Continuous enhancement of iturin A production by Bacillus subtilis with a stepwise two-stage glucose feeding strategy

Process optimized for production of iturin A in biofilm reactor by Bacillus velezensis ND

In this research, to provide an optimal growth medium for the production of iturin A, the concentrations of key amino acid precursors were optimized in shake flask cultures using the response surface method. The optimized medium were applied in a biofilm reactor for batch fermentation, resulting in enhanced production of iturin A. On this basis, a step-wise pH control strategy and a combined step-wise pH and temperature control strategy were introduced to further improve the production of iturin A. Finally, the fed-batch fermentation was performed based on combined step-wise pH and temperature control. The titer and productivity of iturin A reached 7.86 ± 0.23 g/L and 65.50 ± 1.92 mg/L/h, respectively, which were 37.65 and 65.20% higher than that before process optimization.

Microbial lipopeptides: their pharmaceutical and biotechnological potential, applications, and way forward

As lead molecules, cyclic lipopeptides with antibacterial, antifungal, and antiviral properties have garnered a lot of attention in recent years. Because of their potential, cyclic lipopeptides have earned recognition as a significant class of antimicrobial compounds with applications in pharmacology and biotechnology. These lipopeptides, often with biosurfactant properties, are amphiphilic, consisting of a hydrophilic moiety, like a carboxyl group, peptide backbone, or carbohydrates, and a hydrophobic moiety, mostly a fatty acid. Besides, several lipopeptides also have cationic groups that play an important role in biological activities. Antimicrobial lipopeptides can be considered as possible substitutes for antibiotics that are conventional to address the current drug-resistant issues as pharmaceutical industries modify the parent antibiotic molecules to render them more effective against antibiotic-resistant bacteria and fungi, leading to the development of more resistant microbial strains. Bacillus species produce lipopeptides, which are secondary metabolites that are amphiphilic and are typically synthesized by non-ribosomal peptide synthetases (NRPSs). They have been identified as potential biocontrol agents as they exhibit a broad spectrum of antimicrobial activity. A further benefit of lipopeptides is that they can be produced and purified biotechnologically or biochemically in a sustainable manner using readily available, affordable, renewable sources without harming the environment. In this review, we discuss the biochemical and functional characterization of antifungal lipopeptides, as well as their various modes of action, method of production and purification (in brief), and potential applications as novel antibiotic agents.

Bacillus subtilis engineered for topical delivery of an antifungal agent

Fungal skin infections are a common condition affecting 20-25 percent of the world population. While these conditions are treatable with regular application of an antifungal medication, we sought to develop a more convenient, longer-lasting topical antifungal platform that could increase patient adherence to treatment regimens by using Bacillus subtilis, a naturally antifungal bacteria found on the skin, for drug production and delivery. In this study, we engineered B. subtilis for increased production of the antifungal lipopeptide iturin A by overexpression of the pleiotropic regulator DegQ. The engineered strain had an over 200% increase in iturin A production as detected by HPLC, accompanied by slower growth but the same terminal cell density as determined by absorbance measurements of liquid culture. In an in vitro antifungal assay, we found that despite its higher iturin A production, the engineered strain was less effective at reducing the growth of a plug of the pathogenic fungus Trichophyton mentagrophytes on an agar plate compared to the parent strain. The reduced efficacy of the engineered strain may be explained by its reduced growth rate, which highlights the need to address trade-offs between titers (e.g. measured drug production) and other figures of merit (e.g. growth rate) during metabolic engineering.

Enhanced biosurfactant production by Bacillus subtilis SPB1 using developed fed-batch fermentation: effects of glucose levels and feeding systems

Biosurfactants stand for highly useful and promising compounds. They basically serve for a variety of applications in multiple industries and aspects of human life. Therefore, it is highly required to improve their production yield especially through the development of new and more efficient fermentation processes. In this aim, batch and fed-batch were studied and compared in terms of their effective biosurfactant production by Bacillus subtilis SPB1. Experiments of fed-batch fermentations were carried out through three different glucose feeding strategies, namely the pulsed, the constant Donespeed and the exponential feeding. The comparison between different fermentation processes revealed that fed-batch process proved to be a more efficient cultivation strategy than the batch process in terms of cell biomass, biosurfactant production and productivity. Among the three different feeding strategies, the exponential feeding process achieved the highest fermentation results of final biosurfactant concentration. The latter increased more than twofolds compared to batch fermentation.

