Enhance nisin yield via improving acid-tolerant capability of Lactococcus lactis F44

New advances in biological preservation technology for aquatic products

Aquatic products, characterized by their high moisture content, abundant nutrients, and neutral pH, create an optimal environment for the rapid proliferation of spoilage organisms, lipid oxidation, and autolytic degradation. These factors collectively expedite the spoilage and deterioration of aquatic products during storage and transportation within the supply chain. To maintain the quality and extend the shelf-life of aquatic products, appropriate preservation methods must be implemented. The growing consumer preference for bio-preservatives, is primarily driven by consumer demands for naturalness and concerns about environmental sustainability. The present review discusses commonly employed bio-preservatives derived from plants, animals, and microorganisms and their utilization in the preservation of aquatic products. Moreover, the preservation mechanisms of bio-preservatives, including antioxidant activity, inhibition of spoilage bacteria and enzyme activity, and the formation of protective films are reviewed. Integration of bio-preservation techniques with other methods, such as nanotechnology, ozone technology, and coating technology that enhance the fresh-keeping effect are discussed. Importantly, the principal issues in the application of bio-preservation technology for aquatic products and their countermeasures are presented. Further studies and the identification of new bio-preservatives that preserve the safety and quality of aquatic products should continue.

Current challenges and development strategies of bacteriocins produced by lactic acid bacteria applied in the food industry

Given the great importance of natural biopreservatives in the modern food industry, lactic acid bacteria (LAB)-producing bacteriocins have gained considerable attention due to their antimicrobial activity against foodborne pathogens and spoilage bacteria. Although numerous LAB-producing bacteriocins have demonstrated efficiency in preserving food quality in various applications, only a limited number of these compounds have been commercially approved to date. The currently unclear gastrointestinal metabolism of bacteriocins may pose safety risks, as well as cytotoxicity and immunogenicity, which need to be seriously considered before their application. A more noteworthy concern lies in whether bacteriocins induce an imbalance in the gut microbiota, thereby leading to alterations in the abundance of health-associated microorganisms and their metabolites in the gastrointestinal tract. Accordingly, this review presents unique insights into the challenges arising from metabolic interactions between LAB-producing bacteriocins and the gastrointestinal tract. Besides, the application of bacteriocins in the food industry faces challenges arising from the low production yield, weak stability, and insufficient antimicrobial activity. The corresponding development strategies are proposed for conducting the systematic and comprehensive evaluation of the potential safety risks of bacteriocins and their metabolites. The strategies also focus on the rational design to increase the activity and stability, the fermentation control to enhance the production yield, and the hurdle and embedding technology to improve the application effects. It definitively discloses the perspective of bacteriocins to become natural, sustainable, safe, and eco-friendly biological preservatives for the advancement of the food industry.

Production of bacterial cellulose (BC)/nisin composite with enhanced antibacterial and mechanical properties through co-cultivation of Komagataeibacter xylinum and Lactococcus lactis subsp. lactis

By employing co-cultivation technique on Komagataeibacter xylinum and Lactococcus lactis subsp. lactis, bacterial cellulose (BC)/nisin films with improved antibacterial activity and mechanical properties were successfully produced. The findings demonstrated that increased nisin production is associated with an upregulation of gene expression. Furthermore, results from Scanning electronic microscopy (SEM), Fourier transform infrared (FTIR), X-ray diffraction (XRD), and Thermogravimetric analysis (TG) confirmed the integration of nisin within BC. While being biocompatible with human cells, the BC/nisin composites exhibited antimicrobial activity. Moreover, mechanical property analyses showed a noticeable improvement in Young's modulus, tensile strength, and elongation at break by 161, 271, and 195 %, respectively. Additionally, the nisin content in fermentation broth was improved by 170 % after co-culture, accompanied by an 8 % increase in pH as well as 10 % decrease in lactate concentration. Real-time reverse transcription PCR analysis revealed an upregulation of 11 nisin-related genes after co-cultivation, with the highest increase in nisA (5.76-fold). To our knowledge, this is the first study which demonstrates that an increase in secondary metabolites after co-culturing is modulated by gene expression. This research offers a cost-effective approach for BC composite production and presents a technique to enhance metabolite concentration through the regulation of relevant genes.

Bifidobacterium longum subsp. infantis as widespread bacteriocin gene clusters carrier stands out among the Bifidobacterium

