RMSCNN: A Random Multi-Scale Convolutional Neural Network for Marine Microbial Bacteriocins Identification

The abuse of traditional antibiotics has led to an increase in the resistance of bacteria and viruses. Similar to the function of antibacterial peptides, bacteriocins are more common as a kind of peptides produced by bacteria that have bactericidal or bacterial effects. More importantly, the marine environment is one of the most abundant resources for extracting marine microbial bacteriocins (MMBs). Identifying bacteriocins from marine microorganisms is a common goal for the development of new drugs. Effective use of MMBs will greatly alleviate the current antibiotic abuse problem. In this work, deep learning is used to identify meaningful MMBs. We propose a random multi-scale convolutional neural network method. In the scale setting, we set a random model to update the scale value randomly. The scale selection method can reduce the contingency caused by artificial setting under certain conditions, thereby making the method more extensive. The results show that the classification performance of the proposed method is better than the state-of-the-art classification methods. In addition, some potential MMBs are predicted, and some different sequence analyses are performed on these candidates. It is worth mentioning that after sequence analysis, the HNH endonucleases of different marine bacteria are considered as potential bacteriocins.

Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci

New ecosystems are being actively mined for new bioactive compounds. Because of the large amount of unexplored biodiversity, bacteria from marine environments are especially promising. Further, host-associated microbes are of special interest because of their low toxicity and compatibility with host health. Here, we identified and characterized biosynthetic gene clusters encoding antimicrobial compounds in host-associated enterococci recovered from fecal samples of wild marine animals remote from human-affected ecosystems. Putative biosynthetic gene clusters in the genomes of 22 Enterococcus strains of marine origin were predicted using antiSMASH5 and Bagel4 bioinformatic software. At least one gene cluster encoding a putative bioactive compound precursor was identified in each genome. Collectively, 73 putative antimicrobial compounds were identified, including 61 bacteriocins (83.56%), 10 terpenes (13.70%), and 2 (2.74%) related to putative nonribosomal peptides (NRPs). Two of the species studied, Enterococcus avium and Enterococcus mundtti, are rare causes of human disease and were found to lack any known pathogenic determinants but yet possessed bacteriocin biosynthetic genes, suggesting possible additional utility as probiotics. Wild marine animal-associated enterococci from human-remote ecosystems provide a potentially rich source for new antimicrobial compounds of therapeutic and industrial value and potential probiotic application.

Discovery of Novel Type II Bacteriocins Using a New High-Dimensional Bioinformatic Algorithm

Antimicrobial compounds first arose in prokaryotes by necessity for competitive self-defense. In this light, prokaryotes invented the first host defense peptides. Among the most well-characterized of these peptides are class II bacteriocins, ribosomally-synthesized polypeptides produced chiefly by Gram-positive bacteria. In the current study, a tensor search protocol-the BACIIα algorithm-was created to identify and classify bacteriocin sequences with high fidelity. The BACIIα algorithm integrates a consensus signature sequence, physicochemical and genomic pattern elements within a high-dimensional query tool to select for bacteriocin-like peptides. It accurately retrieved and distinguished virtually all families of known class II bacteriocins, with an 86% specificity. Further, the algorithm retrieved a large set of unforeseen, putative bacteriocin peptide sequences. A recently-developed machine-learning classifier predicted the vast majority of retrieved sequences to induce negative Gaussian curvature in target membranes, a hallmark of antimicrobial activity. Prototypic bacteriocin candidate sequences were synthesized and demonstrated potent antimicrobial efficacy in vitro against a broad spectrum of human pathogens. Therefore, the BACIIα algorithm expands the scope of prokaryotic host defense bacteriocins and enables an innovative bioinformatics discovery strategy. Understanding how prokaryotes have protected themselves against microbial threats over eons of time holds promise to discover novel anti-infective strategies to meet the challenge of modern antibiotic resistance.

