilm-associated genes pgaD (biofilm PGA synthesis protein), slrR (biofilm formation regulator), and kpsC (capsular polysaccharide export protein) were identified as pivotal in the elimination of ARGs, which can serve as effective indicators for assessing antibiotic resistance in groundwater. Collectively, this study demonstrates that BOF as an environmentally friendly fertilizer could markedly reduce the vertical migration risks of ARGs and proposes Bacillus biofilm formation related genes as reliable indicators for monitoring antibiotic resistance in groundwater.

Characteristics and biological mechanism of protein degradation by the black solider fly (Hermetia illucens L.) larvae gut strain Bacillus subtilis S4

The black solider fly larvae (BSFL) can efficiently convert nitrogen in organic waste into insect protein. Bacillus subtilis S4, an efficient protein-degrading bacterium from the BSFL gut, was isolated and identified to explore the mechanism of nutrient metabolism underlying BSFL nitrogen utilization. Results showed that B. subtilis S4 could effectively increase larval biomass in a bean stem bioconversion system. In vitro high-performance liquid chromatography analysis showed that B. subtilis S4 completely degraded casein into Val, Ile, Phe, Leu, Tyr, Lys, Gly, and Met. Various protease genes with secretion expression ability were annotated in B. subtilis S4. They included peptidoglycan DL - endopeptidase, aminopeptidase, extracellular metalloprotease, peptidoglycan endopeptidase, and peptidase M15. Therefore, the BSFL intestinal microbe B. subtilis S4 could effectively degrade protein and promote larval biomass accumulation, which could provide novel insights into the combined conversion of organic waste into proteins by microbes and insects.

Wingless strain created using binary transgenic CRISPR/Cas9 alleviates concerns about mass rearing of Hermetia illucens

Larvae of the black soldier fly Hermetia illucens have potential as a natural waste recycler and subsequent use as protein-rich feed for livestock. A common question about the insect-farming processes is, what about the concerns of mass escape of insects from large populations? Here, we present a binary transgenic CRISPR/Cas9 system to generate wingless strain with the potential to address this issue. We identified gonad-specific promoters in vivo and evaluated use of the two strongest promoters, nanos and exuperantia, to drive Cas9 expression. We found that crossing the Hiexu-Cas9 with transgenic sgRNA-expressing insects resulted in higher knockout efficiency of the marker gene white. The Hiexu-Cas9 strain exhibited a maternal deposition of Cas9 that caused more effective knockout in the progeny of female Cas9-expressing individuals. Using this system, we generated wingless mutants lacking mating ability, which can be maintained in colony through a genetic cross of two single strain. These insects are less likely to escape and would be unable to successfully mate if they did escape. Taken together, this study validates effective genetic tools that can be used for gene function studies and industrial applications in black soldier fly and provides an approach to alleviate the concern about massive rearing.

Exploring the role of the microbiome of the H. illucens (black soldier fly) for microbial synergy in optimizing black soldier fly rearing and subsequent applications

The symbiotic microbiome in the insect's gut is vital to the host insect's development, improvement of health, resistance to disease, and adaptability to the environment. The black soldier fly (BSF) can convert organic substrates into a protein- and fat-rich biomass that is viable for various applications. With the support of a selective microbiome, BSF can digest and recycle different organic waste, reduce the harmful effects of improper disposal, and transform low-value side streams into valuable resources. Molecular and systems-level investigations on the harbored microbial populations may uncover new biocatalysts for organic waste degradation. This article discusses and summarizes the efforts taken toward characterizing the BSF microbiota and analyzing its substrate-dependent shifts. In addition, the review discusses the dynamic insect-microbe relationship from the functional point of view and focuses on how understanding this symbiosis can lead to alternative applications for BSF. Valorization strategies can include manipulating the microbiota to optimize insect growth and biomass production, as well as exploiting the role of BSF microbiota to discover new bioactive compounds based on BSF immunity. Optimizing the BSF application in industrial setup and exploiting its gut microbiota for innovative biotechnological applications are potential developments that could emerge in the coming decade.

