Spore-adsorption: Mechanism and applications of a non-recombinant display system

Probiotic spore-based antigen delivery: a novel oral vaccine strategy against Vibrio infections in aquaculture

BACKGROUND

Vibriosis is a deadly illness caused by various species of the Vibrio genus. Due to its high incidence in aquaculture plants, vibriosis is responsible for significant economic losses. Currently, anti-vibriosis treatments rely on antibiotics. However, the global rise in antibiotic resistance necessitates the development of alternative approaches. Novel vaccines and effective probiotics have been proposed as potential alternative to antibiotics in fighting bacterial infections. Here we propose a combined vaccine/probiotic strategy based on the use of probiotic bacterial spores for the oral delivery of Vibrio antigens. Spores of various species of the Bacillus genus are widely used as probiotics and have been shown to efficiently display antigens in a non-recombinant way.

RESULTS

Spores of various probiotic strains were analyzed to assess their effectiveness in displaying a heterologous model protein, and B. megaterium MV30 was identified as the most efficient strain. MV30 spores were then used to display two antigens of Vibrio harveyi, the entire Hsp33 protein of 33 kDa and a 239 amino acids fragment of OmpK (OmpK21/260), identified as the most immunogenic part of the protein. While Hsp33 is a stable protein, OmpK21/260 is unstable at conditions mimicking those encountered in an aquaculture plant and the interaction with MV30 spores reduced such instability. The protective ability of the combined probiotic/vaccination strategy was assayed on Medaka fish (Oryzias latipes), as a model. In a challenge experiment with a virulent strain of Vibrio harveyi, a protective effect was observed with MV30 spores alone and such effect was significantly increased when the same spores displayed either one of the two antigens.

CONCLUSION

Our results support the use of probiotics and oral vaccines as a valid alternative to antibiotics and point to the application of probiotic spore-based antigen delivery as a novel strategy to fight pathogenic infections.

Transcriptomic analysis of Bacillus licheniformis 2709 reveals the molecular mechanism of alkaline protease biosynthesis regulated by the DegS/DegU two-component system

The DegS/DegU two-component signal transduction system (TCS), plays significant roles in a broad range of bacterial responses to the complicated environment in Bacillus subtilis. However, few efforts have been made to explore the physiological functions of DegS/DegU in alkaline protease (AprE) biosynthesis in the industrial strain Bacillus licheniformis 2709. In this study, it was found that the biosynthesis of AprE is severely hampered in degS and degU deficient mutants compared with the original strain. To investigate the underlying mechanisms responsible for changing the AprE productivity, transcriptome profile analysis was conducted to compare the differentially expressed genes (DEGs) among the deficient mutants and the control. At the peak of AprE production in degS mutant, a total of 810 DEGs including 125 up-regulated and 685 down-regulated were identified compared to the control, which were mainly annotated in 15 pathways, including oxidative phosphorylation, amino acid metabolism and ABC transporters. Besides, the transcriptomic analysis of degU mutant revealed that 307 genes were significantly up-regulated and 604 genes were down-regulated, among which, rho was identified and further functionally verified. Systematic comparison of DEGs under different conditions elucidated self-repression mechanism of DegU on aprE expression in B. licheniformis 2709, which was confirmed by the inducible expression of degU::gfp in this study. The study will yield valuable insight into how the DegS/DegU TCS regulates aprE expression in industrial strain with respect to protease production, and facilitates genetic strain improvement aiming at biological containment and effectiveness of biotechnological processes.

Immobilization of alginate C-5 epimerases using Bacillus subtilis spore display

Alginates are the most abundant polysaccharides found in brown seaweed, composed of (1→4)-linked β-D-mannuronate (M) and its C-5 epimer, α-L-guluronate (G). The G-blocks of alginate possess viscosifying and gelling properties, making alginates valuable industrial polysaccharides. Alginate epimerases are enzymes epimerizing M to G, enhancing the usability and value of alginate. The three alginate epimerases AlgE1, AlgE4, and AlgE6 were immobilized using Bacillus subtilis spores displaying the epimerases fused to the spore crust protein CotY. To our knowledge, this is the first display of immobilized alginate-modifying enzymes. Activity assays of the four AlgE4-displaying spore strains showed that AlgE4 produced MG-blocks from polyM alginate. AlgE4 was tested linked by its N- and C-termini. Two linkers with different flexibility were tested, both containing a TEV protease cleavage site. Immobilizing alginate epimerases on B. subtilis spores resulted in a recyclable system that is easy to isolate and reuse, thus opening possibilities for industrial application. Recyclability was demonstrated by performing five consecutive reactions with the same batch of AlgE4 spores, with the spores retaining 24% of the starting activity after four rounds of reuse. TEV cleavage of spore-displayed enzyme was optimized using spores displaying a green fluorescent protein, and these optimized conditions were used to cleave AlgE4 off the spores. The cleavage of four AlgE4-displaying spores was successful, but cleavage efficiency varied depending on which terminus of AlgE4 was fused to CotY.

