Increasing fengycin production by strengthening the fatty acid synthesis pathway and optimizing fermentation conditions

An Integrated Pipeline and Overexpression of a Novel Efflux Transporter, YoeA, Significantly Increases Plipastatin Production in Bacillus subtilis

Plipastatin, an antimicrobial peptide produced by Bacillus subtilis, exhibits remarkable antimicrobial activity against a diverse range of pathogenic bacteria and fungi. However, the practical application of plipastatin has been significantly hampered by its low yield in wild Bacillus species. Here, the native promoters of both the plipastatin operon and the sfp gene in the mono-producing strain M-24 were replaced by the constitutive promoter P43, resulting in plipastatin titers being increased by 27% (607 mg/mL) and 50% (717 mg/mL), respectively. Overexpression of long chain fatty acid coenzyme A ligase (LCFA) increased the yield of plipastatin by 105% (980 mg/mL). A new efflux transporter, YoeA, was identified as a MATE (multidrug and toxic compound extrusion) family member, overexpression of yoeA enhanced plipastatin production to 1233 mg/mL, an increase of 157%, and knockout of yoeA decreased plipastatin production by 70%; in contrast, overexpression or knockout of yoeA in mono-producing surfactin and iturin engineered strains only slightly affected their production, demonstrating that YoeA acts as the major exporter for plipastatin. Co-overexpression of lcfA and yoeA improved plipastatin production to 1890 mg/mL, which was further elevated to 2060 mg/mL after abrB gene deletion. Lastly, the use of optimized culture medium achieved 2514 mg/mL plipastatin production, which was 5.26-fold higher than that of the initial strain. These results suggest that multiple strain engineering is an effective strategy for increasing lipopeptide production, and identification of the novel transport efflux protein YoeA provides new insights into the regulation and industrial application of plipastatin.

Strategies for improving fengycin production: a review

Fengycin is an important member of the lipopeptide family with a wide range of applications in the agricultural, food, medical and cosmetic industries. However, its commercial application is severely hindered by low productivity and high cost. Therefore, numerous studies have been devoted to improving the production of fengycin. We summarize these studies in this review with the aim of providing a reference and guidance for future researchers. This review begins with an overview of the synthesis mechanism of fengycin via the non-ribosomal peptide synthetases (NRPS), and then delves into the strategies for improving the fengycin production in recent years. These strategies mainly include fermentation optimization and metabolic engineering, and the metabolic engineering encompasses enhancement of precursor supply, application of regulatory factors, promoter engineering, and application of genome-engineering (genome shuffling and genome-scale metabolic network model). Finally, we conclude this review with a prospect of fengycin production.

Production of Lipopeptides from Bacillus velezensis BVQ121 and Their Application in Chitosan Antibacterial Coating

The extracellular substance of Bacillus has antibacterial effects inhibiting multiple foodborne pathogens and plays important roles in food production. This study found one Bacillus velezensis BVQ121 strain producing antibacterial lipopeptides (BVAL). After optimization of the fermentation conditions, the BVAL yield was the highest at 1.316 ± 0.03 g/L in reality with the initial pH 6.0, temperature 31 °C, and shaker speed 238 rpm when the optimal nitrogen and carbon sources were used in Landy medium for fermentation. The antibacterial components were identified as iturin, surfactin, and fengycin by HPLC and MALDI-TOF-MS. The MIC was at 2 mg/mL and MBC was at 5 mg/mL. The 6% weight ratio of nanocellulose dosage in chitosan solution could improve the tensile length and strength of the film, and the antibacterial performance was enhanced by the addition of BVAL. The addition of BVAL had no effect on the color and ductility of the film and improved its antibacterial effect. The shelf life of pigeon eggs can be extended by more than 10 days to resist bacterial infections after coating with the chitosan-nanocellulose-BVAL film solution.