A novel enterocin T1 with anti-Pseudomonas activity produced by Enterococcus faecium T1 from Chinese Tibet cheese

An enterocin-producing Enterococcus faecium T1 was isolated from Chinese Tibet cheese. The enterocin was purified by SP-Sepharose and reversed phase HPLC. It was identified as unique from other reported bacteriocins based on molecular weight (4629 Da) and amino acid compositions; therefore it was subsequently named enterocin T1. Enterocin T1 was stable at 80-100 °C and over a wide pH range, pH 3.0-10.0. Protease sensitivity was observed to trypsin, pepsin, papain, proteinase K, and pronase E. Importantly, enterocin T1 was observed to inhibit the growth of numerous Gram-negative and Gram-positive bacteria including Pseudomonas putida, Pseudomonas aeruginosa, Pseudomonas fluorescens, Escherichia coli, Salmonella typhimurium, Shigella flexneri, Shigella sonnei, Staphylococcus aureus, Listeria monocytogenes. Take together, these results suggest that enterocin T1 is a novel bacteriocin with the potential to be used as a bio-preservative to control Pseudomonas spp. in food.

Class I and Class II Lanthipeptides Produced by Bacillus spp

The increasing number of multidrug-resistant pathogens, along with the small number of new antimicrobials under development, leads to an increased need for novel alternatives. Class I and class II lanthipeptides (also known as lantibiotics) have been considered promising alternatives to classical antibiotics. In addition to their relevant medical applications, they are used as probiotics, prophylactics, preservatives, and additives in cosmetics and personal-care products. The genus Bacillus is a prolific source of bioactive compounds including ribosomally and nonribosomally synthesized antibacterial peptides. Accordingly, there is significant interest in the biotechnological potential of members of the genus Bacillus as producers of antimicrobial lanthipeptides. The present review focuses on aspects of the biosynthesis, gene cluster organization, structure, antibacterial spectrum, and bioengineering approaches of lanthipeptides produced by Bacillus strains. Their efficacy and potency against some clinically relevant strains, including MRSA and VRE, are also discussed. Although no lanthipeptides are currently in clinical use, the information herein highlights the potential of these compounds.

Genetic characterization and expression of leucocin B, a class IId bacteriocin from Leuconostoc carnosum 4010

Leuconostoc carnosum 4010 is an antimicrobial strain used as a protective culture in vacuum-packed meats. In this study, we showed that, in addition to antilisterial class IIa bacteriocins leucocin A and C, the strain also produces class IId bacteriocin leucocin B, the antimicrobial activity of which is limited to the genera Leuconostoc and Weissella. Two novel genes, lebBI encoding the leucocin B precursor with a double-glycine-type leader and putative immunity protein LebI, were identified on L. carnosum 4010 plasmid pLC4010-1. LebI contains three transmembrane spans and shares 55% identity with the mesentericin B105 immunity protein. Genes lebBI were shown to be transcribed in 4010 by RT-PCR analysis. The secretion of leucocin B in L. carnosum 4010 was shown by spot-on-lawn and SDS-gel overlay methods with a Leuconostoc strain sensitive to leucocin B but resistant to leucocins A and C. In addition, leucocins A and B from L. carnosum 4010 were cloned as SSusp45 fusions in heterologous host Lactococcus lactis and the secretion of active bacteriocins was detected on indicator plates.

[Structure, function, and biosynthesis of thiazoleoxazole modified microcins]

Recent advances in a large-scale genome sequencing and data analysis led to discovery of a large number of diverse ribosomally-synthesized posttranslationally-modified natural products. One bourgeoning family of such compounds, characterized by the presence of thiazole and oxazoleheterocycles derived from cysteine and serine residues, is referred to as thiazoleoxazole modified microcins. This review brings together known information about classification, structure, and biosynthesis of thiazole-oxazole modified microcins, their biological activity and potential applications.