IMPORTANCE

Seaweed is a scalable resource that requires no fresh water, fertilizer, or arable land, making it an important biomass for bioeconomies. Alginates are a major component of brown seaweed and are widely used in food, feed, technical, and pharmacological industries. To tailor the functional properties of alginates, alginate epimerases have shown to be promising for postharvest valorization of alginate. This study investigates an efficient and easy method to produce immobilized alginate epimerases, thus opening new industrial use cases. In this study, the alginate epimerases are immobilized on the surface of Bacillus subtilis spores. The bacterium forms spores in reaction to nutrient starvation, which are highly resistant to external influences and can be repurposed as a stable protein display platform for numerous applications due to its ease of genomic manipulation and cultivation.

A multifarious bacterial surface display: potential platform for biotechnological applications

Bacterial-cell surface display represents a novel field of protein engineering, which is grounds for presenting recombinant proteins or peptides on the surface of host cells. This technique is primarily used for endowing cellular activity on the host cells and enables several biotechnological applications. In this review, we comprehensively summarize the speciality of bacterial surface display, specifically in gram-positive and gram-negative organisms and then we depict the practical cases to show the importance of bacterial cell surface display in biomedicine and bioremediation domains. We manifest that among other display systems such as phages and ribosomes, the cell surface display using bacterial cells can be used to avoid the loss of combinatorial protein libraries and also open the possibility of isolating target-binding variants using high-throughput selection platforms. Thus, it is becoming a robust tool for functionalizing microbes to serve as a potential implement for various bioengineering purposes.

Heyndrickxia coagulans spore-based nanoparticle generator for improved oral insulin delivery and hypoglycemic therapy

Due to the two major physiological barriers restricted by mucus penetration and epithelia transport, oral insulin therapy using nano-delivery system remains challenging. Heyndrickxia coagulans spores can survive the harsh conditions of gastrointestinal tract (GIT), and penetrate in the mucus through germination to probiotics with their amphipathic proteinaceous coat shedding in the gut epithelium, which makes it possible to be functionalized with hydrophilic peptide/protein and form nanoparticles (NPs) in vivo. Inspired by the natural physiological properties of spores, novel deoxycholic acid-modified Heyndrickxia coagulans spores loaded with insulin (DA-Spore/Ins) as the generators of autonomous bio-based nanoparticles were designed to solve these absorption barriers to enhance oral insulin delivery. The DA-Spore/Ins delivery system achieved preferable drug protection and rapid mucus penetration through its germination in the intestinal microenvironment. Meanwhile, DA-Spore/Ins NPs could be spontaneously formed by the self-assembly of the disintegrated DA-covalently amphipathic protein coat and the hydrophilic protein/peptides drug. This can efficiently transport through the epithelial cells through the bile acid pathway. In vivo studies indicated that DA-Spore/Ins delivery system achieved an oral relative bioavailability of 15.1 % and superior hypoglycemic effect in type I diabetic rats characterized by good biocompatibility. These studies suggested that the intrinsic biological characteristics of Heyndrickxia coagulans spore-based nanogenerators rendered their promising application in oral insulin or other protein drug therapy.