Enhanced iturin a production in a two-compartment biofilm reactor by Bacillus velezensis ND

In this study, a two-compartment biofilm reactor was designed for iturin A production. The biofilm reactor consists of a stirred-tank fermentor containing exclusively suspended cells and a packing column where the biofilm is attached. Polyester fiber with sphere shape and rough surfaces was chosen as the carrier of biofilm in packing column. Batch, fed-batch, and repeated-batch fermentation using Bacillus velezensis ND in the biofilm reactor were studied. Compared to conventional suspended cell fermentations, the productivity of iturin A in batch and fed-batch biofilm fermentation were increased by 66.7% and 63.3%, respectively. Maximum itutin A concentration of 6.8 ± 0.1 g/L and productivity of 46.9 ± 0.2 mg/L/h were obtained in fed-batch biofilm fermentation. Repeated-batch fermentation showed high stability, with almost same profile as batch fermentation. After a step-wise temperature control strategy was introduced in the biofilm reactor, productivity of iturin A was increased by 131.9% compared to suspended cell reactor. This superior performance of biofilm reactor confirms that it has great potential in industrial production of iturin A.

Characterization of Bacillus velezensis UTB96, Demonstrating Improved Lipopeptide Production Compared to the Strain B. velezensis FZB42

Bacillus strains can produce various lipopeptides, known for their antifungal properties. This makes them attractive metabolites for applications in agriculture. Therefore, identification of productive wild-type strains is essential for the development of biopesticides. Bacillus velezensis FZB42 is a well-established strain for biocontrol of plant pathogens in agriculture. Here, we characterized an alternative strain, B. velezensis UTB96, that can produce higher amounts of all three major lipopeptide families, namely surfactin, fengycin, and iturin. UTB96 produces iturin A. Furthermore, UTB96 showed superior antifungal activity towards the soybean fungal pathogen Diaporthe longicolla compared to FZB42. Moreover, the additional provision of different amino acids for lipopeptide production in UTB96 was investigated. Lysine and alanine had stimulatory effects on the production of all three lipopeptide families, while supplementation of leucine, valine and isoleucine decreased the lipopeptide bioproduction. Using a 45-litre bioreactor system for upscaling in batch culture, lipopeptide titers of about 140 mg/L surfactin, 620 mg/L iturin A, and 45 mg/L fengycin were achieved. In conclusion, it becomes clear that B. velezensis UTB96 is a promising strain for further research application in the field of agricultural biological controls of fungal diseases.

Enhanced production of iturin A by strengthening fatty acid synthesis modules in Bacillus amyloliquefaciens

Iturin A is a biosurfactant with various applications, and its low synthesis capability limits its production and application development. Fatty acids play a critical role in cellular metabolism and target product syntheses, and the relationship between fatty acid supplies and iturin A synthesis is unclear. In this study, we attempted to increase iturin A production via strengthening fatty acid synthesis pathways in Bacillus amyloliquefaciens. First, acetyl-CoA carboxylase AccAD and ACP S-malonyltransferase fabD were overexpressed via promoter replacement, and iturin A yield was increased to 1.36 g/L by 2.78-fold in the resultant strain HZ-ADF1. Then, soluble acyl-ACP thioesterase derived from Escherichia coli showed the best performance for iturin A synthesis, as compared to those derived from B. amyloliquefaciens and Corynebacterium glutamicum, the introduction of which in HZ-ADF1 further led to a 57.35% increase of iturin A yield, reaching 2.14 g/L. Finally, long-chain fatty acid-CoA ligase LcfA was overexpressed in HZ-ADFT to attain the final strain HZ-ADFTL2, and iturin A yield reached 2.96 g/L, increasing by 6.59-fold, and the contents of fatty acids were enhanced significantly in HZ-ADFTL2, as compared to the original strain HZ-12. Taken together, our results implied that strengthening fatty acid supplies was an efficient approach for iturin A production, and this research provided a promising strain for industrial production of iturin A.