Characteristic of bacteriocines and their application

Bacteriocines are small peptides with anti-bacterial properties. They are produced both by Gram-positive and Gram-negative bacteria. Until now, a few hundred bacteriocines were described. Classification of bacteriocines undergoes continuous alterations, as new developments regarding their structure, amino acid sequence and recognised mechanism of their action are available. Some of bacteriocins (lantibiotics) contain atypical amino acids, such as lantionine (Lan), methyllantionine (MeLan), dehydroalanine (Dha), dehydrobutyrine (Dhb), or D-alanine (D-Ala). The best recognized bacteriocines are produced by lactic acid bacteria, including nisine produced by strains of Lactococcus lactis. These bacteriocines have been recognized to be fully safe for humans. At present, nisine is used in food industry, as a preserving agent. Other lactic acid bacteria bacteriocines and probiotic preparations provide an alternative for antibiotics, and are used in food and in animal feed.

Class IIa bacteriocins: diversity and new developments

Class IIa bacteriocins are heat-stable, unmodified peptides with a conserved amino acids sequence YGNGV on their N-terminal domains, and have received much attention due to their generally recognized as safe (GRAS) status, their high biological activity, and their excellent heat stability. They are promising and attractive agents that could function as biopreservatives in the food industry. This review summarizes the new developments in the area of class IIa bacteriocins and aims to provide uptodate information that can be used in designing future research.

[Characteristic, properties, prospect of application of bacteriocins]

Literary data and own research results dedicated to bacteriocin investigations have been analysed. Bacteriocins as one of the most widespread factors of bacterial antagonism, which are distinguished by the majority of microorganisms and characterized by bactericidal action in respect of representatives of phylogenetically related species have been considered. Allowing for their high lytic activity and narrow action specificity, the prospects for the use of the bacteriocins as possible alternative antibacterial remedies are examined. The basic approaches to bacteriocin classification, their variety, structure, killer properties and mechanisms of lytic action are presented. The perspective trends of the use and possible significance of these antibacterial substances in medicine are indicated.

Lantibiotics: peptides of diverse structure and function

The current need for antibiotics with novel target molecules has coincided with advances in technical approaches for the structural and functional analysis of the lantibiotics, which are ribosomally synthesized peptides produced by gram-positive bacteria. These peptides have antibiotic or morphogenetic activity and are structurally defined by the presence of unusual amino acids introduced by posttranslational modification. Lantibiotics are complex polycyclic molecules formed by the dehydration of select Ser and Thr residues and the intramolecular addition of Cys thiols to the resulting unsaturated amino acids to form lanthionine and methyllanthionine bridges, respectively. Importantly, the structural and functional diversity of the lantibiotics is much broader than previously imagined. Here we discuss this growing collection of molecules and introduce some recently discovered peptides, review advances in enzymology and protein engineering, and discuss the regulatory networks that govern the synthesis of the lantibiotics by the producing organisms.

A novel lantibiotic acting on bacterial cell wall synthesis produced by the uncommon actinomycete Planomonospora sp

Important classes of antibiotics acting on bacterial cell wall biosynthesis, such as beta-lactams and glycopeptides, are used extensively in therapy and are now faced with a challenge because of the progressive spread of resistant pathogens. A discovery program was devised to target novel peptidoglycan biosynthesis inhibitors capable of overcoming these resistance mechanisms. The microbial products were first screened according to their differential activity against Staphylococcus aureus and its L-form. Then, activities insensitive to the addition of a beta-lactamase cocktail or d-alanyl-d-alanine affinity resin were selected. Thirty-five lantibiotics were identified from a library of broth extracts produced by 40,000 uncommon actinomycetes. Five of them showed structural characteristics that did not match with any known microbial metabolite. In this study, we report on the production, structure determination, and biological activity of one of these novel lantibiotics, namely, planosporicin, which is produced by the uncommon actinomycete Planomonospora sp. Planosporicin is a 2194 Da polypeptide originating from 24 proteinogenic amino acids. It contains lanthionine and methyllanthionine amino acids generating five intramolecular thioether bridges. Planosporicin selectively blocks peptidoglycan biosynthesis and causes accumulation of UDP-linked peptidoglycan precursors in growing bacterial cells. On the basis of its mode of action and globular structure, planosporicin can be assigned to the mersacidin (20 amino acids, 1825 Da) and the actagardine (19 amino acids, 1890 Da) subgroup of type B lantibiotics. Considering its spectrum of activity against Gram-positive pathogens of medical importance, including multi-resistant clinical isolates, and its efficacy in vivo, planosporicin represents a potentially new antibiotic to treat emerging pathogens.