Screening of oxytetracycline-degrading strains in the intestine of the black soldier fly larvae and their degradation characteristics

The presence of excessive antibiotic residues poses a significant threat to human health and the environment. This study was designed to identify an effective oxytetracycline (OTC)-degrading strain through the screening of the intestine of black soldier fly larvae (BSFL). A strain designated "B2" was selected using a series of traditional microbial screening methods. It could be identified as Enterococcus faecalis by Gram staining and 16S rDNA sequencing, with a similarity of 99.93%. Its ability to degrade OTC was then assessed using high-performance liquid chromatography (HPLC). The degradation of the strain was characterized using a one-way test to assess the effects of the substrate concentration, inoculum amount, and initial pH on the degrading bacteria. The results indicate that strain B2 exhibited optimal OTC-degrading performance at a substrate concentration of 50 mg/L, with an inoculum amount of 6% and a pH value of 5.0. Specifically, strain B2 achieved degradation rates of 71.11%, 56.14%, and 45.03%. These findings demonstrate the effectiveness of strain B2 in degrading OTC, indicating its potential for use in environmental remediation efforts.

Bioconversion of sulfamethazine-contaminated chicken manure by black soldier fly larvae: Effects on antibiotic resistance genes and microbial communities

Sulfamethazine (SM2), a widely detected antibiotic in livestock manure, poses environmental and health risks due to its persistence and the proliferation of antibiotic resistance genes (ARGs). In this study, we investigated the degradation of SM2 and the elimination of sulfonamide ARGs (sul1 and sul2) in chicken manure contaminated with varying concentration of SM2 by black soldier fly larvae (BSFL). Quantitative PCR and 16S rRNA gene sequencing were employed to monitor changes in sulfa ARGs and microbial community composition within both the larvae gut and chicken manure. During the 12-day test period, BSFL exhibited strong tolerance to SM2, significantly reducing SM2 concentrations by 80.54%-92.22% across different treatment groups. Concurrently, the abundance of sul1 and sul2 decreased by 79.27% and 79.92% in chicken manure, respectively. Additionally, microbial genera such as Firmicutes (47.18-65%) and Bacillus (9.32-10.25%), which were enriched in both the BSFL gut and chicken manure, were identified as potential contributors to SM2 degradation. These findings provide a promising biotechnological strategy for mitigating antibiotic contamination in livestock manure.

Biosafety assessment of laying hens fed different treatments of black soldier flies (Hermetia illucens) under doxycycline stress

The black soldier fly (BSF, Hermetia illucens) is a resource insect that can utilize livestock and poultry feces. However, BSFs may also increase the risk of transmission of antibiotic resistance genes (AGRs) that are widespread in livestock and poultry farm environments. Therefore, we aimed to evaluate the biosecurity risks of different BSF treatments in the laying chicken food chain using the "chicken manure-BSF-laying hens" model. Our results indicated that different BSF treatments significantly affected antibiotic residue, ARGs, MGEs, bacterial antibiotic resistance, and bacterial microbial community composition in the food chain of laying hens fed BSFs. These risks can be effectively reduced through starvation treatment and high-temperature grinding treatment. Comprehensive risk assessment analysis revealed that starvation combined with high-temperature milling (Group H) had the greatest effect.

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".

Safety and transfer of veterinary drugs from substrate to black soldier fly larvae

There is an increasing interest in edible insects in Europe for feed and food purposes. Quantitative information on the transfer of chemical hazards from substrates to larvae is needed to evaluate food and feed safety aspects. This evaluation is especially needed when organic substrates or residual streams such as manure will be applied as substrate, contributing to a circular food system. This study investigated the transfer of veterinary drugs from spiked substrate to black soldier fly larvae (Hermetia illucens). Veterinary drugs that are commonly administered to chicken, fattening pigs, and cattle and regularly detected in manure were included: three different antibiotics (enrofloxacin, oxytetracycline, sulfamethoxazole), three coccidiostats (narasin, salinomycin, toltrazuril) and one antiparasitic drug (eprinomectin). The chemicals were spiked to insect substrate to reach final concentrations of 0.5 and 5 mg/kg for the antibiotics and the antiparasitic drug, and 5 and 50 mg/kg for the coccidiostats. Black soldier fly larvae were reared for 1 week on the spiked substrates, and the transfer of the veterinary drugs to the larvae and frass was quantified using liquid chromatography coupled with tandem mass spectrometry. Only oxytetracycline and eprinomectin reduced the average weight and/or survival of the black soldier fly larvae. The transfer of the veterinary drugs to the larvae was on average 19.2% for oxytetracycline, 12% for enrofloxacin, 9.5% for narasin, 8.1% for eprinomectin, 3.9% for salinomycin, 4.2% for toltrazuril, and 0.2% for sulfamethoxazole, relative to concentrations in the substrate. Mass-balance calculations revealed that the larvae seem to metabolise veterinary drugs, and indeed, metabolites of enrofloxacin, sulfamethoxazole, and toltrazuril were detected in the larvae and frass. In conclusion, insect-rearing substrates should be evaluated for the presence of veterinary drug residues to ensure feed (and food) safety, as well as because of possible effects on insect growth.