Bifidobacterium is the dominant genus, particularly in the intestinal tract niche of healthy breast-fed infants, and many of these strains have been proven to elicit positive effects on infant development. In addition to its effective antimicrobial activity against detrimental microorganisms, it helps to improve the intestinal microbiota balance. The isolation and identification of bacteriocins from Bifidobacterium have been limited since the mid-1980s, leading to an underestimation of its ability for bacteriocin production. Here, we employed a silicon-based search strategy to mine 354 putative bacteriocin gene clusters (BGCs), most of which have never been reported, from the genomes of 759 Bifidobacterium strains distributed across 9 species. Consistent with previous reports, most Bifidobacterium strains did not carry or carry only a single BGC; however, Bifidobacterium longum subsp. infantis, in contrast to other Bifidobacterium species, carried numerous BGCs, including lanthipeptides, lasso peptides, thiopeptides, and class IId bacteriocins. The antimicrobial activity of the crude bacteriocins and transcription analysis confirmed its potential for bacteriocin biosynthesis. Additionally, we investigated the association of bacteriocins with the phylogenetic positions of their homologs from other genera and niches. In conclusion, this study re-examines a few Bifidobacterium species traditionally regarded as a poor source of bacteriocins. These bacteriocin genes impart a competitive advantage to Bifidobacterium in colonizing the infant intestinal tract. IMPORTANCE Development of the human gut microbiota commences from birth, with bifidobacteria being among the first colonizers of the newborn intestinal tract and dominating it for a considerable period. To date, the genetic basis for the successful adaptation of bifidobacteria to this particular niche remains unclear since studies have mainly focused on glycoside hydrolase and adhesion-related genes. Bacteriocins are competitive factors that help producers maintain colonization advantages without destroying the niche balance; however, they have rarely been reported in Bifidobacterium. The advancement in sequencing methods and bacteriocin databases enables the use of a silicon-based search strategy for the comprehensive and rapid re-evaluation of the bacteriocin distribution of Bifidobacterium. Our study revealed that B. infantis carries abundant bacteriocin biosynthetic gene clusters for the first time, presenting new evidence regarding the competitive interactions of Bifidobacterium in the infant intestinal tract.

Acid-tolerant bacteria and prospects in industrial and environmental applications

Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F₁-F₀-ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents. KEY POINTS: • Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail • The activity of decarboxylase systems for acid tolerance depends on pH • Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria.

Bioengineering of a Lactococcus lactis subsp. lactis strain enhances nisin production and bioactivity

Lactococcus lactis subsp. lactis is a food bacterium that has been utilized for decades in food fermentation and the development of high-value industrial goods. Among these, nisin, which is produced by several strains of L. lactis subsp. lactis, plays a crucial role as a food bio-preservative. The gene expression for nisin synthesis was evaluated using qPCR analysis. Additionally, a series of re-transformations of the strain introducing multiple copies of the nisA and nisRK genes related to nisin production were developed. The simultaneous expression of nisA and nisZ genes was used to potentiate the effective inhibition of foodborne pathogens. Furthermore, qPCR analysis indicated that the nisA and nisRK genes were expressed at low levels in wild-type L. lactis subsp. lactis. After several re-transformations of the strain with the nisA and nisRK genes, a high expression of these genes was obtained, contributing to improved nisin production. Also, co-expression of the nisA and nisZ genes resulted in extremely effective antibacterial action. Hence, this study would provide an approach to enhancing nisin production during industrial processes and antimicrobial activity.

Response mechanisms to acid stress of acid-resistant bacteria and biotechnological applications in the food industry

Acid-resistant bacteria are more and more widely used in industrial production due to their unique acid-resistant properties. In order to survive in various acidic environments, acid-resistant bacteria have developed diverse protective mechanisms such as sensing acid stress and signal transduction, maintaining intracellular pH homeostasis by controlling the flow of H⁺, protecting and repairing biological macromolecules, metabolic modification, and cross-protection. Acid-resistant bacteria have broad biotechnological application prospects in the food field. The production of fermented foods with high acidity and acidophilic enzymes are the main applications of this kind of bacteria in the food industry. Their acid resistance modules can also be used to construct acid-resistant recombinant engineering strains for special purposes. However, they can also cause negative effects on foods, such as spoilage and toxicity. Herein, the aim of this paper is to summarize the research progress of molecular mechanisms against acid stress of acid-resistant bacteria. Moreover, their effects on the food industry were also discussed. It is useful to lay a foundation for broadening our understanding of the physiological metabolism of acid-resistant bacteria and better serving the food industry.

CRISPR/Cas tools for enhancing the biopreservation ability of lactic acid bacteria in aquatic products

Lactic acid bacteria (LAB) plays a crucial role in aquatic products biopreservation as it can inhibit many bacteria, in particular the specific spoilage organisms (SSOs) of aquatic products, by competing for nutrients or producing one or more metabolites which have antimicrobial activity, such as bacteriocins. Lactobacillus spp. and Lactococcus spp. are the most commonly used Lactic acid bacterias in aquatic products preservation. The improvement of gene editing tools is particularly important for developing new lactic acid bacteria strains with superior properties for aquatic products biopreservation. This review summarized the research progress of the most widely used CRISPR/Cas-based genome editing tools in Lactobacillus spp. and Lactococcus spp. The genome editing tools based on homologous recombination and base editor were described. Then, the research status of CRISPRi in transcriptional regulation was reviewed briefly. This review may provide a reference for the application of CRISPR/Cas-based genome editing tools to other lactic acid bacteria species.

Breeding of a High-Nisin-Yielding Bacterial Strain and Multiomics Analysis

Nisin is a green, safe and natural food preservative. With the expansion of nisin application, the demand for nisin has gradually increased, which equates to increased requirements for nisin production. In this study, Lactococcus lactis subsp. lactis lxl was used as the original strain, and the compound mutation method was applied to induce mutations. A high-yielding and genetically stable strain (Lactobacillus lactis A32) was identified, with the nisin titre raised by 332.2% up to 5089.29 IU/mL. Genome and transcriptome sequencing was used to analyse A32 and compare it with the original lxl strain. The comparative genomics results show that 107 genes in the A32 genome had mutations and most base mutations were not located in the four well-researched nisin-related operons, nisABTCIPRK, nisI, nisRK and nisFEG: 39 single-nucleotide polymorphisms (SNPs), 34 insertion mutations and 34 deletion mutations. The transcription results show that the expression of 92 genes changed significantly, with 27 of these differentially expressed genes upregulated, while 65 were downregulated. Our findings suggest that the output of nisin increased in L. lactis strain A32, which was accompanied by changes in the DNA replication-related gene dnaG, the ABC-ATPase transport-related genes patM and tcyC, the cysteine thiometabolism-related gene cysS, and the purine metabolism-related gene purL. Our study provides new insights into the traditional genetic mechanisms involved nisin production in L. lactis, which could provide clues for a more efficient metabolic engineering process.