Diversity of enterococcal bacteriocins and their grouping in a new classification scheme

Enterococci are lactic acid bacteria of importance in food, public health and medical microbiology. Many strains produce bacteriocins, some of which have been well characterized. This review describes the structural and genetic characteristics of enterocins, the bacteriocins produced by enterococci. Some of these can be grouped with typical bacteriocins produced by lactic acid bacteria according to traditional classification, whereas others are atypical and structurally distinct from the general classes of bacteriocins. These atypical enterocins recently played an important role in and prompted reclassification of the class II bacteriocins into a new scheme. In this review, a more simplified classification scheme for enterocins based on amino acid sequence homologies is proposed. Enterocins are of interest for their diversity and potential for use as food biopreservatives. The emergence of multiple antibiotic-resistant enterococci among agents of nosocomial disease and the presence of virulence factors among food isolates requires a careful safety evaluation of isolates intended for potential biotechnical use. Nevertheless, enterococcal bacteriocins produced by heterologous hosts or added as cell-free preparations may still be attractive for application in food preservation.

[Posttranslationally modified microcins]

Microcins are antibacterial compounds that are encoded in the bacterial genome and synthesized via ribosomal translation. Microcins play an important role in microbial ecology and are promising as antibiotics. To exert their effect, most microcins are incorporated in the membrane of sensitive cells to increase its permeability. The review considers the known classes of posttranslationally modified microcins. These microcins are unusual in structure and inhibit the grown of sensitive cells by entering their cytoplasm and affecting intracellular targets, such as DNA gyrase, DNA-dependent RNA polymerase, and aspartyl-tRNA synthase.

Open L-lactic acid fermentation of food refuse using thermophilic Bacillus coagulans and fluorescence in situ hybridization analysis of microflora

In the production of commercially useful poly-L-lactic acid plastic from biomass wastes, a feasible fermentation process to produce optically active L-lactic acid would be required. Here, model kitchen refuse (MKR) was inoculated with Bacillus coagulans NBRC12583 under nonsterilized openculture conditions. At temperatures below 45 degrees C, a racemic mixture of D- and L-lactic acids was accumulated, whereas only L-lactic acid was selectively accumulated by incubation at 50-65 degrees C. At 45 degrees C, the results of fermentation could not be consistently reproduced. To analyze microflora in this type of mixed culture system, whole-cell fluorescence in situ hybridization (FISH) using 16S rRNA-targeted oligonucleotide probes for B. coagulans, Bcoa191, and LAC722(L), a group-specific probe for a wide range of mesophilic lactic acid bacteria was applied. The dominancy of mesophilic lactic acid bacteria at lower temperatures, and that of B. coagulans at higher temperatures were confirmed. By using a saccharified liquid of collected kitchen refuse, 86 g/l of L-lactic acid was accumulated under nonsterile conditions by a 5-d incubation at 55 degrees C, pH 6.5, with 53% carbon yield and 97% optical purity. To conclude, high temperature open lactic acid fermentation is a simple and promising method for producing high-grade L-lactic acid from biomass waste, and FISH analysis of such mixed-culture systems is helpful for monitoring the microflora in these cultures.

