Heterologous Biosynthesis of Five New Class II Bacteriocins From Lactobacillus paracasei CNCM I-5369 With Antagonistic Activity Against Pathogenic Escherichia coli Strains

Understanding bacteriocin heterologous expression: A review

Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.

Bacteriocin diversity, function, discovery and application as antimicrobials

Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.

Heterologous Expression of Plantaricin 423 and Mundticin ST4SA in Saccharomyces cerevisiae

Antimicrobial peptides or bacteriocins are excellent candidates for alternative antimicrobials, but high manufacturing costs limit their applications. Recombinant gene expression offers the potential to produce these peptides more cost-effectively at a larger scale. Saccharomyces cerevisiae is a popular host for recombinant protein production, but with limited success reported on antimicrobial peptides. Individual recombinant S. cerevisiae strains were constructed to secrete two class IIa bacteriocins, plantaricin 423 (PlaX) and mundticin ST4SA (MunX). The native and codon-optimised variants of the plaA and munST4SA genes were cloned into episomal expression vectors containing either the S. cerevisiae alpha mating factor (MFα1) or the Trichoderma reesei xylanase 2 (XYNSEC) secretion signal sequences. The recombinant peptides retained their activity and stability, with the MFα1 secretion signal superior to the XYNSEC secretion signal for both bacteriocins. An eight-fold increase in activity against Listeria monocytogenes was observed for MunX after codon optimisation, but not for PlaX-producing strains. After HPLC-purification, the codon-optimised genes yielded 20.9 mg/L of MunX and 18.4 mg/L of PlaX, which displayed minimum inhibitory concentrations (MICs) of 108.52 nM and 1.18 µM, respectively, against L. monocytogenes. The yields represent a marked improvement relative to an Escherichia coli expression system previously reported for PlaX and MunX. The results demonstrated that S. cerevisiae is a promising host for recombinant bacteriocin production that requires a simple purification process, but the efficacy is sensitive to codon usage and secretion signals.

Enterocin DD14 can inhibit the infection of eukaryotic cells with enveloped viruses

Bacteriocins are ribosomally synthesized bacterial peptides endowed with antibacterial, antiprotozoal, anticancer and antiviral activities. In the present study, we evaluated the antiviral activities of two bacteriocins, enterocin DD14 (EntDD14) and lacticaseicin 30, against herpes simplex virus type 1 (HSV-1), human coronavirus 229E (HCoV-229E) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Vero, Huh7 and Vero E6 cells, respectively. In addition, the interactions of these bacteriocins with the envelope glycoprotein D of HSV-1 and the receptor binding domains of HCoV-229E and SARS-CoV-2 have been computationally evaluated using protein-protein docking and molecular dynamics simulations. HSV-1 replication in Vero cells was inhibited by EntDD14 and, to a lesser extent, by lacticaseicin 30 added to cells after virus inoculation. EntDD14 and lacticaseicin 30 had no apparent antiviral activity against HCoV-229E; however, EntDD14 was able to inhibit SARS-CoV-2 in Vero E6 cells. Further studies are needed to elucidate the antiviral mechanism of these bacteriocins.

Postbiotics: Functional Food Materials and Therapeutic Agents for Cancer, Diabetes, and Inflammatory Diseases

Postbiotics are (i) "soluble factors secreted by live bacteria, or released after bacterial lysis, such as enzymes, peptides, teichoic acids, peptidoglycan-derived muropeptides, polysaccharides, cell-surface proteins and organic acids"; (ii) "non-viable metabolites produced by microorganisms that exert biological effects on the hosts"; and (iii) "compounds produced by microorganisms, released from food components or microbial constituents, including non-viable cells that, when administered in adequate amounts, promote health and wellbeing". A probiotic- and prebiotic-rich diet ensures an adequate supply of these vital nutrients. During the anaerobic fermentation of organic nutrients, such as prebiotics, postbiotics act as a benevolent bioactive molecule matrix. Postbiotics can be used as functional components in the food industry by offering a number of advantages, such as being added to foods that are harmful to probiotic survival. Postbiotic supplements have grown in popularity in the food, cosmetic, and healthcare industries because of their numerous health advantages. Their classification depends on various factors, including the type of microorganism, structural composition, and physiological functions. This review offers a succinct introduction to postbiotics while discussing their salient features and classification, production, purification, characterization, biological functions, and applications in the food industry. Furthermore, their therapeutic mechanisms as antibacterial, antiviral, antioxidant, anticancer, anti-diabetic, and anti-inflammatory agents are elucidated.