Biocontrol manufacturing and agricultural applications of Bacillus velezensis

Many microorganisms have been reported as bioagents for producing ecofriendly, cost-effective, and safe products. Some Bacillus species of bacteria can be used in agricultural applications. Bacillus velezensis in particular has shown promising results for controlling destructive phytopathogens and in biofungicide manufacturing. Some B. velezensis strains can promote plant growth and display antibiotic activities against plant pathogen agents. In this review, we focus on the often-overlooked potential properties of B. velezensis as a bioagent for applications that will extend beyond the traditional agricultural uses. We delve into its versatility and future prospects, the challenges such uses may encounter, and some drawbacks associated with B. velezensis-based products.

Improvement of lipopeptide production in Bacillus subtilis HNDF2-3 by overexpression of the sfp and comA genes

Bacillus subtilis HNDF2-3 can produce a variety of lipopeptide antibiotics with lower production. To improve its lipopeptide production, three genetically engineered strains were constructed. The results of real-time PCR showed that the highest transcriptional levels of the sfp gene in F2-3sfp, F2-3comA and F2-3sfp-comA were 29.01, 6.65 and 17.50 times of the original strain, respectively, while the highest transcriptional levels of the comA gene in F2-3comA and F2-3sfp-comA were 10.44 and 4.13 times of the original strain, respectively. The results of ELISA showed that the malonyl-CoA transacylase activity of F2-3comA was the highest, reaching 18.53 IU/L at 24 h, the data was 32.74% higher than that of the original strain. The highest total lipopeptide production of F2-3sfp, F2-3comA and F2-3sfp-comA induced by IPTG at optimal concentration were 33.51, 46.05 and 38.96% higher than that of the original strain, respectively. The results of HPLC showed that iturin A production of F2-3sfp-comA was the highest, which was 63.16% higher than that of the original strain. This study laid the foundation for further construction of genetically engineered strains with high lipopeptide production.

An Engineered Microbial Consortium Provides Precursors for Fengycin Production by Bacillus subtilis

Fengycin has great potential for applications in biological control because of its biosafety and degradability. In this study, the addition of exogenous precursors increased fengycin production by Bacillus subtilis. Corynebacterium glutamicum was engineered to produce high levels of precursors (Thr, Pro, Val, and Ile) to promote the biosynthesis of fengycin. Furthermore, recombinant C. glutamicum and Yarrowia lipolytica providing amino acid and fatty acid precursors were co-cultured to improve fengycin production by B. subtilis in a three-strain artificial consortium, in which fengycin production was 2100 mg·L-1. In addition, fengycin production by the consortium in a 5 L bioreactor reached 3290 mg·L-1. Fengycin had a significant antifungal effect on Rhizoctonia solani, which illustrates its potential as a food preservative. Taken together, this work provides a new strategy for improving fengycin production by a microbial consortium and metabolic engineering.

Construction of Bacillus subtilis for efficient production of fengycin from xylose through CRISPR-Cas9

Fengycin is a multifunctional peptide antibiotic produced mainly by Bacillus species and the purpose of this research was to construct a Bacillus subtilis strain that can produce fengycin with the xylose as the substrate with CRSIPR-Cas9. Hence, at the beginning of this study, functional sfp and degQ were expressed in B. subtilis 168 strain to give the strain the ability to produce the fengycin with the titer of 71.21 mg/L. Subsequently, the native promoter PppsA of the cluster responsible for the fengycin synthesis was replaced by the Pveg promoter, resulting in a further 5.22-fold increase in fengycin titer. To confer xylose utilization capacity to B. subtilis, deletion of araR and constitutive overexpression of araE were performed, and the xylose consumption rate of the engineered strain BSUY06 reached 0.29 g/L/h, which is about 6.25-fold higher than that of the parent strain BSUY04-1. In the final phase of this study, the fermentation characteristics were observed and the initial xylose concentration was optimized. In this study, 40 g/L xylose was proved to be the most suitable initial concentration for growth and fengycin fermentation, which leading to a fengycin titer of 430.86 mg/L. This study demonstrated that lignocellulose, the clean and sustainable substrate with xylose as the second largest sugar, is a potential substrate for the production of fengycin.