Permeabilization and lysis induced by bacteriocins and its effect on aldehyde formation by Lactococcus lactis

Permeabilization induced by lacticin 3147, lactococcins A, B and M, enterocin AS-48 and nisin, bacteriocins described as cell membrane-pore forming and lytic agents, enhanced in all cases aldehyde formation by Lactococcus lactis IFPL730. Nevertheless, the conversion of isoleucine into 2-methylbutyraldehyde depended not only on the degree of permeabilization but also on the bacteriocin that caused the cell membrane damage. The highest values of 2-methylbutyraldehyde corresponded to cell suspensions containing lacticin 3147 and lactococcins, treatments that provoked further lysis in addition to induced permeabilization.

The continuing story of class IIa bacteriocins

Many bacteria produce antimicrobial peptides, which are also referred to as peptide bacteriocins. The class IIa bacteriocins, often designated pediocin-like bacteriocins, constitute the most dominant group of antimicrobial peptides produced by lactic acid bacteria. The bacteriocins that belong to this class are structurally related and kill target cells by membrane permeabilization. Despite their structural similarity, class IIa bacteriocins display different target cell specificities. In the search for new antibiotic substances, the class IIa bacteriocins have been identified as promising new candidates and have thus received much attention. They kill some pathogenic bacteria (e.g., Listeria) with high efficiency, and they constitute a good model system for structure-function analyses of antimicrobial peptides in general. This review focuses on class IIa bacteriocins, especially on their structure, function, mode of action, biosynthesis, bacteriocin immunity, and current food applications. The genetics and biosynthesis of class IIa bacteriocins are well understood. The bacteriocins are ribosomally synthesized with an N-terminal leader sequence, which is cleaved off upon secretion. After externalization, the class IIa bacteriocins attach to potential target cells and, through electrostatic and hydrophobic interactions, subsequently permeabilize the cell membrane of sensitive cells. Recent observations suggest that a chiral interaction and possibly the presence of a mannose permease protein on the target cell surface are required for a bacteria to be sensitive to class IIa bacteriocins. There is also substantial evidence that the C-terminal half penetrates into the target cell membrane, and it plays an important role in determining the target cell specificity of these bacteriocins. Immunity proteins protect the bacteriocin producer from the bacteriocin it secretes. The three-dimensional structures of two class IIa immunity proteins have been determined, and it has been shown that the C-terminal halves of these cytosolic four-helix bundle proteins specify which class IIa bacteriocin they protect against.

Purification and sequencing of cerein 7B, a novel bacteriocin produced by Bacillus cereus Bc7

Cerein 7B is a new bacteriocin produced simultaneously with cerein 7A by Bacillus cereus Bc7 in liquid brain heart infusion cultures. Both bacteriocins are not synergistic. The two peptides have been purified to homogeneity by hydrophobic interaction, cation exchange and reverse-phase liquid chromatography. They can be distinguished by their N-terminal amino acid sequences N-Gly-Trp-Gly-Asp-Val-Leu (7A) and N-Gly-Trp-Trp-Asn-Ser-Trp-Gly-Lys (7B). Pre-cerein 7B is 74 amino acids long and contains an 18 aminoacid double-glycine type leader sequence that is removed to produce the mature bacteriocin. The leader peptide sequence is related to that of sec-independent secretion signals suggesting that cerein 7B belongs to class II sec-independent bacteriocins.

A novel bacteriocin, thuricin 17, produced by plant growth promoting rhizobacteria strain Bacillus thuringiensis NEB17: isolation and classification

AIMS

The aim of this study was to identify and characterize a compound produced by the plant growth promoting bacterium, Bacillus thuringiensis non-Bradyrhizobium Endophytic Bacterium 17.

METHODS AND RESULTS

The bacterial peptide was analysed and purified via HPLC. Using the disk diffusion assay this peptide inhibited the growth of 16/19 B. thuringiensis strains, 4/4 Bacillus cereus strains, among others, as well as a Gram-negative strain Escherichia coli MM294 (pBS42). Both bactericidal and bacteristatic effects were observed on B. cereus ATCC 14579 and bactericidal effects were observed on B. thuringiensis ssp. thuringiensis Bt1267. The molecular weight of the peptide was estimated via SDS-PAGE and confirmed with Matrix Assisted Laser Desorption Ionization Quadrapole Time of Flight mass spectrometry; its weight is 3162 Da. The peptide is biologically active after exposure to 100 degrees C for 15 min, and within the pH range 1.00-9.25. Its activity disappeared when treated with proteinase K and protease, but not with alpha-amylase or catalase.