Potential Impact of Combined Inhibition by Bacteriocins and Chemical Substances of Foodborne Pathogenic and Spoilage Bacteria: A Review

In recent years, food safety caused by foodborne pathogens and spoilage bacteria has become a major public health problem worldwide. Bacteriocins are a kind of antibacterial peptide synthesized by microbial ribosomes, and are widely used as food preservatives. However, when used individually bacteriocins may have limitations such as high cost of isolation and purification, narrow inhibitory spectrum, easy degradation by enzymes, and vulnerability to complex food environments. Numerous studies have demonstrated that co-treatment with bacteriocins and a variety of chemical substances can have synergistic antibacterial effects on spoilage microorganisms and foodborne pathogens, effectively prolonging the shelf life of food and ensuring food safety. Therefore, this paper systematically summarizes the synergistic bacteriostatic strategies of bacteriocins in combination with chemical substances such as essential oils, plant extracts, and organic acids. The impacts of bacteriocins when used individually and in combination with other chemical substances on different food substrates are clarified, and bacteriocin-chemical substance compositions that enhance antibacterial effectiveness and reduce the potential negative effects of chemical preservatives are highlighted and discussed. Combined treatments involving bacteriocins and different kinds of chemical substances are expected to be a promising new antibacterial method and to become widely used in both the food industry and biological medicine.

Isolation, identification, and biochemical characterization of five Lacticaseibacillus strains from Oggtt: A traditional fermented and dried buttermilk

This study investigates the isolation and characterization of the main lactic acid bacteria responsible for fermentation of Oggtt, a dried fermented buttermilk. Five isolates with Gram-positive staining and negative catalase and oxidase activity were identified using phenotypic and genotypic methods, and their antagonistic, exopolysaccharides and organic acid production, proteolytic activity, and antioxidant capacity were assessed. The isolates are classified as Lacticaseibacillus paracasei Ogt_1, Lacticaseibacillus casei Ogt_2, Lacticaseibacillus paracasei Ogt_3, Lacticaseibacillus paracasei Ogt_4, and Lacticaseibacillus paracasei Ogt_5. All strains possessed high antagonistic activity against Proteus vulgaris, Staphylococcus aureus, and Escherichia coli. All strains produced high levels of lactic acid (11177.3-15404.9 μg/ml), tartaric acid (2197.8-4058.5 μg/ml), and exopolysaccharides(20.86-239.9 mg/L) and possessed high proteolytic and antioxidant activity at variable manners. Overall, this study indicates the isolation of important Lacticaseibacillus strains from Oggtt, which could be used as starter cultures for developing functional foods.

The Efficacy of Probiotics as Antiviral Agents for the Treatment of Rotavirus Gastrointestinal Infections in Children: An Updated Overview of Literature

Enteric viruses, including the rotavirus, norovirus, and adenoviruses, are the most common cause of acute gastroenteritis. The rotavirus disease is especially prevalent among children, and studies over the past decade have revealed complex interactions between rotaviruses and the gut microbiota. One way to treat and prevent dysbiosis is the use of probiotics as an antiviral agent. This review focuses on the latest scientific evidence on the antiviral properties of probiotics against rotavirus gastroenteric infections in children. A total of 19 studies exhibited a statistically significant antiviral effect of probiotics. The main probiotics that were effective were Saccharomyces cerevisiae var. boulardii, Lacticaseibacillus rhamnosus GG, and various multi-strain probiotics. The underlying mechanism of the probiotics against rotavirus gastroenteric infections in children included immune enhancement and modulation of intestinal microbiota leading to shortening of diarrhoea. However, several clinical studies also found no significant difference in the probiotic group compared to the placebo group even though well-known strains were used, thus showing the importance of correct dosage, duration of treatment, quality of probiotics and the possible influence of other factors, such as the production process of probiotics and the influence of immunisation on the effect of probiotics. Therefore, more robust, well-designed clinical studies addressing all factors are warranted.