Optimization of iturin A production from Bacillus subtilis ZK-H2 in submerge fermentation by response surface methodology

In this research, single-factor and response surface experiments were conducted in the fed-batch fermentation process to improve the yield of iturin A. The effect of adding various concentrations of precursor amino acids l-asparagine (Asn), l-aspartic acid (Asp), l-glutamic acid (Glu), l-glutamine (Gln), l-Serine (Ser) and l-proline (Pro) at different adding times (3 and 12 h) on iturin A production and cell growth was studied. The respective addition of amino acids (Asp 0.28 g/L; Asn 0.36 g/L; Glu 0.20, 0.28 and 0.360 g/L; Gln 0.20, 0.28 and 0.36 g/L; Pro 0.12, 0.20, 0.28 and 0.36 g/L) at 3 h was shown to improve cell growth but did not affect the yield of iturin A. Meanwhile, the individual addition of the same amino acids at 12 h improved cell growth and increased the yield of iturin A. Excellent correlation was obtained between the predicted and measured values, suggesting that the regression model was accurate and reliable; highly significant (P < 0.0001), and the determination coefficient (R²= 0.975). When 0.0752 g/L Asn; 0.1992 g/L Gln and 0.1464 g/L Pro were added at 12 h, the yield of iturin A reached 0.85 g/L, which is 32.81%-fold higher than that of the initial process. Therefore, this study obtained optimal parameters for iturin A production by the experimental method, and process validation gave high iturin A yields (0.85 g/L) during a 60 h fermentation. These findings could guide an up-scaling of the fermentation process.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s13205-020-02540-7) contains supplementary material, which is available to authorized users.

The unconventional adverse effects of fungal pretreatment on iturin A fermentation by Bacillus amyloliquefaciens CX-20

Fungal pretreatment is the most common strategy for improving the conversion of rapeseed meal (RSM) into value-added microbial products. It was demonstrated that Bacillus amyloliquefaciens CX-20 could directly use RSM as the sole source of all nutrients except the carbon source for iturin A fermentation with high productivity. However, whether fungal pretreatment has an impact on iturin A production is still unknown. In this study, the effects of fungal pretreatment and direct bio-utilization of RSM for iturin A fermentation were comparatively analysed through screening suitable fungal species, and evaluating the relationships between iturin A production and the composition of solid fermented RSM and liquid hydrolysates. Three main unconventional adverse effects were identified. (1) Solid-state fermentation by fungi resulted in a decrease of the total nitrogen for B. amyloliquefaciens CX-20 growth and metabolism, which caused nitrogen waste from RSM. (2) The released free ammonium nitrogen in liquid hydrolysates by fungal pretreatment led to the reduction of iturin A. (3) The insoluble precipitates of hydrolysates, which were mostly ignored and wasted in previous studies, were found to have beneficial effects on producing iturin A. In conclusion, our study verifies the unconventional adverse effects of fungal pretreatment on iturin A production by B. amyloliquefaciens CX-20 compared with direct bio-utilization of RSM.

Simultaneous hydrolysis with lipase and fermentation of rapeseed cake for iturin A production by Bacillus amyloliquefaciens CX-20

BACKGROUND

Rapeseed cake (RSC), as the intermediate by-product of oil extraction from the seeds of Brassica napus, can be converted into rapeseed meal (RSM) by solvent extraction to remove oil. However, compared with RSM, RSC has been rarely used as a raw material for microbial fermentation, although both RSC and RSM are mainly composed of proteins, carbohydrates and minerals. In this study, we investigated the feasibility of using untreated low-cost RSC as nitrogen source to produce the valuable cyclic lipopeptide antibiotic iturin A using Bacillus amyloliquefaciens CX-20 in submerged fermentation. Especially, the effect of oil in RSC on iturin A production and the possibility of using lipases to improve the iturin A production were analyzed in batch fermentation.

RESULTS

The maximum production of iturin A was 0.82 g/L at the optimal initial RSC and glucose concentrations of 90 and 60 g/L, respectively. When RSC was substituted with RSM as nitrogen source based on equal protein content, the final concentration of iturin A was improved to 0.95 g/L. The production of iturin A was further increased by the addition of different lipase concentrations from 0.1 to 5 U/mL into the RSC medium for simultaneous hydrolysis and fermentation. At the optimal lipase concentration of 0.5 U/mL, the maximal production of iturin A reached 1.14 g/L, which was 38.15% higher than that without any lipase supplement. Although rapeseed oil and lipase were firstly shown to have negative effects on iturin A production, and the effect would be greater if the concentration of either was increased, their respective negative effects were reduced when used together.