CONCLUSIONS

We conclude that this is the first report of a bacteriocin produced by a plant growth promoting rhizobacteria (B. thuringiensis) species and have named the bacteriocin thuricin 17.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our work has characterized a bacteriocin produced by a plant growth promoting bacterium. This strain is previously reported to increase soya bean nodulation.

Bacteriocins: developing innate immunity for food

Bacteriocins are bacterially produced antimicrobial peptides with narrow or broad host ranges. Many bacteriocins are produced by food-grade lactic acid bacteria, a phenomenon which offers food scientists the possibility of directing or preventing the development of specific bacterial species in food. This can be particularly useful in preservation or food safety applications, but also has implications for the development of desirable flora in fermented food. In this sense, bacteriocins can be used to confer a rudimentary form of innate immunity to foodstuffs, helping processors extend their control over the food flora long after manufacture.

Bacteriocins: developing innate immunity for food

Bacteriocins are bacterially produced antimicrobial peptides with narrow or broad host ranges. Many bacteriocins are produced by food-grade lactic acid bacteria, a phenomenon which offers food scientists the possibility of directing or preventing the development of specific bacterial species in food. This can be particularly useful in preservation or food safety applications, but also has implications for the development of desirable flora in fermented food. In this sense, bacteriocins can be used to confer a rudimentary form of innate immunity to foodstuffs, helping processors extend their control over the food flora long after manufacture.

Expression of mptC of Listeria monocytogenes induces sensitivity to class IIa bacteriocins in Lactococcus lactis

Sensitivity to class IIa bacteriocins from lactic acid bacteria was recently associated with the mannose phosphotransferase system (PTS) permease, , in Listeria monocytogenes. To assess the involvement of this protein complex in class IIa bacteriocin activity, the mptACD operon, encoding , was heterologously expressed in an insensitive species, namely Lactococcus lactis, using the NICE double plasmid system. Upon induction of the cloned operon, the recombinant Lc. lactis became sensitive to leucocin A. Pediocin PA-1 and enterocin A also showed inhibitory activity against Lc. lactis cultures expressing mptACD. Furthermore, the role of the three genes of the mptACD operon was investigated. Derivative plasmids containing various combinations of these three genes were made from the parental mptACD plasmid by divergent PCR. The results showed that expression of mptC alone is sufficient to confer sensitivity to class IIa bacteriocins in Lc. lactis.

Shigella flexneri strains produce bacteriocins active against members of the human microbial intestinal flora

The principal aim of this work was to detect the bacteriocinogenic capacity of S. flexneri strains on members of the human intestinal flora. A total of 49 bacteriocinogenic S. flexneri strains were isolated from individuals of both sexes and different ages. The bacteriocins were detected by means of the drop method using E. coli and B. fragilis as target strains. The serotypes of the S. flexneri were determined. The producer capacity of bacteriocins was analysed in 10 different colonies of the same cellular clone and also the arbitrary units were determined. The highest number of bacteriocinogenic S. flexneri strains were obtained from diarrhoeal individuals from 0-10 years old and the S. flexneri serotype 2a was the most abundant. It was demonstrated that E. coli and B. fragilis isolated from the normal intestinal flora of healthy individuals were susceptible to the bacteriocinogenic S. flexneri strains. By means of the determination of arbitrary units per ml of the bacteriocin, it was demonstrated that colonies from a single colony isolate of a same clone of bacteriocinogenic S. flexneri produce different quantities of bacteriocin.

pbp2229-mediated nisin resistance mechanism in Listeria monocytogenes confers cross-protection to class IIa bacteriocins and affects virulence gene expression