Postbiotics: From emerging concept to application

The microbiome innovation has resulted in an umbrella term, postbiotics, which refers to non-viable microbial cells, metabolic byproducts and their microbial components released after lysis. Postbiotics, modulate immune response, gene expression, inhibit pathogen binding, maintain intestinal barriers, help in controlling carcinogenesis and pathogen infections. Postbiotics have antimicrobial, antioxidant, and immunomodulatory properties with favorable physiological, immunological, neuro-hormonal, regulatory and metabolic reactions. Consumption of postbiotics relieves symptoms of various diseases and viral infections such as SARS-CoV-2. Postbiotics can act as alternatives for pre-probiotic specially in immunosuppressed patients, children and premature neonates. Postbiotics are used to preserve and enhance nutritional properties of food, elimination of biofilms and skin conditioning in cosmetics. Postbiotics have numerous advantages over live bacteria with no risk of bacterial translocation from the gut to blood, acquisition of antibiotic resistance genes. The process of extraction, standardization, transport, and storage of postbiotic is more natural. Bioengineering techniques such as fermentation technology, high pressure etc., may be used for the synthesis of different postbiotics. Safety assessment and quality assurance of postbiotic is important as they may induce stomach discomfort, sepsis and/or toxic shock. Postbiotics are still in their infancy compared to pre- and pro- biotics but future research in this field may contribute to improved physiological functions and host health. The current review comprehensively summarizes new frontiers of research in postbiotics.

Structure of Lacticaseicin 30 and Its Engineered Variants Revealed an Interplay between the N-Terminal and C-Terminal Regions in the Activity against Gram-Negative Bacteria

Lacticaseicin 30 is one of the five bacteriocins produced by the Gram-positive Lacticaseibacillus paracasei CNCM I-5369. This 111 amino acid bacteriocin is noteworthy for being active against Gram-negative bacilli including Escherichia coli strains resistant to colistin. Prediction of the lacticaseicin 30 structure using the Alphafold2 pipeline revealed a largely helical structure including five helix segments, which was confirmed by circular dichroism. To identify the structural requirements of the lacticaseicin 30 activity directed against Gram-negative bacilli, a series of variants, either shortened or containing point mutations, was heterologously produced in Escherichia coli and assayed for their antibacterial activity against a panel of target strains including Gram-negative bacteria and the Gram-positive Listeria innocua. Lacticaseicin 30 variants comprising either the N-terminal region (amino acids 1 to 39) or the central and C-terminal regions (amino acids 40 to 111) were prepared. Furthermore, mutations were introduced by site-directed mutagenesis to obtain ten bacteriocin variants E6G, T7P, E32G, T33P, T52P, D57G, A74P, Y78S, Y93S and A97P. Compared to lacticaseicin 30, the anti-Gram-negative activity of the N-terminal peptide and variants E32G, T33P and D57G remained almost unchanged, while that of the C-terminal peptide and variants E6G, T7P, T52P, A74P, Y78S, Y93S and A97P was significantly altered. Finally, the N-terminal region was further shortened to keep only the first 20 amino acid part that was predicted to include the first helix. The anti-Gram-negative activity of this truncated peptide was completely abolished. Overall, this study shows that activity of lacticaseicin 30, one of the rare Gram-positive bacteriocins inhibiting Gram-negative bacteria, requires at least two helices in the N-terminal region and that the C-terminal region carries amino acids playing a role in modulation of the activity. Taken together, these data will help to design forthcoming variants of lacticaseicin 30 as promising therapeutic agents to treat infections caused by Gram-negative bacilli.

Potential of New Bacterial Strains for a Multiproduct Bioprocess Application: A Case Study Using Isolates of Lactic Acid Bacteria from Pineapple Silage of Costa Rican Agro-Industrial Residues

Lactic acid bacteria (LAB) with potential for the development of multi-product processes are necessary for the valorization of side streams obtained during the biotechnological production of lactic acid (LA). In this study, 14 LAB strains isolated from pineapple agro-industrial residues in Costa Rica were cultivated in microplates, and the six strains with the highest growth were selected for fermentation in microbioreactors to evaluate the production of LA and acetic acid, and the consumption of glucose. Lacticaseibacillus paracasei 6710 and L. paracasei 6714 presented the highest OD600 values (1.600 and 1.602, respectively); however, the highest LA (in g/L) production was observed in L. paracasei 6714 (14.50 ± 0.20) and 6712 (14.67 ± 0.42). L. paracasei 6714 was selected for bioreactor fermentation and reached a maximum OD600 of 6.3062 ± 0.141, with a LA yield of 84.9% and a productivity of 1.06 g L−1 h−1 after 21 h of fermentation. Finally, lipoteichoic acid (LTA) detection from biomass was performed and the antimicrobial activity of the compounds present in the supernatant was studied. LTA was detected from L. paracasei 6714 biomass, and its supernatant caused significant inhibition of foodborne surrogate microorganisms. LAB isolated from pineapple silage have biotechnological potential for multiproduct processes.