Genomic insights into antimicrobial potential and optimization of fermentation conditions of pig-derived Bacillus subtilis BS21

Bacillus spp. have been widely used as probiotic supplements in animal feed as alternatives to antibiotics. In the present study, we screened a Bacillus subtilis strain named BS21 from pig feces. Antimicrobial activities, whole genome mining and UHPLC-MS/MS analysis were used to explore its antimicrobial mechanism. Strain BS21 showed Significant growth inhibition against a variety of animal pathogens, including Escherichia coli, Salmonella enterica Pullorum, Salmonella enterica Typhimurium, Citrobacter rodentium, Shigella flexneri and Staphylococcus aureus. Seven gene clusters involved in antimicrobial biosynthesis of secondary metabolites were encoded by strain BS21 genome, including four non-ribosomal peptides (bacillibactin, fengycin, surfactin and zwittermicin A), one ribosomal peptide (subtilosin A), one dipeptide (bacilysin) and one polyketide (bacillaene). Among them, production of surfactin, fengycin, bacillibactin, bacilysin and bacillaene was detected in the supernatant of B. subtilis strain BS21. To develop the potential application of BS21 in animal production, medium components and fermentation parameters optimization was carried out using response surface methodology (RSM). Production of antimicrobial secondary metabolites of strain BS21 was increased by 43.4%, and the best medium formula after optimization was corn flour 2%, soybean meal 1.7% and NaCl 0.5% with optimum culture parameters of initial pH 7.0, temperature 30°C, rotating speed at 220 rpm for 26 h. Our results suggested that strain BS21 has the potential for large-scale production and application as a potential source of probiotics and alternative to antibiotics for animal production.

Antimicrobial peptides from Bacillus spp. and strategies to enhance their yield

Antibiotic resistance is a growing concern that is affecting public health globally. The search for alternative antimicrobial agents has become increasingly important. Antimicrobial peptides (AMPs) produced by Bacillus spp. have emerged as a promising alternative to antibiotics, due to their broad-spectrum antimicrobial activity against resistant pathogens. In this review, we provide an overview of Bacillus-derived AMPs, including their classification into ribosomal (bacteriocins) and non-ribosomal peptides (lipopeptides and polyketides). Additionally, we delve into the molecular mechanisms of AMP production and describe the key biosynthetic gene clusters involved. Despite their potential, the low yield of AMPs produced under normal laboratory conditions remains a challenge to large-scale production. This review thus concludes with a comprehensive summary of recent studies aimed at enhancing the productivity of Bacillus-derived AMPs. In addition to medium optimization and genetic manipulation, various molecular strategies have been explored to increase the production of recombinant antimicrobial peptides (AMPs). These include the selection of appropriate expression systems, the engineering of expression promoters, and metabolic engineering. Bacillus-derived AMPs offer great potential as alternative antimicrobial agents, and this review provides valuable insights on the strategies to enhance their production yield, which may have significant implications for combating antibiotic resistance. KEY POINTS: • Bacillus-derived AMP is a potential alternative therapy for resistant pathogens • Bacillus produces two main classes of AMPs: ribosomal and non-ribosomal peptides • AMP yield can be enhanced using culture optimization and molecular approaches.

The viability of spores is the key factor for microbial induced calcium carbonate precipitation

While previous studies mainly focused on the total number of spores as an index to predict the calcium precipitation activity (CPA) of bacterial strains, the effect of viability of spores on microbial-induced calcium precipitation (MICP) has remained highly ignored. Therefore, for the first time, we have attempted to optimize the sporulation process in terms of viable spore production and, most importantly, aimed to build a correlation between viable spores and CPA. The results have shown that for the sporulation of Bacillus sp. H4, starch and peptone are the optimal carbon and nitrogen sources, respectively. One gram per liter of sodium chloride promotes CPA and production of viable spores, whereas an increase of sodium chloride concentration beyond 8 g L^-1 significantly reduces CPA without reducing the quantity of viable spores. Exogenous conditions such as seed age, inoculation quantity, and liquid volume only pose slight influence on the sporulation and CPA. Conclusively, the spores produced under optimized conditions are more morphologically uniform and display a 20% increase in CPA compared to pre-optimized spores. Furthermore, by combining the results of heatmap analysis, it can be concluded that not only the quantity, but also the quality of viable spores is important for bacterial strain to develop high CPA and effective MICP process. This study sheds light on the breadth of biomineralization activity based on viable spores and is an imperative step toward the intelligible design of MICP-based engineering solutions. KEY POINTS: • Viability of spores is a key controlling factor in calcium precipitation activity (CPA). • Spores produced under optimized conditions display a 20% increase in CPA. • Quality of viable spores is imperative for bacterial strains to develop high CPA.