It was previously shown that enhanced nisin resistance in some mutants was associated with increased expression of three genes, pbp2229, hpk1021, and lmo2487, encoding a penicillin-binding protein, a histidine kinase, and a protein of unknown function, respectively. In the present work, we determined the direct role of the three genes in nisin resistance. Interruption of pbp2229 and hpk1021 eliminated the nisin resistance phenotype. Interruption of hpk1021 additionally abolished the increase in pbp2229 expression. The results indicate that this nisin resistance mechanism is caused directly by the increase in pbp2229 expression, which in turn is brought about by the increase in hpk1021 expression. We also found a degree of cross-protection between nisin and class IIa bacteriocins and investigated possible mechanisms. The expression of virulence genes in one nisin-resistant mutant and two class IIa bacteriocin-resistant mutants of the same wild-type strain was analyzed, and each mutant consistently showed either an increase or a decrease in the expression of virulence genes (prfA-regulated as well as prfA-independent genes). Although the changes mostly were moderate, the consistency indicates that a mutant-specific change in virulence may occur concomitantly with bacteriocin resistance development.

Purification of antilisterial bacteriocins

In recent years, numerous contamination outbreaks, involving various pathogens (i.e., Listeria and Salmonella), have increased concern over food preservation. Research efforts have focused on the discovery of new molecules targeting such foodborne pathogens and therefore able to inhibit and or kill them. Lactic acid bacteria (LAB) extensively used in fermented foods for thousands of years not only improve their flavor and texture but also inhibit pathogenic and spoilage microorganisms. LAB inhibitory activity is primarily owing to pH decrease and competition for substrates. Antagonistic activity of LAB also depends on secreted antimicrobial compounds with a poor selectivity, such as metabolic compounds (i.e., hydrogen peroxide, acetoin, and others) or more specific ones like bacteriocins. The latter are proteinaceous compounds, ribosomally synthesized and subsequently secreted by Gram-positive as well as Gram-negative bacteria. Their antimicrobial activity is generally restricted to strains phylogenetically related to the producers.A classification of bacteriocins produced by LAB was first proposed by Klaenhammer in 1993 and was modified by Nes et al. in 1996; class I and class II bacteriocins are the most abundant and thoroughly studied. Bacteriocins from both classes exhibit antilisterial activity. Class I bacteriocins, namely, lantibiotics, have been widely studied, and among them, nisin is used in many countries as a preservative in food products. These bacteriocins are characterized by the presence, in their primary structure, of post-translationally modified amino acid residues (i.e., lanthionine and methylanthionine) that are formed. Class II bacteriocins, containing three subclasses, consist of small peptides that do not bear any modified amino acid residue. The most studied subclass corresponds to class IIa, also termed anti-Listeria bacteriocins. These peptides share strong structural homologies in their N-terminal domain, with the presence of one disulfide bond and a net positive charge. Their C-terminal domain is more variable but appears quite hydrophobic. Moreover, some of these bacteriocins, namely, sakacin G, pediocin PA-1, enterocin A, coagulin, and divercin V41, are characterized by the presence of a second disulfide bond in the C-terminal region.

[Bacteriocins: criteria, classification, characteristics, methods of detection]

The review on bacteriocins of Gram negative and Gram positive bacteria. Criteria making it possible to regard antagonistic substances as bateriocins or bacteriocin-like substances and on their classification are presented. Examples of bacteriocins naming depending on the taxonomic position of the producer culture are given. Information on the physico-chemical and biological properties of bacteriocins and their purification is presented as well as on detection tools of bacteriocins in microorganisms and evaluation of the producer activity of the bacteriological culture.