Application of Biotechnology in Specific Spoilage Organisms of Aquatic Products

Aquatic products are delicious and have high nutritive value, however, they are highly perishable during storage due to the growth and metabolism of microorganisms. The spoilage process of aquatic products was demonstrated to be highly related to the composition of microorganisms, in which the specific spoilage organisms (SSOs) are the main factors. In this article, the spoilage indicators of SSOs were systematically described, which could make a comprehensive evaluation of the quality of aquatic products. Quorum sensing (QS) regulates the growth, metabolism and characteristics of SSOs, the common signaling molecules and the QS system in the major SSOs of aquatic products were discussed. Moreover, we compared various technologies for the analysis of SSOs in aquatic products. Besides, quality control techniques based on microbiota regulating of aquatic products, including physical, chemical and biological preservation strategies, were also compared. In conclusion, novel preservation technologies and hurdle techniques are expected to achieve comprehensive inhibition of SSOs.

A novel co-cultivation strategy to generate low-crystallinity bacterial cellulose and increase nisin yields

In this study, a co-culturing Enterobacter sp. and Lactococcus lactis strategy was developed to alter bacterial cellulose (BC) properties and increase nisin yields. We generated high nisin yields (6260 IU/mL) by altering inoculum ratios and inoculation times in a novel co-culture system. Critically, these were 85% higher than L. lactis monocultures. By monitoring fermentation broth pH and lactic acid yields, the pH was higher and lactic acid yields lower during co-culture conditions when compared with L. lactis monocultures, suggesting that co-culturing was more suitable for L. lactis nisin production. We also determined BC film yields and properties (BC, BC-N, and BC-N after nisin release). BC yields produced by co-culturing were not very different from Enterobacter sp. monocultures, but crystallinity was significantly altered. Collectively, our co-culture system adequately and economically modified BC fibers by interfering with self-assembly and crystallization processes during BC synthesis, with significantly improved nisin yields.

Systems-level analysis of the global regulatory mechanism of CodY in Lactococcus lactis metabolism and nisin immunity modulation

Bacteria adapt to the constantly changing environment by regulating their metabolism. The global transcriptional regulator CodY is known to regulate metabolism in low G+C Gram-positive bacteria. Systems-level identification of its direct targets by proteome and ChIP-seq assays was rarely reported. Here, we identified CodY serves as an activator or a repressor of hundreds of genes involved in nitrogen metabolism, carbohydrate metabolism, and transcription through iTRAQ proteome and ChIP-seq. Combined with EMSA experiment, apart from the genes associated with amino acid biosynthesis (ilvD, leuA, optS, ybbD, dtpT, and pepN), genes involved in cell wall synthesis (murD and ftsW) and nisin immunity (nisI) were identified to be regulated by CodY. Moreover, it was demonstrated that CodY activated the transcription of nisI and contributed to the nisin immunity by nisin resistance assay. Intriguingly, CodY showed a self-regulation through binding to the motif 'AAAGGTGTGACAACT'in the CDS region of codY verified by DNase I footprinting assay and MEME analysis. In addition, a novel conserved AT-rich motif 'AATWTTCTGACAATT' was obtained in L. lactis F44. This study provides new insights into the comprehensive CodY regulation in L. lactis by controlling metabolism, nisin immunity and self-expression. Importance Lactococcus lactis, a widely used lactic acid bacteria (LAB) in the food fermentation, has been the model strain in genetic engineering, and its application has extended from food to microbial cell factory. CodY is a global regulator in low G+C Gram-positive bacteria. Its function and direct target genes in genome-level were rarely known in L. lactis. In this study, we described the comprehensive regulation mechanism of CodY. It widely modulated the metabolism of nitrogen and carbohydrate, cell wall synthesis and nisin immunity in L. lactis F44, and its expression level was regulated by feedback control.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Engineering Lactococcus lactis as a multi-stress tolerant biosynthetic chassis by deleting the prophage-related fragment

Background

In bioengineering, growth of microorganisms is limited because of environmental and industrial stresses during fermentation. This study aimed to construct a nisin-producing chassis Lactococcus lactis strain with genome-streamlined, low metabolic burden, and multi-stress tolerance characteristics.

