Isolation and characterization of a novel temperate bacteriophage from gut-associated Escherichia within black soldier fly larvae (Hermetia illucens L. [Diptera: Stratiomyidae])

Protocol for establishing CRISPR-Cas12a for efficient genome editing of Pseudomonas aeruginosa phages

We developed an efficient type V CRISPR-Cas12a system tailored specifically for Pseudomonas aeruginosa phages, showcasing its remarkable cleavage activity and the ability to precisely introduce genetic modifications, including point mutations, deletions, and insertions, into phage genomes. Here, we present a protocol for establishing CRISPR-Cas12a for genome editing of Pseudomonas aeruginosa phages. We describe steps for the construction of pCRISPR-12a plasmid and guide RNA and the utilization of the type V CRISPR-Cas12a system for precise genetic editing of phages. For complete details on the use and execution of this protocol, please refer to Chen et al.1.

Black Soldier Fly (Hermetia illucens) Microbiome and Microbe Interactions: A Scoping Review

Black soldier fly (Hermetia illucens, BSF) is farmed worldwide to convert organic waste into usable biomaterials. Studies on the larval microbiome have been carried out to check for symbiotic or pathogenic microbes and their respective functions and fates. Some studies tested these microbes for industrial applications, while others tested the effects of exogenous microbes as probiotics or for substrate pre-processing to improve larval fitness, bioconversion rates, or nutritional qualities. This review examined all peer-reviewed literature on these topics to consolidate many disparate findings together. It followed the PRISMA guidelines for scoping reviews. The results found no evidence of globally conserved core microbes, as diet strongly correlated with gut microbiome, but some genera appeared most frequently in BSF larval guts worldwide regardless of diet. The gut microbes undoubtably assist in digestion, including pathogen suppression, and so microbial probiotics show promise for future investigations. However, the common gut microbes have not been explored as probiotics themselves, which would be a promising direction for future work. The impacts of BSF bioconversion on pathogens varied, so each rearing facility should investigate and manage their pathogen risks independently. The data summarized in this study provide useful reference points for future investigations into BSF-microbe interactions.

Characterization and Comparative Genomic Analysis of vB_BceM_CEP1: A Novel Temperate Bacteriophage Infecting Burkholderia cepacia Complex

The increasing prevalence of multidrug-resistant bacteria imminently threatens public health and jeopardizes nearly all aspects of modern medicine. The Burkholderia cepacia complex (Bcc) comprises Burkholderia cepacia and the related species of Gram-negative bacteria. Members of the Bcc group are opportunistic pathogens responsible for various chronic illnesses, including cystic fibrosis and chronic granulomatous disease. Phage therapy is emerging as a potential solution to combat the antimicrobial resistance crisis. In this study, a temperate phage vB_BceM_CEP1 was isolated from sewage and fully characterized. Transmission electron microscopy indicated that vB_BceM_CEP1 belongs to the family Peduoviridae. The isolated phage demonstrated enhanced environmental stability and antibiofilm potential. One-step growth analysis revealed a latent period of 30 min and an average burst size of 139 plaque-forming units per cell. The genome of vB_BceM_CEP1 consists of 32,486 bp with a GC content of 62.05%. A total of 40 open reading frames were annotated in the phage genome, and none of the predicted genes was annotated as tRNA. Notably, genes associated with antibiotic resistance, host virulence factors, and toxins were absent from the vB_BceM_CEP1 genome. Based on its unique phenotype and phylogeny, the isolated phage vB_BceM_CEP1 is classified as a new temperate phage with lytic activity. The findings of this study enhance our understanding of the diversity of Bcc phages.

Development of the CRISPR-Cas12a system for editing of Pseudomonas aeruginosa phages

Pseudomonas aeruginosa is a common opportunistic pathogen. The potential efficacy of phage therapy has attracted the attention of researchers, but efficient gene-editing tools are lacking, limiting the study of their biological properties. Here, we designed a type V CRISPR-Cas12a system for the gene editing of P. aeruginosa phages. We first evaluated the active cutting function of the CRISPR-Cas12a system in vitro and discovered that it had a higher gene-cutting efficiency than the type II CRISPR-Cas9 system in three different P. aeruginosa phages. We also demonstrated the system's ability to precisely edit genes in Escherichia coli phages, Salmonella phages, and P. aeruginosa phages. Using the aforementioned strategies, non-essential P. aeruginosa phage genes can be efficiently deleted, resulting in a reduction of up to 5,215 bp (7.05%). Our study has provided a rapid, efficient, and time-saving tool that accelerates progress in phage engineering.