LC-MS and Transcriptome Analysis of Lipopeptide Biosynthesis by Bacillus velezensis CMT-6 Responding to Dissolved Oxygen

Dissolved oxygen (DO) is an key factor for lipopeptide fermentation. To better understand the link between oxygen supply and lipopeptide productivity in Bacillus velezensis CMT-6, the mechanism of DO on the synthesis of antimicrobial lipopeptides by Bacillus velezensis CMT-6 was examined. The production of surfactin and iturin of CMT-6 was detected by liquid chromatography–mass spectrometer (LC-MS) under different DO conditions and transcriptome analysis was performed. At 100 and 200 rpm, the lipopeptides productions were 2753.62 mg/L and 3452.90 mg/L, respectively. There was no significant change in the yield of iturin but that of surfactin increased by 64.14%. Transcriptome analysis revealed that the enriched differential genes were concentrated in the GO term of oxidation–reduction process. The marked enrichment of the lipopeptides synthesis pathway, including microbial metabolism in diverse environments and carbon metabolism in the two-component system, were observed. More importantly, the expression levels of the four surfactin synthetase genes increased at higher DO, however, the iturin synthetase gene expression did not. Furthermore, modular surfactin synthetase was overexpressed (between 9- and 49-fold) at 200 rpm but not at 100 rpm, which is suggestive of efficient surfactin assembly resulting in surfactin overproduction. This study provides a theoretical basis for constructing engineering strains with high lipopeptide production to adapt to different DO.

Assessment of Lipopeptide Mixtures Produced by Bacillus subtilis as Biocontrol Products against Apple Scab (Venturia inaequalis)

Apple scab is an important disease conventionally controlled by chemical fungicides, which should be replaced by more environmentally friendly alternatives. One of these alternatives could be the use of lipopeptides produced by Bacillus subtilis. The objective of this work is to study the action of the three families of lipopeptides and different mixtures of them in vitro and in vivo against Venturia inaequalis. Firstly, the antifungal activity of mycosubtilin/surfactin and fengycin/surfactin mixtures was determined in vitro by measuring the median inhibitory concentration. Then, the best lipopeptide mixture ratio was produced using Design of Experiment (DoE) to optimize the composition of the culture medium. Finally, the lipopeptides mixtures efficiency against V. inaequalis was assessed in orchards as well as the evaluation of the persistence of lipopeptides on apple. In vitro tests show that the use of fengycin or mycosubtilin alone is as effective as a mixture, with the 50–50% fengycin/surfactin mixture being the most effective. Optimization of culture medium for the production of fengycin/surfactin mixture shows that the best composition is glycerol coupled with glutamic acid. Finally, lipopeptides showed in vivo antifungal efficiency against V. inaequalis regardless of the mixture used with a 70% reduction in the incidence of scab for both mixtures (fengycin/surfactin or mycosubtilin/surfactin). The reproducibility of the results over the two trial campaigns was significantly better with the mycosubtilin/surfactin mixture. The use of B. subtilis lipopeptides to control this disease is very promising.

Systemically engineering Bacillus amyloliquefaciens for increasing its antifungal activity and green antifungal lipopeptides production