Results

The Cre-loxP recombination system was applied to reduce the genome and obtain the target chassis strain. A prophage-related fragment (PRF; 19,739 bp) in the L. lactis N8 genome was deleted, and the mutant strain L. lactis N8-1 was chosen for multi-stress tolerance studies. Nisin immunity of L. lactis N8-1 was increased to 6500 IU/mL, which was 44.44% higher than that of the wild-type L. lactis N8 (4500 IU/mL). The survival rates of L. lactis N8-1 treated with lysozyme for 2 h and lactic acid for 1 h were 1000- and 10,000-fold higher than that of the wild-type strain, respectively. At 39 ℃, the L. lactis N8-1 could still maintain its growth, whereas the growth of the wild-type strain dramatically dropped. Scanning electron microscopy showed that the cell wall integrity of L. lactis N8-1 was well maintained after lysozyme treatment. Tandem mass tags labeled quantitative proteomics revealed that 33 and 9 proteins were significantly upregulated and downregulated, respectively, in L. lactis N8-1. These differential proteins were involved in carbohydrate and energy transport/metabolism, biosynthesis of cell wall and cell surface proteins.

Conclusions

PRF deletion was proven to be an efficient strategy to achieve multi-stress tolerance and nisin immunity in L. lactis, thereby providing a new perspective for industrially obtaining engineered strains with multi-stress tolerance and expanding the application of lactic acid bacteria in biotechnology and synthetic biology. Besides, the importance of PRF, which can confer vital phenotypes to bacteria, was established.

MiniBacillus PG10 as a Convenient and Effective Production Host for Lantibiotics

Efficient bacterial cell factories are important for the screening and characterization of potent antimicrobial peptides such as lantibiotics. Although lantibiotic production systems have been established in Lactococcus lactis and Escherichia coli, the industrial workhorse Bacillus subtilis has been left relatively unexplored as a lantibiotic production host. Therefore, we tested different B. subtilis strains for their ability to produce lantibiotic peptides by using the subtilin modification and transport enzymes derived from the natural subtilin producer B. subtilis ATCC 6633. Our study shows that although B. subtilis ATCC 6633 and 168 are able to produce various processed lantibiotic peptides, an evident advantage of using either the 8-fold protease-deficient strain WB800 or the genome-minimized B. subtilis 168 strain PG10 is the lack of extracellular serine protease activity. Consequently, leader processing of lantibiotic precursor peptides is circumvented and thus potential toxicity toward the production host is prevented. Furthermore, PG10 provides a clean secondary metabolic background and therefore appears to be the most promising B. subtilis lantibiotic production host. We demonstrate the production of various lantibiotic precursor peptides by PG10 and show different options for their in vitro activation. Our study thus provides a convenient B. subtilis-based lantibiotic production system, which facilitates the search for novel antimicrobial peptides.

d-Methionine and d-Phenylalanine Improve Lactococcus lactis F44 Acid Resistance and Nisin Yield by Governing Cell Wall Remodeling

Lactococcus lactis encounters various environmental challenges, especially acid stress, during its growth. The cell wall can maintain the integrity and shape of the cell under environmental stress, and d-amino acids play an important role in cell wall synthesis. Here, by analyzing the effects of 19 different d-amino acids on the physiology of L. lactis F44, we found that exogenously supplied d-methionine and d-phenylalanine increased the nisin yield by 93.22% and 101.29%, respectively, as well as significantly increasing the acid resistance of L. lactis F44. The composition of the cell wall in L. lactis F44 with exogenously supplied d-Met or d-Phe was further investigated via a vancomycin fluorescence experiment and a liquid chromatography-mass spectrometry assay, which demonstrated that d-Met could be incorporated into the fifth position of peptidoglycan (PG) muropeptides and d-Phe could be added to the fourth and fifth positions. Moreover, overexpression of the PG synthesis gene murF further enhanced the levels of d-Met and d-Phe involved in PG and increased the survival rate under acid stress and the nisin yield of the strain. This study reveals that the exogenous supply of d-Met or d-Phe can change the composition of the cell wall and influence acid tolerance as well as nisin yield in L. lactis IMPORTANCE As d-amino acids play an important role in cell wall synthesis, we analyzed the effects of 19 different d-amino acids on L. lactis F44, demonstrating that d-Met and d-Phe can participate in peptidoglycan (PG) synthesis and improve the acid resistance and nisin yield of this strain. murF overexpression further increased the levels of d-Met and d-Phe incorporated into PG and contributed to the acid resistance of the strain. These findings suggest that d-Met and d-Phe can be incorporated into PG to improve the acid resistance and nisin yield of L. lactis, and this study provides new ideas for the enhancement of nisin production.

Safety Aspects of Genetically Modified Lactic Acid Bacteria

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.

Co-production of Nisin and γ-Aminobutyric Acid by Engineered Lactococcus lactis for Potential Application in Food Preservation

Microbiological contamination and oxidative damage are the two main challenges in maintaining quality and improving shelf-life of foods. Here, we developed a Lactococcus lactis fermentation system that could simultaneously produce nisin, an antimicrobial peptide, and γ-aminobutyric acid (GABA), an antioxidant agent. In this system, we metabolically engineered a nisin producing strain L. lactis F44 for GABA production by expression of glutamate decarboxylase and glutamate/GABA antiporter. GABA biosynthesis could facilitate nisin production through enhancing acid resistance of the strain. By applying a two-stage pH-control fermentation strategy, the engineered strain yielded up to 9.12 g/L GABA, which was 2.2 times higher than that of pH-constant fermentation. Furthermore, we demonstrated the potential application of the freeze-dried fermentation product as a preservative to improve the storage performance of meat and fruit. These results suggested that the fermentation product of nisin-GABA co-producing strain could serve as a cost-effective, easily prepared, and high-performance food preservative.