Black soldier fly-based bioconversion of biosolids: Microbial community dynamics and fate of antibiotic resistance genes

Biosolids as by-products of wastewater treatment can contain a large spectrum of pathogens and antibiotic resistance genes (ARGs). Insect-based bioconversion using black soldier fly larvae (BSFL) is an emerging technology that has shown to reduce significant amounts of biosolids quickly and produce larvae biomass containing low heavy metal concentrations. However, to the best of our knowledge, this is the first study investigating the transfer of pathogens and ARGs from biosolids into the process' end-products, BSFL and frass. We hypothesized that BSF-based bioconversion can decrease the abundance of pathogenic bacteria and ARGs in biosolids. In this study, we performed BSFL feeding trials with biosolids blended or not blended with wheat bran, and wheat bran alone as a low bioburden diet (control). We conducted 16S rRNA amplicon sequencing to monitor changes of the BSFL-associated microbial community and the fate of biosolids-associated pathogens. A diverse set of ARGs (ermB, intl1, sul1, tetA, tetQ, tetW, and blaCTX-M-32) were quantified by qPCR and were linked to changes in substrate- and BSFL-associated microbiomes. BSF-based bioconversion of biosolids-containing substrates led to a significant reduction of the microbial diversity, the abundance of several pathogenic bacteria and the investigated ARGs (< 99 %). Feeding with a high bioburden biosolid diet resulted in a higher microbial diversity, and the accumulation of pathogenic bacteria and ARGs in the BSFL. Results of this study demonstrated that BSF-based bioconversion can be a suitable waste management technology to (1) reduce significant amounts of biosolids and (2) reduce the presence of pathogens and ARGs. However, the resulting larvae biomass would need to undergo further post-treatment to reduce the pathogenic load to allow them as animal feed.

Evolution of microbiome composition, antibiotic resistance gene loads, and nitrification during the on-farm composting of the solid fraction of pig slurry using two bulking agents

Composting is a nature-based method used to stabilize organic matter and to transform nitrogen from animal farm manure or solid fraction of slurry (SFS). The use of composted material as source of nutrients for agriculture is limited by its potential to facilitate the propagation of biological hazards like pathogens and antibiotic-resistant bacteria and their associated antibiotic-resistance genes (ARG). We show here an experimental on-farm composting (one single batch) of pig SFS, performed under realistic conditions (under dry continental Mediterranean climate) for 280 days, and using two different bulking agents (maize straw and tree pruning residues) for the initial mixtures. The observed reduction in potentially pathogenic bacteria (80-90%) and of ARG loads (60-100%) appeared to be linked to variations in the microbiome composition occurring during the first 4 months of composting, and concurrent with the reduction of water-soluble ammonium and organic matter loads. Nitrification during the composting has also been observed for both composting piles. Similar patterns have been demonstrated at small scale and the present study stresses the fact that the removal can also occur at full scale. The results suggest that adequate composition of the starting material may accelerate the composting process and improve its global performance. While the results confirm the sanitization potential of composting, they also issue a warning to limit ARG loads in soils and in animal and human gut microbiomes, as the only way to limit their presence in foodstuffs and, therefore, to reduce consumers' exposure.

Co-digestion of chicken manure and sewage sludge in black soldier fly larvae bioconversion system: bacterial biodiversity and nutrients quality of residues for biofertilizer application

Black soldier fly larvae (BSFL) bioconversion system is emerging as an effective approach for organic waste pollution treatment. Co-digestion of different organic matters with BSFL can be an effective way to realize the innovative biowaste circular economy. In this study, organic waste mixture of chicken manure and sewage sludge was chosen as substrate for BSFL growth. The bacterial biodiversity and nutrients quality of BSFL residue were evaluated through gene sequencing and other characterizations to confirm their application potential as biofertilizers. The dominant bacteria in BSFL residue were Firmicutes (75.39%) at phylum level, Bacilli (71.61%) at class level and Pseudogracilibacillus (11.08%) at genus level. Antibiotic resistance genes (ARGs) were used to assess the harmlessness of BSFL residue. After BSFL treatment, 36.2% decrease in ARGs was observed. Taking nutrients quality into consideration, dissolved organic carbon, dissolved nitrogen, available phosphorous, and available potassium significantly increased in the co-digestion system. These results demonstrated that co-digestion of chicken manure and excess sludge in BSFL bioconversion system could improve the nutrients quality of residues. However, removal of ARGs in the bioconversion process should be further explored to eliminate environmental concerns associated with application of BSFL residue as biofertilizers.

Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure

The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.