The biosynthesis of antifungal lipopeptides iturin and fengycin has attracted broad interest; however, there is a bottleneck in its low yield in wild strains. Because the key metabolic mechanisms in the lipopeptides synthesis pathway remain unclear, genetic engineering approaches are all ending up with a single or a few gene modifications. The aim of this study is to develop a systematic engineering approach to improve the antifungal activity and biosynthesis of iturin and fengycin in Bacillus amyloliquefaciens. First, blocking the carbon overflow metabolic pathway to increase precursor supply of the branched-chain amino acids by knockout of bdh, disrupting sporulation to extend the stage for producing antifungal lipopeptides by deletion of kinA, blocking of siderophore synthesis to enhance the availability of amino acids and fatty acids by deletion of dhbF, and increasing Spo0A∼P by deletion of rapA, could improve the antifungal activity by 24%, 10%, 13% and 18%, respectively. Second, the double knockout strain ΔbdhΔkinA, triple knockout strain ΔbdhΔkinAΔdhbF and quadruple knockout strain ΔkinAΔbdhΔdhbFΔrapA could improve the antifungal activity by 38%, 44% and 53%, respectively. Finally, overexpression of sfp in ΔkinAΔbdhΔdhbFΔrapA further increased the antifungal activity by 65%. After purifying iturin and fengycin as standards for quantitative analysis of lipopeptides, we found the iturin titer was 17.0 mg/L in the final engineered strain, which was 3.2-fold of the original strain. After fermentation optimization, the titer of iturin and fengycin reached 31.1 mg/L and 175.3 mg/L in flask, and 123.5 mg/L and 1200.8 mg/L in bioreactor. Compared to the original strain, the iturin and fengycin titer in bioreactor increased by 22.8-fold and 15.9-fold in the final engineered strain, respectively. This study may pave the way for the commercial production of green antifungal lipopeptides, and is also favorable for understanding the regulatory and biosynthetic mechanism of iturin and fengycin.

Transcriptome Analysis of Bacillus amyloliquefaciens Reveals Fructose Addition Effects on Fengycin Synthesis

Fengycin is a lipopeptide produced by Bacillus that has a strong inhibitory effect on filamentous fungi; however, its use is restricted due to poor production and low yield. Previous studies have shown that fengycin biosynthesis in B. amyloliquefaciens was found to be significantly increased after fructose addition. This study investigated the effect of fructose on fengycin production and its regulation mechanism in B. amyloliquefaciens by transcriptome sequencing. According to the RNA sequencing data, 458 genes were upregulated and 879 genes were downregulated. Transcriptome analysis results showed that fructose changed the transcription of amino acid synthesis, fatty acid metabolism, and energy metabolism; alterations in these metabolic pathways contribute to the synthesis of fengycin. In an MLF medium (modified Landy medium with fructose), the expression level of the fengycin operon was two-times higher than in an ML medium (modified Landy medium). After fructose was added to B. amyloliquefaciens, the fengycin-synthesis-associated genes were activated in the process of fengycin synthesis.

Production of fengycin from D-xylose through the expression and metabolic regulation of the Dahms pathway

D-Xylose is a key component of lignocellulosic biomass and the second-most abundant carbohydrate on the planet. As one of the most powerful cyclo-lipopeptide antibiotics, fengycin displays strong wide-spectrum antifungal and antiviral, as well as potential anti-cancer activity. Pyruvate is a key metabolite linking the biosynthesis of fatty acids and amino acids, the precursors for fengycin. In this study, the genes encoding the Dahms xylose-utilization pathway were integrated into the amyE site of Bacillus subtilis 168, and based on the metabolic characteristics of the Dahms pathway, the acetate kinase (ackA) and lactate dehydrogenase (ldh) genes were knocked out. Then, the metabolic control module II was designed to convert glycolaldehyde, another intermediate of the Dahms pathway, in addition to pathways for the conversion of acetaldehyde into malic acid and oxaloacetic acid, resulting in strain BSU03. In the presence of module II, the content of acetic and lactic acid decreased significantly, and the xylose uptake efficiency increased. At the same time, the yield of fengycin increased by 87% compared to the original strain. Additionally, the underlying factors for the increase of fengycin titer were revealed through metabonomic analysis. This study therefore demonstrates that this regulation approach can not only optimize the intracellular fluxes for the Dahms pathway, but is also conducive to the synthesis of secondary metabolites similar to fengycin. KEY POINTS: • The expression and effect of the Dahms pathway on the synthesis of fengycin in Bacillus subtilis 168. • The expression of regulatory module II can promote the metabolic rate of the Dahms pathway and increase the synthesis of the fengycin.