Higher nisin yield is reached with glutathione and pyruvate compared with heme in Lactococcus lactis N8

There are different studies that aim to enhance the production of nisin by Lactococcus lactis since its chemical synthesis is not possible. In this study, glutathione (GSH) and pyruvate, which are known to reduce the oxidative stress of cells, have been shown to trigger the production of nisin at both transcriptional and translational levels in L. lactis cells grown under aerobic condition. Presence of GSH and pyruvate caused more nisin yield than the heme-supplemented medium. Moreover, the expression of genes that encode stress-related enzymes were apparently upregulated in the presence of GSH and pyruvate. It can be concluded that GSH and pyruvate contribute to the defense system of L. lactis cells and so that higher biomass was obtained which in turn enhance nisin production. Antioxidant effect of GSH and pyruvate was known; however, their stimulating effect on nisin production was shown for the first time in this study.

Microbial response to acid stress: mechanisms and applications

Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.

Systemic understanding of Lactococcus lactis response to acid stress using transcriptomics approaches

During fermentation, acid stress caused by the accumulation of acidic metabolites seriously affects the metabolic activity and production capacity of microbial cells. To elucidate the acid stress-tolerance mechanisms of microbial cells, we performed genome mutagenesis combined with high-throughput technologies to screen acid stress-tolerant strains. Mutant strain Lactococcus lactis WH101 showed a 16,000-fold higher survival rate than that of the parent strain after 5 h of acid shock at pH 4.0 and maintained higher ATP, NH₄⁺, and intracellular pH (pH_i) levels during acid stress. Additionally, comparative transcriptomics analysis revealed enhanced regulation of carbohydrate metabolism and sugar transport to provide additional energy, amino acid metabolism and transport to maintain pH_i homeostasis and ATP generation, and fatty acid metabolism to enhance cellular acid tolerance. Moreover, overexpression of identified components resulted in 12.6- and 12.9-fold higher survival rates after acid shock for 3 h at pH 4.0 in L. lactis (ArcB) and L. lactis (MalQ) compared to the control strain, respectively. These findings provide valuable insight into the acid stress-response mechanisms of L. lactis and promote the further development of robust industrial strains.

Enhanced acid-stress tolerance in Lactococcus lactis NZ9000 by overexpression of ABC transporters

Background

Microbial cell factories are widely used in the production of acidic products such as organic acids and amino acids. However, the metabolic activity of microbial cells and their production efficiency are severely inhibited with the accumulation of intracellular acidic metabolites. Therefore, it remains a key issue to enhance the acid tolerance of microbial cells. In this study, we investigated the effects of four ATP-binding cassette (ABC) transporters on acid stress tolerance in Lactococcus lactis.

Results

Overexpressing the rbsA, rbsB, msmK, and dppA genes exhibited 5.8-, 12.2-, 213.7-, and 5.2-fold higher survival rates than the control strain, respectively, after acid shock for 3 h at pH 4.0. Subsequently, transcriptional profile alterations in recombinant strains were analyzed during acid stress. The differentially expressed genes associated with cold-shock proteins (csp), fatty acid biosynthesis (fabH), and coenzyme A biosynthesis (coaD) were up-regulated in the four recombinant strains during acid stress. Additionally, some genes were differentially expressed in specific recombinant strains. For example, in L. lactis (RbsB), genes involved in the pyrimidine biosynthetic pathway (pyrCBDEK) and glycine or betaine transport process (busAA and busAB) were up-regulated during acid stress, and the argG genes showed up-regulations in L. lactis (MsmK). Finally, we found that overexpression of the ABC transporters RbsB and MsmK increased intracellular ATP concentrations to protect cells against acidic damage in the initial stage of acid stress. Furthermore, L. lactis (MsmK) consistently maintained elevated ATP concentrations under acid stress.

Conclusions

This study elucidates the common and specific mechanisms underlying improved acid tolerance by manipulating ABC transporters and provides a further understanding of the role of ABC transporters in acid-stress tolerance.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1188-8) contains supplementary material, which is available to authorized users.

The genome and transcriptome of Lactococcus lactis ssp. lactis F44 and G423: Insights into adaptation to the acidic environment

Nisin, as a common green (environmentally friendly), nontoxic antibacterial peptide secreted by Lactococcus lactis, is widely used to prevent the decomposition of meat and dairy products and maintains relatively high stability at low pH. However, the growth of Lc. lactis is frequently inhibited by high lactic acid concentrations produced during fermentation. This phenomenon has become a great challenge in enhancing the nisin yield for this strain. Here, the shuffled strain G423 that could survive on a solid plate at pH 3.7 was generated through protoplast fusion-mediated genome shuffling. The nisin titer of G423 peaked at 4,543 IU/mL, which was 59.9% higher than that of the same batch of the initial strain Lc. lactis F44. The whole genome comparisons between G423 and F44 indicated that 6 large fragments (86,725 bp) were inserted in G423 compared with that of Lc. lactis F44. Transcriptome data revealed that 4 novel noncoding transcripts, and the significantly upregulated genes were involved in multiple processes in G423. In particular, the expression of genes involved in cell wall and membrane biosynthesis was obviously perturbed under acidic stress. Quantitative real-time PCR analysis showed that the transcription of noncoding small RNA NC-1 increased by 2.35-fold at pH 3.0 compared with that of the control (pH 7.0). Overexpression assays indicated that small RNA NC-1 could significantly enhance the acid tolerance and nisin production of G423 and F44. Our work provided new insights into the sophisticated genetic mechanisms involved in Lc. lactis in an acidic environment, which might elucidate its potential application in food and dairy industries.