Probiotic Spores of Shouchella clausii SF174 and Displayed Bromelain Show Beneficial Additive Potential

Probiotics have health-beneficial properties mainly due to either a direct action on the host or the modulation of the host microbiota. Health-beneficial properties have also been associated with a variety of plant-derived molecules, widely used as dietary supplements. This study explores the possibility of combining the actions of probiotics and of plant-derived molecules by developing beneficial, probiotic-carrying, heterologous molecules. To this extent, spores of SF174, a well-characterized probiotic strain of Shouchella clausii (formerly Bacillus clausii), were used to bind bromelain, a plant-derived mixture of endopeptidases with beneficial effects. Probiotic spores displaying bromelain maintained their antioxidant activity and acquired the endopeptidase activity of the heterologous molecule. The endopeptidase activity was stabilized by the interaction with the spore and largely preserved from degradation at simulated gastric conditions. Under conditions mimicking those encountered in the intestine, as well as upon spore germination, active bromelain was released from the spore surface. The in vitro results reported in this study support the idea that probiotics carrying beneficial heterologous molecules combine the health properties of the probiotic with those of the delivered molecule and pave the way for the development of a novel class of functional probiotics.

Yeast surface display technology: Mechanisms, applications, and perspectives

Microbial cell surface display technology, which relies on genetically fusing heterologous target proteins to the cell wall through fusion with cell wall anchor proteins, has emerged as a promising and powerful method with diverse applications in biotechnology and biomedicine. Compared to classical intracellular or extracellular expression (secretion) systems, the cell surface display strategy stands out by eliminating the necessity for enzyme purification, overcoming substrate transport limitations, and demonstrating enhanced activity, stability, and selectivity. Unlike phage or bacterial surface display, the yeast surface display (YSD) system offers distinct advantages, including its large cell size, ease of culture and genetic manipulation, the use of generally regarded as safe (GRAS) host cell, the ability to ensure correct folding of complex eukaryotic proteins, and the potential for post-translational modifications. To date, YSD systems have found widespread applications in protein engineering, waste biorefineries, bioremediation, and the production of biocatalysts and biosensors. This review focuses on detailing various strategies and mechanisms for constructing YSD systems, providing a comprehensive overview of both fundamental principles and practical applications. Finally, the review outlines future perspectives for developing novel forms of YSD systems and explores potential applications in diverse fields.

Functional modification of gut bacteria for disease diagnosis and treatment

Intestinal bacteria help keep humans healthy by regulating lipid and glucose metabolism as well as the immunological and neurological systems. Oral treatment using intestinal bacteria is limited by the high acidity of stomach fluids and the immune system's attack on foreign bacteria. Scientists have created coatings and workarounds to overcome these limitations and improve bacterial therapy. These preparations have demonstrated promising outcomes, with advances in synthetic biology and optogenetics improving their focused colonization and controlled release. Engineering bacteria preparations have become a revolutionary therapeutic approach that converts intestinal bacteria into cellular factories for medicinal chemical synthesis. The present paper discusses various aspects of engineering bacteria preparations, including wrapping materials, biomedical uses, and future developments.

Important role of Bacillus subtilis as a probiotic and vaccine carrier in animal health maintenance

Bacillus subtilis is a widespread Gram-positive facultative aerobic bacterium that is recognized as generally safe. It has shown significant application value and great development potential in the animal farming industry. As a probiotic, it is frequently used as a feed growth supplement to effectively replace antibiotics due to its favourable effects on regulating the intestinal flora, improving intestinal immunity, inhibiting harmful microorganisms, and secreting bioactive substances. Consequently, the gut health and disease resistance of farmed animals can be improved. Both vegetative and spore forms of B. subtilis have also been utilized as vaccine carriers for delivering the antigens of infectious pathogens for over a decade. Notably, its spore form is regarded as one of the most prospective for displaying heterologous antigens with high activity and stability. Previously published reviews have predominantly focused on the development and applications of B. subtilis spore surface display techniques. However, this review aims to summarize recent studies highlighting the important role of B. subtilis as a probiotic and vaccine carrier in maintaining animal health. Specifically, we focus on the beneficial effects and underlying mechanisms of B. subtilis in enhancing disease resistance among farmed animals as well as its potential application as mucosal vaccine carriers. It is anticipated that B. subtilis will assume an even more prominent role in promoting animal health with in-depth research on its characteristics and genetic manipulation tools.