Genomic analysis and experimental pathogenic characterization of Riemerella anatipestifer isolates from chickens in China

Waterfowl have a high likelihood of being infected with Riemerella anatipestifer. Although the pathogen is found in domestic ducks, turkeys, geese, and wild birds, there is little information available about the consequences of infection during egg laying and hatching in chickens. Here, we present the first report of a novel sequence type of R. anatipestifer S63 isolated from chickens in China. On the basis of pan-genome analysis, we showed S63's genome occupies a distinct branch with other R. anatipestifer isolates from other hosts. Galleria mellonella larval tests indicated that S63 is less virulent than R. anatipestifer Ra36 isolated from ducks. Ducks and hens are susceptible to S63 infection. There is no mortality rate for chickens or ducks, but adult chickens experience neurological symptoms that reduce egg production and hatching rates. In chickens, S63 might be passed vertically from parents to offspring, resulting in "jelly-like" lifeless embryos. Using quantitative PCR, S63 was detected in the brain, liver, reproductive organs, and embryos. As far as we know, this is the first report of R. anatipestifer in hens, a disease that can reduce egg productivity, lower hatching rates, and produce jelly-like lifeless embryos, and the first report to raise the possibility that hens can be infected by roosters via semen.

Genome sequence of Shiga toxin-producing Escherichia coli jumbo bacteriophage vB_EcoM_JNE01

Bacteriophage vB_EcoM_JNE01 was isolated from chicken farm sewage using Escherichia coli O157:H7 as the host bacteria. The total length of the vB_EcoM_JNE01 genome is 355,583 bp, with 584 open reading frames and 36% G+C content. It shares an 80% nucleotide identity with 59% query coverage with the bacteriophage PBECO4 (NC_027364).

Genetic diversity of RNA viruses infecting invertebrate pests of rice

Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

Insects as an alternative protein source for poultry nutrition: a review

This review summarizes the most relevant scientific literature related to the use of insects as alternative protein sources in poultry diets. The black soldier fly, the housefly, the beetle, mealworms, silkworms, earthworms, crickets, and grasshoppers are in the spotlight because they have been identified as an important future source of sustainable animal proteins for poultry feeding. Insect meals meet poultry requirements in terms of nutritional value, essential amino acid composition, nutrient digestibility, and feed acceptance. Furthermore, they are enriched with antimicrobial peptides and bioactive molecules that can improve global health. Results from poultry studies suggest equivalent or enhanced growth performances and quality of end-products as compared to fish meal and soybean meal. To outline this body of knowledge, this article states established threads of research about the nutrient profiles and the digestibility of insect meals, their subsequent effects on the growth and laying performances of poultry as well as the quality of meat, carcass, and eggs. To fully exploit insect-derived products, the effects of insect bioactive molecules (antimicrobial peptides, fatty acids, and polysaccharides) were addressed. Furthermore, as edible insects are likely to take a meaningful position in the feed and food chain, the safety of their derived products needs to be ensured. Some insights into the current knowledge on the prevalence of pathogens and contaminants in edible insects were highlighted. Finally, the effect of insect farming and processing treatment on the nutritive value of insect larvae was discussed. Our overview reveals that using insects can potentially solve problems related to reliance on other food sources, without altering the growth performances and the quality of meat and eggs.

Temperate phage influence virulence and biofilm-forming of Salmonella Typhimurium and enhance the ability to contaminate food product

Salmonella is a food-borne zoonotic pathogen that threatens food safety and public health security. Temperate phages can influence bacterial virulence and phenotype and play an important role in bacterial evolution. However, most studies on Salmonella temperate phages focus on prophage induced by bacteria, with few reports on Salmonella temperate phages isolated in the environment. Moreover, whether temperate phages drive bacterial virulence and biofilm formation in food and animal models remains unknown. In this study, Salmonella temperate phage vB_Sal_PHB48 was isolated from sewage. TEM and phylogenetic analysis indicated that phage PHB48 belongs to the Myoviridae family. Additionally, Salmonella Typhimurium integrating PHB48 was screened and designated as Sal013⁺. Whole genome sequencing revealed that the integration site was specific and we confirmed that the integration of PHB48 did not change the O-antigen and coding sequences of Sal013. Our in vitro and in vivo studies showed that the integration of PHB48 could significantly enhance the virulence and biofilm formation of S. Typhimurium. More importantly, the integration of PHB48 significantly improved the colonization and contamination ability of bacteria in food samples. In conclusion, we isolated Salmonella temperate phage directly from the environment and systematically clarified that PHB48 enhanced the virulence and biofilm-forming ability of Salmonella. In addition, we found that PHB48 increased the colonization and contamination ability of Salmonella in food samples. These results indicated that the highly pathogenic Salmonella induced by temperate phage was more harmful to food matrices and public health security. Our results could enhance the understanding of the evolutionary relationship between bacteriophages and bacteria, and raise public awareness of large-scale outbreaks resulting from Salmonella virulence enhancement in food industry.