CONCLUSIONS

Appropriate relative concentrations of lipase and rapeseed oil were demonstrated to support optimal iturin A production. And simultaneous hydrolysis with lipase and fermentation was an effective way to produce iturin A from RSC using B. amyloliquefaciens CX-20.

Establishment of a rapeseed meal fermentation model for iturin A production by Bacillus amyloliquefaciens CX-20

Iturin A is an important broad-spectrum antifungal cyclic lipopeptide used as an ideal potential biological control agent. However, its application is limited mainly due to the producer strains' low productivity and the high production costs. Here, a potentially industrial strain Bacillus amyloliquefaciens CX-20 was proved to use low-cost rapeseed meal (RSM) as the sole source of all nutrients except the carbon source for the high productivity of iturin A. A fermentation model was first established to analyse the specific roles of different RSM components on iturin A production. Proteins and minerals in RSM were confirmed to play positive role, whereas fibre had negative effect. And the maximal concentration of iturin A was predicted to be more than 1.64 g l-1 by the established evaluation model. Moreover, submerged fermentation of B. amyloliquefaciens CX-20 demonstrated a strong ability to hydrolyse RSM and release water-soluble nutrients. This fermentation broth, a mixture of Bacillus, iturin A and RSM hydrolysate, could simultaneously combat clubroot disease and promote the growth of Brassica napus. In conclusion, this study provides a promising strategy to achieve full utilization of RSM for the production of a combination of value-added biological control agent and biofertilizer.

Influence of Phenotypic Dissociation in Bacillus subtilis Strain ET-1 on Iturin A Production

Iturin A is a very important cyclic lipopeptide produced by several B. subtilis strains and has large commercial and therapeutic application potentials but its production on industrial scale has not been realized yet. In the present study, we have observed that the strain ET-1 of Bacillus subtilis, a producer of Iturin A, can present at least three different colony morphologies, which we arbitrarily called Rough, Smooth, and Mucoid morphotypes (R-, S-, and M-form). Performing HPLC analysis, a significant difference between the amounts of Iturin A produced by the three morphotypes was found. The morphotype R-form showed the highest productivity with yields about 10 and 100 times higher than morphotypes S and M, respectively. The results show that the production of Iturin A by B. subtilis could be strongly influenced by the phenotypic heterogeneity of cells within the inoculum. Indeed, we have observed that, pasteurizing the inoculum before seeding in order to improve the homogeneity removing the phenotypes less able to synthesize the Iturin A, its yields in a bench-scale production could be significantly improved. This can represent an important control factor also at industrial scale to improve the Iturin A yields, the robustness, the replicability, and consequently the cost-effectiveness of fermentation processes.

Enhanced production of antifungal lipopeptide iturin A by Bacillus amyloliquefaciens LL3 through metabolic engineering and culture conditions optimization

Background

Iturins, which belong to antibiotic cyclic lipopeptides mainly produced by Bacillus sp., have the potential for application in biomedicine and biocontrol because of their hemolytic and antifungal properties. Bacillus amyloliquefaciens LL3, isolated previously by our lab, possesses a complete iturin A biosynthetic pathway as shown by genomic analysis. Nevertheless, iturin A could not be synthesized by strain LL3, possibly resulting from low transcription level of the itu operon.

Results

In this work, enhanced transcription of the iturin A biosynthetic genes was implemented by inserting a strong constitutive promoter C2up into upstream of the itu operon, leading to the production of iturin A with a titer of 37.35 mg l⁻¹. Liquid chromatography-mass spectrometry analyses demonstrated that the strain produced four iturin A homologs with molecular ion peaks at m/z 1044, 1058, 1072 and 1086 corresponding to [C₁₄ + 2H]²⁺, [C₁₅ + 2H]²⁺, [C₁₆ + 2H]²⁺ and [C₁₇ + 2H]²⁺. The iturin A extract exhibited strong inhibitory activity against several common plant pathogens. The yield of iturin A was improved to 99.73 mg l⁻¹ by the optimization of the fermentation conditions using a response surface methodology. Furthermore, the yield of iturin A was increased to 113.1 mg l⁻¹ by overexpression of a pleiotropic regulator DegQ.