Improved acid-stress tolerance of Lactococcus lactis NZ9000 and Escherichia coli BL21 by overexpression of the anti-acid component recT

Acid accumulation caused by carbon metabolism severely affects the fermentation performance of microbial cells. Here, different sources of the recT gene involved in homologous recombination were functionally overexpressed in Lactococcus lactis NZ9000 and Escherichia coli BL21, and their acid-stress tolerances were investigated. Our results showed that L. lactis NZ9000 (ERecT and LRecT) strains showed 1.4- and 10.4-fold higher survival rates against lactic acid (pH 4.0), respectively, and that E. coli BL21 (ERecT) showed 16.7- and 9.4-fold higher survival rates than the control strain against lactic acid (pH 3.8) for 40 and 60 min, respectively. Additionally, we found that recT overexpression in L. lactis NZ9000 improved their growth under acid-stress conditions, as well as increased salt- and ethanol-stress tolerance and intracellular ATP concentrations in L. lactis NZ9000. These findings demonstrated the efficacy of recT overexpression for enhancing acid-stress tolerance and provided a promising strategy for insertion of anti-acid components in different hosts.

The increase of O-acetylation and N-deacetylation in cell wall promotes acid resistance and nisin production through improving cell wall integrity in Lactococcus lactis

Cell wall is closely related to bacterial robustness and adsorption capacity, playing crucial roles in nisin production in Lactococcus lactis. Peptidoglycan (PG), the essential component of cell wall, is usually modified with MurNAc O-acetylation and GlcNAc N-deacetylation, catalyzed by YvhB and XynD, respectively. In this study, increasing the two modifications in L. lactis F44 improved autolysis resistance by decreasing the susceptibility to PG hydrolases. Furthermore, both modifications were positively associated with overall cross-linkage, contributing to cell wall integrity. The robust cell wall rendered the yvhB/xynD-overexpression strains more acid resistant, leading to the increase of nisin production in fed-batch fermentations by 63.7 and 62.9%, respectively. Importantly, the structural alterations also reduced nisin adsorption capacity, resulting in reduction of nisin loss. More strikingly, the co-overexpression strain displayed the highest nisin production (76.3% higher than F44). Our work provides a novel approach for achieving nisin overproduction via extensive cell wall remodeling.

Innovative approaches to nisin production

Nisin is a bacteriocin produced by Lactococcus lactis that has been approved by the Food Drug Administration for utilization as a GRAS status food additive. Nisin can inhibit spore germination and demonstrates antimicrobial activity against Listeria, Clostridium, Staphylococcus, and Bacillus species. Under some circumstances, it plays an immune modulator role and has a selective cytotoxic effect against cancer cells, although it is notable that the high production cost of nisin-a result of the low nisin production yield of producer strains-is an important factor restricting intensive use. In recent years, production of nisin has been significantly improved through genetic modifications to nisin producer strains and through innovative applications in the fermentation process. Recently, 15,400 IU ml^-1 nisin production has been achieved in L. lactis cells following genetic modifications by eliminating the factors that negatively affect nisin biosynthesis or by increasing the cell density of the producing strains in the fermentation medium. In this review, innovative approaches related to cell and fermentation systems aimed at increasing nisin production are discussed and interpreted, with a view to increasing industrial nisin production.

Enhancing nisin yield by engineering a small noncodding RNA anti41 and inhibiting the expression of glnR in Lactococcus lactis F44

OBJECTIVES

To engineer a small nonconding RNA anti41 to enhance nisin yield by inhibiting the expression of glnR in Lactococcus lactis F44.

RESULTS

We constructed a screening library to determine appropriate artificial sRNAs and obtained a sRNA anti41 that can produce approximately three fold of the inhibitory effect on GlnR. Moreover, the transcription levels of the direct inhibitory targets of GlnR (glnP, glnQ, amtB, and glnK) were dramatically upregulated in the anti41 overexpression strain (F44-anti41), thereby confirming the inhibitory effect of anti41 on GlnR. In addition, anti41 overexpression improved the survival rate of cells by approximately three fold under acid stress, promoted cell growth, and increased nisin yield by 29.83%.

CONCLUSIONS

We were able to provide a novel strategy for the construction of robust high-producing industrial strains.

Contribution of YthA, a PspC Family Transcriptional Regulator of Lactococcus lactis F44 Acid Tolerance and Nisin Yield: a Transcriptomic Approach