Disarm The Bacteria: What Temperate Phages Can Do

In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.

The Use of Probiotics during Rearing of Hermetia illucens: Potential, Caveats, and Knowledge Gaps

Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to optimize yield and quality. However recently, research has started to focus more on the associated microbes in the larval digestive system and their substrates and the effect of manipulating the composition of these communities on insect performance as a form of microbiome engineering. Here we present an overview of the existing literature on the use of microorganisms during rearing of the BSFL to optimize the productivity of this insect. These studies have had variable outcomes and potential explanations for this variation are offered to inspire future research that might lead to a better success rate for microbiome engineering in BSFL.

Black Soldier Fly Larvae Influence Internal and Substrate Bacterial Community Composition Depending on Substrate Type and Larval Density

Saprophagous fly larvae interact with a rich community of bacteria in decomposing organic matter. Larvae of some species, such as the black soldier fly, can process a wide range of organic residual streams into edible insect biomass and thus produce protein as a sustainable component of livestock feed. The microbiological safety of the insects and substrates remains a point of concern. Substrate-associated bacteria can dominate the larval gut microbiota, but the larvae can also alter the bacterial community in the substrate. However, the relative importance of substrate type and larval density in bacterial community dynamics is unknown. We investigated four larval densities (0 [control], 50, 100, or 200 larvae per container [520 mL; diameter, 75 mm]) and three feed substrates (chicken feed, chicken manure, and camelina substrate [50% chicken feed, 50% camelina oilseed press cake]) and sampled the bacterial communities of the substrates and larvae at three time points over 15 days. Although feed substrate was the strongest driver of microbiota composition over time, larval density significantly altered the relative abundances of several common bacterial genera, including potential pathogens, in each substrate and in larvae fed chicken feed. Bacterial communities of the larvae and substrate differed to a higher degree in chicken manure and camelina than in chicken feed. This supports the substrate-dependent impact of black soldier fly larvae on bacteria both within the larvae and in the substrate. This study indicates that substrate composition and larval density can alter bacterial community composition and might be used to improve insect microbiological safety.

IMPORTANCE Black soldier fly larvae can process organic side streams into nutritious insect biomass, yielding a sustainable ingredient of animal feed. In processing such organic residues, the larvae impact the substrate and its microbiota. However, their role relative to the feed substrate in shaping the bacterial community is unknown. This may be important for the waste management industry to determine whether pathogens can be controlled by manipulating the larval density and the timing of harvest. We investigated how the type of feed substrate and the larval density (number of larvae per container) interacted to influence bacterial community composition in the substrates and larvae over time. Substrate type was the strongest driver of bacterial community composition, and the magnitude of the impact of the larvae depended on the substrate type and larval density. Thus, both substrate composition and larval density may be used to improve the microbiological safety of the larvae as animal feed.

Exploring the Benefits of Metal Ions in Phage Cocktail for the Treatment of Methicillin-Resistant Staphylococcus aureus (MRSA) Infection

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is an important zoonotic pathogen worldwide. Infections due to MRSA are associated with higher mortality rates compared with methicillin-susceptible S. aureus. Meanwhile, bacteriophages have been shown to overcome the emergence of MRSA.

Methods

Phage PHB22a, PHB25a, PHB38a, and PHB40a were isolated. Here, we evaluated the ability of a phage cocktail containing phages PHB22a, PHB25a, PHB38a, and PHB40a against MRSA S-18 strain in vivo and in vitro. Phage whole-genome sequencing, host-range determination, lytic activity, and biofilm clearance experiments were performed in vitro. Galleria mellonella larvae and a mouse systemic infection model to evaluate the efficacy of phage therapy in vivo.

Results

The phage cocktail exhibited enhanced antibacterial and anti-biofilm effects compared to the single phage. Phage cocktail contained with Ca²⁺/Zn²⁺ significantly reduced the number of viable bacteria (24-h or 48-h biofilm) by more than 0.81-log compared to the phage cocktail alone. Furthermore, we demonstrated that the addition of Ca²⁺ and Zn²⁺ phage cocktail could increase the survival rate of G. mellonella larvae infected with S. aureus by 10% compared with phage cocktail alone. This was further confirmed in the mouse model, which showed a 2.64-log reduction of host bacteria S-18, when Ca²⁺ and Zn²⁺ were included in the cocktail compared with the phage cocktail alone.

Conclusion

Our results indicated that phage cocktail supplemented with Ca²⁺/Zn²⁺ could effectively remove bacteria in biofilms and mice tissues infected with S. aureus.