Conclusions

To our knowledge, this is the first report on simultaneous production of four iturin A homologs (C₁₄–C₁₇) by a Bacillus strain. In addition, this study suggests that metabolic engineering in combination with culture conditions optimization may be a feasible method for enhanced production of bacterial secondary metabolites.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1121-1) contains supplementary material, which is available to authorized users.

Integrated strategy of temperature shift and mannitol feeding for enhanced production of echinocandin B by Aspergillus nidulans CCTCC M2012300

The production of echinocandin B (ECB) by Aspergillus nidulans CCTCC M2012300 was improved by integrating the temperature-shift and fed-batch control strategies. The kinetic characteristics of batch cultures were analyzed at different culture temperatures, and then a two-stage temperature control strategy was established. In the first 6 days, the temperature was maintained at 30 °C to obtain the maximal cell growth rate; subsequently, 25 °C was used to gain a high ECB formation rate. On the basis of temperature control, the ECB productivity was increased to 143.3 mg/(L day), which was a 1.3-fold improvement compared with the optimal constant-temperature cultivations. The influences of fed-batch cultures were further investigated. A maximal ECB productivity of 170.8 mg/(L day) was obtained through a three-stage mannitol pulse-feeding strategy, which was another 1.2-fold improvement than that of the batch fermentation. This is the first report of the use of a two-stage temperature control fed-batch strategy in ECB fermentation. This strategy was simple and economical to operate and may provide new guidance for the industrial-scale production of ECB.

In Silico Discovery of Novel Ligands for Antimicrobial Lipopeptides for Computer-Aided Drug Design

The increase in antibiotic-resistant strains of pathogens has created havoc worldwide. These antibiotic-resistant pathogens require potent drugs for their inhibition. Lipopeptides, which are produced as secondary metabolites by many microorganisms, have the ability to act as potent safe drugs. Lipopeptides are amphiphilic molecules containing a lipid chain bound to the peptide. They exhibit broad-spectrum activities against both bacteria and fungi. Other than their antimicrobial properties, they have displayed anti-cancer properties as well, but their mechanism of action is not understood. In silico drug design uses computer simulation to discover and develop new drugs. This technique reduces the need of expensive and tedious lab work and clinical trials, but this method becomes a challenge due to complex structures of lipopeptides. Specific agonists (ligands) must be identified to initiate a physiological response when combined with a receptor (lipopeptide). In silico drug design and homology modeling talks about the interaction between ligands and the binding sites. This review summarizes the mechanism of selected lipopeptides, their respective ligands, and in silico drug design.

Kinetic analysis on precursors for iturin A production from Bacillus amyloliquefaciens BPD1

In this study, the precursor effect for iturin A production was quantitatively analyzed. A strain identified as Bacillus amyloliquefaciens BPD1 (Ba-BPD1) was selected due to its ability to produce iturin A. The enhancement of iturin A production in a submerged culture was tested using various additives, including palmitic acid, oils, and complex amino acids. Among these, complex amino acids triggered the highest yield at 559 mg/L. The respective amino acids that contribute to the structure of iturin A were used as precursors. In fact, it was found that the addition of l-proline, l-glutamine, l-asparagine and l-serine could improve iturin A yield in the defined medium. However, during the kinetic analysis, all the amino acids exhibited a lower saturation level than l-serine, which exhibited a high saturation level at 1.2% resulting in an iturin A yield of 914 mg/L. In contrast, a negative effect was observed following the addition of l-tyrosine. To analyze the kinetic behavior of l-serine, three kinetic models were adopted: the kinetic order equation, the Langmuir kinetic equation, and a modified logistic equation. The regression results showed that the modified logistic model was the best fit for the kinetic behavior of l-serine as the major precursor, which could be further referred to the biosynthesis pathway of iturin A. Among the proposed processes for iturin A production, this study achieved the highest iturin A levels as a result of the addition of precursors.