Effects of spore purity on the wet heat resistance of Clostridium perfringens, Bacillus cereus and Bacillus subtilis spores

Heat resistance of spores of Clostridium perfringens 8238 (Hobbs Serotype 2), Bacillus cereus NCTC 11143 (4810/72), and Bacillus subtilis PS533, an isogenic derivative of strain PS832 (a 168 strain) was determined in ground beef at 95 °C. Spore purification was by centrifugation and washing with sterile distilled water (dH2O), followed by sonication and then Histodenz centrifugation for B. subtilis and C. perfringens, and centrifugation and washing with sterile dH2O followed by Histodenz centrifugation for B. cereus. Bags containing inoculated beef samples were submerged in a temperature-controlled water bath and held at 95 °C for predetermined lengths of time. Surviving spore populations were enumerated by plating on mannitol egg yolk polymyxin agar (MYP) agar plates for B. cereus and B. subtilis, and on tryptose-sulfite-cycloserine agar (TSC) agar plates for C. perfringens. Survivor curves were fitted to linear, linear with tail, and Weibull models using the USDA Integrated Pathogen Modeling Program (IPMP) 2013 software. The Weibull model provided a relatively better fit to the data since the root mean square error (RMSE), mean square error (MSE), sum of squared errors (SSE), and Akaike information criterion (AIC) values were lower than the values obtained using the linear or the linear with tail models. Additionally, the Weibull model accurately predicted the observed D-values at 95 °C for the three spore-formers since the accuracy factor (Af) values ranged from 1.03 to 1.08 and the bias factor (Bf) values were either 1.00 or 1.01. Times at 95 °C to achieve a 3-log reduction decreased from 206 min for C. perfringens spores purified with water washes alone to 191 min with water washes followed by sonication and Histodenz centrifugation, from 7.9 min for B. cereus spores purified with water washes alone to 1.4 min with water washes followed by Histodenz centrifugation, and from 20.6 min for B. subtilis spores purified with water washes alone to 6.7 min for water washes followed by sonication and Histodenz centrifugation. Thermal-death-time values reported in this study will assist food processors to design thermal processes to guard against bacterial spores in cooked foods. In addition, clearly spore purity is an additional factor in spore wet heat resistance, although the cause of this effect is not clear.

The Bacterial Spore as a Mucosal Vaccine Delivery System

The development of efficient mucosal vaccines is strongly dependent on the use of appropriate vectors. Various biological systems or synthetic nanoparticles have been proposed to display and deliver antigens to mucosal surfaces. The Bacillus spore, a metabolically quiescent and extremely resistant cell, has also been proposed as a mucosal vaccine delivery system and shown able to conjugate the advantages of live and synthetic systems. Several antigens have been displayed on the spore by either recombinant or non-recombinant approaches, and antigen-specific immune responses have been observed in animals immunized by the oral or nasal route. Here we review the use of the bacterial spore as a mucosal vaccine vehicle focusing on the advantages and drawbacks of using the spore and of the recombinant vs. non-recombinant approach to display antigens on the spore surface. An overview of the immune responses induced by antigen-displaying spores so far tested in animals is presented and discussed.

Bacillus subtilis spores displaying RBD domain of SARS-CoV-2 spike protein

Bacillus subtilis spores are considered to be efficient and useful vehicles for the surface display and delivery of heterologous proteins. In this study, we prepared recombinant spores with the receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein displayed on their surface in fusion with the CotZ or CotY spore coat proteins as a possible tool for the development of an oral vaccine against the SARS-CoV-2 virus. The RBD was attached to the N-terminus or C-terminus of the coat proteins. We also directly adsorbed non-recombinantly produced RBD to the spore surface. SDS-PAGE, western blot and fluorescence microscopy were used to analyze RBD surface expression on purified spores. Results obtained from both display systems, recombinant and non-recombinant, demonstrated that RBD was present on the spore surfaces.