Probiotic-Based Bacteriocin: Immunity Supplementation Against Viruses. An Updated Review

Viral infections are a major cause of severe, fatal diseases worldwide. Recently, these infections have increased due to demanding contextual circumstances, such as environmental changes, increased migration of people and product distribution, rapid demographic changes, and outbreaks of novel viruses, including the COVID-19 outbreak. Internal variables that influence viral immunity have received attention along with these external causes to avert such novel viral outbreaks. The gastrointestinal microbiome (GIM), particularly the present probiotics, plays a vital role in the host immune system by mediating host protective immunity and acting as an immune regulator. Bacteriocins possess numerous health benefits and exhibit antagonistic activity against enteric pathogens and immunobiotics, thereby inhibiting viral infections. Moreover, disrupting the homeostasis of the GIM/host immune system negatively affects viral immunity. The interactions between bacteriocins and infectious viruses, particularly in COVID-19, through improved host immunity and physiology are complex and have not yet been studied, although several studies have proven that bacteriocins influence the outcomes of viral infections. However, the complex transmission to the affected sites and siRNA defense against nuclease digestion lead to challenging clinical trials. Additionally, bacteriocins are well known for their biofunctional properties and underlying mechanisms in the treatment of bacterial and fungal infections. However, few studies have shown the role of probiotics-derived bacteriocin against viral infections. Thus, based on the results of the previous studies, this review lays out a road map for future studies on bacteriocins for treating viral infections.

Natural Bioactive Compounds in Organic and Conventional Fermented Food

Compared to conventional agriculture, organic farming is believed to provide a higher nutritional and health value in its products due to the elimination of harmful contaminants (pesticides, nitrates, heavy metals, etc.). Numerous studies have been conducted to show how the production system affects the quality of food in terms of the content of bioactive compounds. The aim of this study was to compare the content of some bioactive compounds (vitamin C, β-carotene, Ca content) and lactic acid bacteria (LAB) number and their bacteriocinogenic activity in organic and conventional fermented food. Although the results do not provide an unambiguous conclusion regarding the superiority of one production system over the other, the LAB number in organic pickled carrot juice, sauerkraut, yogurt, and kefir was higher than in their conventional counterparts. Their bacteriocinogenic potential against selected pathogens was also higher in most organic products. Organic vegetables contained significantly more vitamin C, and the calcium content in the organic yogurt was higher compared to the conventional version of the product. Relatively similar concentrations of ß-carotene for both production systems were found in carrot juice, while in organic pickled beet juice, there was five-fold less ß-carotene than in conventional juice.

Characterization of a new bacteriocin-like inhibitory peptide produced by Lactobacillus sakei B-RKM 0559

The biopreservation strategy allows extending the shelf life and food safety through the use of indigenous or controlled microbiota and their antimicrobial compounds. The aim of this work was to characterize an inhibitory substance with bacteriocin-like activity (Sak-59) produced by the potentially probiotic L. sakei strain from artisanal traditional Kazakh horse meat product Kazy. The maximum production of Sak-59 occurred at the stationary phase of the L. sakei growth. Sak-59 showed inhibitory activity against gram-positive meat spoilage bacteria strains of Listeria monocytogenes, Staphylococcus aureus, and pathogenic gram-negative bacteria strains of Serratia marcescens and Escherichia coli, but not against the tested Lactobacilli strains. Sak-59 activity, as measured by diffusion assay in agar wells, was completely suppressed after treatment with proteolytic enzymes and remained stable after treatment with α-amylase and lipase, indicating that Sak-59 is a peptide and most likely not glycosylated or lipidated. It was concluded that Sak-59 is a potential new bacteriocin with a characteristic activity spectrum, which can be useful in the food and feed industries.

Current Knowledge of the Mode of Action and Immunity Mechanisms of LAB-Bacteriocins

Bacteriocins produced by lactic acid bacteria (LAB-bacteriocins) may serve as alternatives for aging antibiotics. LAB-bacteriocins can be used alone, or in some cases as potentiating agents to treat bacterial infections. This approach could meet the different calls and politics, which aim to reduce the use of traditional antibiotics and develop novel therapeutic options. Considering the clinical applications of LAB-bacteriocins as a reasonable and desirable therapeutic approach, it is therefore important to assess the advances achieved in understanding their modes of action, and the resistance mechanisms developed by the producing bacteria to their own bacteriocins. Most LAB-bacteriocins act by disturbing the cytoplasmic membrane through forming pores, or by cell wall degradation. Nevertheless, some of these peptides still have unknown modes of action, especially those that are active against Gram-negative bacteria. Regarding immunity, most bacteriocin-producing strains have an immunity mechanism involving an immunity protein and a dedicated ABC transporter system. However, these immunity mechanisms vary from one bacteriocin to another.