The Expansion of a Single Bacteriophage Leads to Bacterial Disturbance in Gut and Reduction of Larval Growth in Musca domestica

The housefly larvae gut microbiota influences larval health and has become an important model to study the ecology and evolution of microbiota-host interactions. However, little is known about the phage community associated with the housefly larval gut, although bacteriophages are the most abundant members of the microbiota and have the potential to shape gut bacterial communities. Changes to bacteriophage composition are associated with disease, but how phages impact insect health remains unclear. We noticed that treating 1-day-old housefly larvae with ~107, ~109, and ~1011 phage particles per ml of bacteriophages led to changes in the growth and development of housefly larvae. Additionally, treating housefly larvae with bacteriophages led to bacterial composition changes in the gut. Changes in the compositions of these gut bacteria are mainly manifested in the increase in harmful bacteria, including Pseudomonas and Providencia and the decrease in beneficial bacteria, including Enterobacter and Klebsiella, after different growth and development periods. The alterations in gut microbiota further influenced the larval growth and development. Collectively, these results indicate that bacteriophages can perturb the intestinal microbiome and impact insect health.

A Novel Tail-Associated O91-Specific Polysaccharide Depolymerase from a Podophage Reveals Lytic Efficacy of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) strains are important zoonotic foodborne pathogens, causing diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome (HUS) in humans. However, antibiotic treatment of STEC infection is associated with an increased risk of HUS. Therefore, there is an urgent need for early and effective therapeutic strategies. Here, we isolated lytic T7-like STEC phage PHB19 and identified a novel O91-specific polysaccharide depolymerase (Dep6) in the C terminus of the PHB19 tailspike protein. Dep6 exhibited strong hydrolase activity across wide ranges of pH (pH 4 to 8) and temperature (20 to 60°C) and degraded polysaccharides on the surface of STEC strain HB10. In addition, both Dep6 and PHB19 degraded biofilms formed by STEC strain HB10. In a mouse STEC infection model, delayed Dep6 treatment (3 h postinfection) resulted in only 33% survival, compared with 83% survival when mice were treated simultaneously with infection. In comparison, pretreatment with Dep6 led to 100% survival compared with that of the control group. Surprisingly, a single PHB19 treatment resulted in 100% survival in all three treatment protocols. Moreover, a significant reduction in the levels of proinflammatory cytokines was observed at 24 h postinfection in Dep6- or PHB19-treated mice. These results demonstrated that Dep6 or PHB19 might be used as a potential therapeutic agent to prevent STEC infection.IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen worldwide. The Shiga-like toxin causes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome (HUS) in humans. Although antibiotic therapy is still used for STEC infections, this approach may increase the risk of HUS. Phages or phage-derived depolymerases have been used to treat bacterial infections in animals and humans, as in the case of the "San Diego patient" treated with a phage cocktail. Here, we showed that phage PHB19 and its O91-specific polysaccharide depolymerase Dep6 degraded STEC biofilms and stripped the lipopolysaccharide (LPS) from STEC strain HB10, which was subsequently killed by serum complement in vitro In a mouse model, PHB19 and Dep6 protected against STEC infection and caused a significant reduction in the levels of proinflammatory cytokines. This study reports the use of an O91-specific polysaccharide depolymerase for the treatment of STEC infection in mice.

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.

Specific Integration of Temperate Phage Decreases the Pathogenicity of Host Bacteria

Temperate phages are considered as natural vectors for gene transmission among bacteria due to the ability to integrate their genomes into a host chromosome, therefore, affect the fitness and phenotype of host bacteria. Many virulence genes of pathogenic bacteria were identified in temperate phage genomes, supporting the concept that temperate phages play important roles in increasing the bacterial pathogenicity through delivery of the virulence genes. However, little is known about the roles of temperate phages in attenuation of bacterial virulence. Here, we report a novel Bordetella bronchiseptica temperate phage, vB_BbrS_PHB09 (PHB09), which has a 42,129-bp dsDNA genome with a G+C content of 62.8%. Phylogenetic analysis based on large terminase subunit indicated that phage PHB09 represented a new member of the family Siphoviridae. The genome of PHB09 contains genes encoding lysogen-associated proteins, including integrase and cI protein. The integration site of PHB09 is specifically located within a pilin gene of B. bronchiseptica. Importantly, we found that the integration of phage PHB09 significantly decreased the virulence of parental strain B. bronchiseptica Bb01 in mice, most likely through disruption the expression of pilin gene. Moreover, a single shot of the prophage bearing B. bronchiseptica strain completely protected mice against lethal challenge with wild-type virulent B. bronchiseptica, indicating the vaccine potential of lysogenized strain. Our findings not only indicate the complicated roles of temperate phages in bacterial virulence other than simple delivery of virulent genes but also provide a potential strategy for developing bacterial vaccines.