To overcome the adverse impacts of environmental stresses during growth, different adaptive regulation mechanisms can be activated in Lactococcus lactis In this study, the transcription levels of eight transcriptional regulators of L. lactis subsp. lactis F44 under acid stress were analyzed using quantitative reverse transcription-PCR. Eight gene-overexpressing strains were then constructed to examine their influences on acid-resistant capability. Overexpressing ythA, a PspC family transcriptional regulator, increased the survival rate by 3.2-fold compared to the control at the lethal pH 3.0 acid shock. Moreover, the nisin yield was increased by 45.50%. The ythA-overexpressing strain FythA appeared to have higher intracellular pH stability and nisin-resistant ability. Subsequently, transcriptome analysis revealed that the vast majority of genes associated with amino acid biosynthesis, including arginine, serine, phenylalanine, and tyrosine, were predominantly upregulated in FythA. Arginine biosynthesis (argG and argH), arginine deiminase pathway, and polar amino acid transport (ysfE and ysfF) were proposed to be the main regulation mechanisms of YthA. Furthermore, the transcription of genes associated with pyrimidine and exopolysaccharide biosynthesis were upregulated. The transcriptional levels of nisIPRKFEG genes were substantially higher in FythA, which directly contributed to the yield and resistance of nisin. Three potential DNA-binding sequences were predicted by computer analysis using the upstream regions of genes with prominent changes. This study showed that YthA could increase acid resistance and nisin yield and revealed a putative regulation mechanism of YthA.IMPORTANCE Nisin, produced by Lactococcus lactis subsp. lactis, is widely used as a safe food preservative. Acid stress becomes the primary restrictive factor of cell growth and nisin yield. In this research, we found that the transcriptional regulator YthA was conducive to enhancing the acid resistance of L. lactis F44. Overexpressing ythA could significantly improve the survival rate and nisin yield. The stability of intracellular pH and nisin resistance were also increased. Transcriptome analysis showed that nisin immunity and the biosynthesis of some amino acids, pyrimidine, and exopolysaccharides were enhanced in the engineered strain. This study elucidates the regulation mechanism of YthA and provides a novel strategy for constructing robust industrial L. lactis strains.

Contribution of YthA, a PspC Family Transcriptional Regulator of Lactococcus lactis F44 Acid Tolerance and Nisin Yield: a Transcriptomic Approach

To overcome the adverse impacts of environmental stresses during growth, different adaptive regulation mechanisms can be activated in Lactococcus lactis In this study, the transcription levels of eight transcriptional regulators of L. lactis subsp. lactis F44 under acid stress were analyzed using quantitative reverse transcription-PCR. Eight gene-overexpressing strains were then constructed to examine their influences on acid-resistant capability. Overexpressing ythA, a PspC family transcriptional regulator, increased the survival rate by 3.2-fold compared to the control at the lethal pH 3.0 acid shock. Moreover, the nisin yield was increased by 45.50%. The ythA-overexpressing strain FythA appeared to have higher intracellular pH stability and nisin-resistant ability. Subsequently, transcriptome analysis revealed that the vast majority of genes associated with amino acid biosynthesis, including arginine, serine, phenylalanine, and tyrosine, were predominantly upregulated in FythA. Arginine biosynthesis (argG and argH), arginine deiminase pathway, and polar amino acid transport (ysfE and ysfF) were proposed to be the main regulation mechanisms of YthA. Furthermore, the transcription of genes associated with pyrimidine and exopolysaccharide biosynthesis were upregulated. The transcriptional levels of nisIPRKFEG genes were substantially higher in FythA, which directly contributed to the yield and resistance of nisin. Three potential DNA-binding sequences were predicted by computer analysis using the upstream regions of genes with prominent changes. This study showed that YthA could increase acid resistance and nisin yield and revealed a putative regulation mechanism of YthA.IMPORTANCE Nisin, produced by Lactococcus lactis subsp. lactis, is widely used as a safe food preservative. Acid stress becomes the primary restrictive factor of cell growth and nisin yield. In this research, we found that the transcriptional regulator YthA was conducive to enhancing the acid resistance of L. lactis F44. Overexpressing ythA could significantly improve the survival rate and nisin yield. The stability of intracellular pH and nisin resistance were also increased. Transcriptome analysis showed that nisin immunity and the biosynthesis of some amino acids, pyrimidine, and exopolysaccharides were enhanced in the engineered strain. This study elucidates the regulation mechanism of YthA and provides a novel strategy for constructing robust industrial L. lactis strains.

Acid or erythromycin stress significantly improves transformation efficiency through regulating expression of DNA binding proteins in Lactococcus lactis F44

Lactococcus lactis is a gram-positive bacterium used extensively in the dairy industry and food fermentation, and its biological characteristics are usually improved through genetic manipulation. However, poor transformation efficiency was the main restriction factor for the construction of engineered strains. In this study, the transformation efficiency of L. lactis F44 showed a 56.1-fold increase in acid condition (pH 5.0); meanwhile, erythromycin stress (0.04 μg/mL) promoted the transformation efficiency more significantly (76.9-fold). Notably, the transformation efficiency of F44e (L. lactis F44 harboring empty pLEB124) increased up to 149.1-fold under the synergistic stresses of acid and erythromycin. In addition, the gene expression of some DNA binding proteins (DprA, RadA, RadC, RecA, RecQ, and SsbA) changed correspondingly. Especially for radA, 25.1-fold improvement was detected when F44e was exposed to pH 5.0. Overexpression of some DNA binding proteins could improve the transformation efficiency. The results suggested that acid or erythromycin stress could improve the transformation efficiency of L. lactis through regulating gene expression of DNA binding proteins. We have proposed a simple but promising strategy for improving the transformation efficiency of L. lactis and other hard-transformed microorganisms.