Gut Microbiota is an Important Source of Bacteriocins and Their In Situ Expression Can Be Explored for Treatment of Bacterial Infections

Bacteriocins are interesting natural antimicrobial peptides that could be deployed quickly to combat certain antimicrobial-resistant bacterial infections. These molecules could be used in conjunction with traditional antibiotics, or even to replace them in some circumstances. To strengthen the concept of "bacteriocinotherapy," we discuss here the benefits associated with production in situ of bacteriocins by commensal bacteria. This on sites production capacity could augment the gut microbiota global resistance plan and provide a backup for bacterial infection treatments.

Potentiating effects of leaderless enterocin DD14 in combination with methicillin on clinical methicillin-resistant Staphylococcus aureus S1 strain

Biofilm formation by pathogenic bacteria as well as their resilience to antibiotic treatments are a major health problem. Here, we sequenced and analyzed the genome of the clinical methicillin-resistant Staphylococcus aureus S1 (MRSA-S1) strain and established its sensitivity to the combination of methicillin and the leaderless two peptides enterocin DD14 (EntDD14). Such sensitivity was assessed in vitro based on the MIC/FIC values as well as on killing curves experiments. Moreover, combination of EntDD14 and methicillin was able to reduce the biofilm formation of Staphylococcus aureus S1 of about ∼30 %. Interestingly, genes thought to be involved in the virulence of MRSA-S1, like nuc and pvl which code, respectively, for nuclease and Panton-Valentine leucocidin, were shown to be downregulated following treatment with EntDD14 and methicillin. Similar effects were registered for other genes such as cflA, cflB and icaB, coding for bacterial ligands clumping factors A, B and intercellular adhesion factor respectively. All these data, suggest that combinations of bacteriocins and antibiotics are useful as a backup for treatment of bacterial infections.

Expression of five class II bacteriocins with activity against Escherichia coli in Lacticaseibacillus paracasei CNCM I-5369, and in a heterologous host

Five open reading frames viz orf010, orf12, orf023, orf030 and orf038 coding class II bacteriocins in Lacticaseibacillus paracasei CNCM I-5369 strain previously isolated from an Algerian dairy product, were found to be expressed after 24 h of growth. The strain has also shown anti-E. coli activity in a narrow pH range between 4.5 and 5. Then, expression and purification of these bacteriocins was conducted in the heterologous host E. coli. This strategy enabled us to purify the peptide encoded by orf030 in large quantities, in contrast to other peptides that were produced but required to be released from the insoluble fraction following 4 M urea and desalting treatments. All peptides heterologously produced were characterized by MALDI TOF Mass spectrometry and successfully tested for their anti-E. coli activity. Furthermore, in silico transcriptional analysis was determined by Findterm tool and with Bagel4 software permitted to locate potential promoters and co-transcription events.

Probiotics at War Against Viruses: What Is Missing From the Picture?

Our world is now facing a multitude of novel infectious diseases. Bacterial infections are treated with antibiotics, albeit with increasing difficulty as many of the more common causes of infection have now developed broad spectrum antimicrobial resistance. However, there is now an even greater challenge from both old and new viruses capable of causing respiratory, enteric, and urogenital infections. Reports of viruses resistant to frontline therapeutic drugs are steadily increasing and there is an urgent need to develop novel antiviral agents. Although this all makes sense, it seems rather strange that relatively little attention has been given to the antiviral capabilities of probiotics. Over the years, beneficial strains of lactic acid bacteria (LAB) have been successfully used to treat gastrointestinal, oral, and vaginal infections, and some can also effect a reduction in serum cholesterol levels. Some probiotics prevent gastrointestinal dysbiosis and, by doing so, reduce the risk of developing secondary infections. Other probiotics exhibit anti-tumor and immunomodulating properties, and in some studies, antiviral activities have been reported for probiotic bacteria and/or their metabolites. Unfortunately, the mechanistic basis of the observed beneficial effects of probiotics in countering viral infections is sometimes unclear. Interestingly, in COVID-19 patients, a clear decrease has been observed in cell numbers of Lactobacillus and Bifidobacterium spp., both of which are common sources of intestinal probiotics. The present review, specifically motivated by the need to implement effective new counters to SARS-CoV-2, focusses attention on viruses capable of co-infecting humans and other animals and specifically explores the potential of probiotic bacteria and their metabolites to intervene with the process of virus infection. The goal is to help to provide a more informed background for the planning of future probiotic-based antiviral research.