CotG Mediates Spore Surface Permeability in Bacillus subtilis

Proteins and glycoproteins that form the surface layers of the Bacillus spore assemble into semipermeable arrays that surround and protect the spore cytoplasm. Such layers, acting like molecular sieves, exclude large molecules but allow small nutrients (germinants) to penetrate. We report that CotG, a modular and abundant component of the Bacillus subtilis spore coat, controls spore permeability through its central region, formed by positively charged tandem repeats. These repeats act as spacers between the N and C termini of the protein, which are responsible for the interaction of CotG with at least one other coat protein. The deletion but not the replacement of the central repeats with differently charged repeats affects the spore resistance to lysozyme and the efficiency of germination-probably by reducing the coat permeability to external molecules. The presence of central repeats is a common feature of the CotG-like proteins present in most Bacillus species, and such a wide distribution of this protein family is suggestive of a relevant role for the structure and function of the Bacillus spore. IMPORTANCE Bacterial spores are quiescent cells extremely resistant to a variety of unphysiological conditions, including the presence of lytic enzymes. Such resistance is also due to the limited permeability of the spore surface, which does not allow lytic enzymes to reach the spore interior. This article proposes that the spore permeability in B. subtilis is mediated by CotG, a modular protein formed by a central region of repeats of positively charged amino acid acting as a "spacer" between the N and C termini. These, in turn, interact with other coat proteins, generating a protein layer whose permeability to external molecules is controlled by the distance between the N and C termini of CotG. This working model is most likely expandable to most sporeformers of the Bacillus genus, since they all have CotG-like proteins, not homologous to CotG of B. subtilis but similarly characterized by central repeats.

Biomimetic Assembly of Spore@ZIF-8 Microspheres for Vaccination

Vaccines have been one of the most powerful weapons to defend against infectious diseases for a long time now. Subunit vaccines are of increasing importance because of their safety and effectiveness. In this work, a Bacillus amyloliquefaciens spore@zeolitic imidazolate framework-8 (ZIF-8) vaccine platform is constructed. The ovalbumin (OVA) is encapsulated in the ZIF-8 shells as a model antigen to form a spore@OVA@ZIF-8 (SOZ) composite. The assembly of ZIF-8 improves the loading content of OVA on the spores and provides OVA with long-term protection. The SOZ composite enhances the immunization efficacy in multiple ways, such as facilitation of antigen uptake and lysosome escape, stimulation of dendritic cells to mature and secrete cytokines, boosting of antibody production and formation of an antigen depot. This platform shows several advantages including easy preparation, cost-effectiveness, long life, convenience of transportation and storage, and no need for the cold chain. These findings may have promising implications for the rational design of safe and effective spore-based composite vaccine platforms.

Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine

Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.

Spore Formers as Beneficial Microbes for Humans and Animals

Microorganisms efficiently colonize the external and internal surfaces of the animal body establishing mutually beneficial interactions and forming site- and individual-specific microbiota. The degradation of complex polysaccharides in the animal gut, the production of useful compounds, protection against pathogenic microorganisms and contribution to the development of an efficient immune system are the main beneficial effects of a balanced microbiota. A dysbiosis, an imbalanced composition of the microbiota, has been associated with a large number of diseases from gastro-intestinal or urogenital disorders to allergies, cardiovascular and autoimmune diseases and even to the onset of certain cancers. A growing body of evidence has indicated that probiotic treatments, aimed at maintaining or rebalancing the microbiota, are useful to treat/prevent those illnesses. Lactic Acid Bacteria and Bifidobacteria are the most common microbes used in probiotic preparations; however, other bacteria and yeast cells are also widely used in commercial products. Here we focus on the use of bacterial spore formers as probiotics. Spore formers have been marketed as probiotics for over 50 years and are now extensively used for the treatment of intestinal disorders and as dietary supplements in humans, as growth promoters and competitive exclusion agents in animals.

An overview and future prospects of recombinant protein production in Bacillus subtilis

Bacillus subtilis is a well-characterized Gram-positive bacterium and a valuable host for recombinant protein production because of its efficient secretion ability, high yield, and non-toxicity. Here, we comprehensively review the recent studies on recombinant protein production in B. subtilis to update and supplement other previous reviews. We have focused on several aspects, including optimization of B. subtilis strains, enhancement and regulation of expression, improvement of secretion level, surface display of proteins, and fermentation optimization. Among them, optimization of B. subtilis strains mainly involves undirected chemical/physical mutagenesis and selection and genetic manipulation; enhancement and regulation of expression comprises autonomous plasmid and integrated expression, promoter regulation and engineering, and fine-tuning gene expression based on proteases and molecular chaperones; improvement of secretion level predominantly involves secretion pathway and signal peptide screening and optimization; surface display of proteins includes surface display of proteins on spores or vegetative cells; and fermentation optimization incorporates medium optimization, process condition optimization, and feeding strategy optimization. Furthermore, we propose some novel methods and future challenges for recombinant protein production in B. subtilis.Key points• A comprehensive review on recombinant protein production in Bacillus subtilis.• Novel techniques facilitate recombinant protein expression and secretion.• Surface display of proteins has significant potential for different applications.