The novel sRNA s015 improves nisin yield by increasing acid tolerance of Lactococcus lactis F44

Nisin, a polycyclic antibacterial peptide produced by Lactococcus lactis, is stable at low pH. Improving the acid tolerance of L. lactis could thus enhance nisin yield. Small non-coding RNAs (sRNAs) play essential roles in acid tolerance by regulating their target mRNAs at the post-transcriptional level. In this study, a novel sRNA, s015, was identified in L. lactis F44 via the use of RNA sequencing, qRT-PCR analysis, and Northern blotting. s015 improved the acid tolerance of L. lactis and boosted nisin yield at low pH. In silico predictions enabled us to construct a library of possible s015 target mRNAs. Statistical analysis and validation suggested that s015 contains a highly conserved region (5'-GAAAAAAAC-3') that likely encompasses the regulatory core of the sRNA. atpG, busAB, cysD, ilvB, tcsR, ung, yudD, and ywdA were verified as direct targets of s015, and the interactions between s015 and its target genes were elucidated. This work provided new insight into the adaptation mechanism of L. lactis under acid stress.

Promoting acid resistance and nisin yield of Lactococcus lactis F44 by genetically increasing D-Asp amidation level inside cell wall

Nisin fermentation by Lactococcus lactis requires a low pH to maintain a relatively higher nisin activity. However, the acidic environment will result in cell arrest, and eventually decrease the relative nisin production. Hence, constructing an acid-resistant L. lactis is crucial for nisin harvest in acidic nisin fermentation. In this paper, the first discovery of the relationship between D-Asp amidation-associated gene (asnH) and acid resistance was reported. Overexpression of asnH in L. lactis F44 (F44A) resulted in a sevenfold increase in survival capacity during acid shift (pH 3) and enhanced nisin desorption capacity compared to F44 (wild type), which subsequently contributed to higher nisin production, reaching 5346 IU/mL, 57.0% more than that of F44 in the fed-batch fermentation. Furthermore, the engineered F44A showed a moderate increase in D-Asp amidation level (from 82 to 92%) compared to F44. The concomitant decrease of the negative charge inside the cell wall was detected by a newly developed method based on the nisin adsorption amount onto cell surface. Meanwhile, peptidoglycan cross-linkage increased from 36.8% (F44) to 41.9% (F44A), and intracellular pH can be better maintained by blocking extracellular H⁺ due to the maintenance of peptidoglycan integrity, which probably resulted from the action of inhibiting hydrolases activity. The inference was further supported by the acmC-overexpression strain F44C, which was characterized by uncontrolled peptidoglycan hydrolase activity. Our results provided a novel strategy for enhancing nisin yield through cell wall remodeling, which contributed to both continuous nisin synthesis and less nisin adsorption in acidic fermentation (dual enhancement).

Lipid-II Independent Antimicrobial Mechanism of Nisin Depends On Its Crowding And Degree Of Oligomerization

Nisin inhibits bacterial growth by generating pores in cell membrane and interrupting cell-wall biosynthesis through specific lipid II interaction. However, the role of the hinge region and C-terminus residues of the peptide in antibacterial action of nisin is largely unknown. Here, using molecular dynamics simulations and experimental approach, we report that at high concentration regimes of nisin, interaction with phospholipids may equally deform the bacterial cell membranes even under significantly varying amounts of lipid-II. Membrane thinning, destabilization and decrease in lipid density depend on the degree of oligomerization of nisin. Growth kinetics of Bacillus subtilis and Escherichia coli interestingly show recovery by extended lag phase under low concentrations of nisin treatment while high concentrations of nisin caused decrease in cell viability as recorded by striking reduction in membrane potential and surface area. The significant changes in the dipole potential and fluorescence anisotropy were observed in negatively charged membranes in the absence of lipid-II with increasing concentration of nisin. The identical correlation of cell viability, membrane potential dissipation and morphology with the concentration regime of nisin, in both Bacillus subtilis (lipid II rich) and Escherichia coli (lipid II impoverished), hints at a non-specific physical mechanism where degree of membrane deformation depends on degree of crowding and oligomerization of nisin.

Relationship between IL-10 gene -819C/T polymorphism and the risk of inflammatory bowel disease: a meta-analysis

BACKGROUND

The -819C/T polymorphism in interleukin 10 (IL-10) gene has been reported to be associated with inflammatory bowel disease (IBD), but the previous results are conflicting.

MATERIALS AND METHODS

The present study aimed at investigating the association between this polymorphism and risk of IBD using a meta-analysis.PubMed, Web of Science,EMBASE,google scholar and China National Knowledge Infrastructure (CNKI) databases were systematically searched to identify relevant publications from their inception to April 2016.Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects models.

RESULTS

A total of 7 case-control studies containing 1890 patients and 2929 controls were enrolled into this meta-analysis, and our results showed no association between IL-10 gene -819C/T polymorphism and IBD risk(TT vs. CC:OR=0.81,95%CI 0.64-1.04;CT vs. CC:OR=0.92,95%CI 0.81-1.05; Dominant model: OR=0.90,95%CI 0.80-1.02; Recessive model: OR=0.84,95%CI 0.66-1.06). In a subgroup analysis by nationality, the -819C/T polymorphism was not associated with IBD in both Asians and Caucasians. In the subgroup analysis stratified by IBD type, significant association was found in Crohn's disease(CD)(CT vs. CC:OR=0.68,95%CI 0.48-0.97).

CONCLUSION

In summary, the present meta-analysis suggests that the IL-10 gene -819C/T polymorphism may be associated with CD risk.