High production system of the antibacterial peptide PLG-1

Propionibacterium thoenii P-127 produces and releases to the growth medium antibacterial agents that can be used as natural preservatives. The concentrations of these antibacterial agents in the growth medium are very low, and their activity can be detected only in concentrated medium, even in a bioreactor. A simple and efficient system to produce propionicin PLG-1 without the use of a bioreactor was investigated. Fermentation in screw-cap bottles without shaking produced antibacterial activity similar to that of fermentation in plates, but in a shorter time. Sodium lactate medium (NaLa) was found to be the most supportive for PLG-1 production compared to lactic acid bacteria media such as M-17 or beet molasses/corn. The initial concentration of the carbon source, sodium lactate, agar concentration, and the initial pH of the medium affected the synthesis of PLG-1. Additions of NaCl up to 1% showed no effect on the antibacterial agent production. The optimal conditions for production of the antibacterial agent were fermentation for 9 days in screw-cap bottles in modified NaLa medium (M-NaLa) containing 1% yeast extract, 1% tryptic soy broth, 0.9% lactic acid, and 0.6% agar, adjusted to pH of 9.

Bacteriocins: evolution, ecology, and application

Microbes produce an extraordinary array of microbial defense systems. These include classical antibiotics, metabolic by-products, lytic agents, numerous types of protein exotoxins, and bacteriocins. The abundance and diversity of this potent arsenal of weapons are clear. Less clear are their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the most abundant and diverse family of microbial defense systems: the bacteriocins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics. In the latter half of this review we focus on the potential role bacteriocins may play in addressing human health concerns and the current role they serve in food preservation.

The effect of bovicin HC5, a bacteriocin from Streptococcus bovis HC5, on ruminal methane production in vitro

Methane represents a loss of feed energy to ruminant animals, and nutritionists have sought methods of inhibiting ruminal methane production. When mixed ruminal bacteria (approximately 400 mg protein ml(-1)) from a cow fed timothy hay were incubated in vitro with carbon dioxide and hydrogen (0.5 atm) for less than 8 h, the first-order rate of methane production was 17 micromol ml(-1). Semi-purified bacteriocin from Streptococcus bovis HC5 (bovicin HC5) inhibited methane production, by as much as 50%, and even a low concentration of bovicin HC5 (128 activity units (AU) ml(-1)) caused a significant decrease. Mixed ruminal bacteria that were transferred successively retained their ability to produce methane from carbon dioxide and hydrogen, and the first-order rate of methane production did not decrease. Cultures that were treated with bovicin HC5 (128 AU ml(-1)) gradually lost their ability to produce methane, and methane was not detected after four transfers. These latter results indicated that ruminal methanogens could not adapt and become resistant to bovicin HC5. When the chromosomal DNA was amplified with 16S rDNA primers specific to archaea, digested with restriction enzymes (HhaI and HaeIII) and separated on agarose gels, approximately 12 fragments were observed. DNA from control and treated cultures (third transfer) had the same fragment pattern indicating bovicin HC5 was not selective. Given the perception that the routine use of antibiotics in animal feeds should be avoided, bacteriocins may provide an alternative strategy for decreasing ruminal methane production.

[Production of bacteriocins by gram-positive bacteria and the mechanisms of transcriptional regulation]

The mechanisms of production of bacteriocins in Gram-positive bacteria and the main distinctions of these bacteriocins from the bacteriocins of Gram-negative bacteria (colicins) are outlined. A classification of antibacterial peptides is presented, and most of known class I and II peptides are pointed out. In Gram-positive bacteria, the cases of bacteriocin-associated quorum sensing are examined. For these cases, the structure of loci containing the genes of regulatory systems, transport, immunity, processing, and posttranslational modification of antibacterial peptides are described. All known regulatory sites for class II bacteriocins are presented. A description of the putative regulatory sites found by us and their classification are provided. The evolutionary tree of transcriptional response regulators is shown to correspond to the tree of their recognition sites.

Ribosomally synthesized antibacterial peptides in Gram positive bacteria

The emergence of multidrug-resistant pathogens that has caused a serious problem in hospitals worldwide, has intensified the search for novel drugs, in order to replace or to be used in complement with the existing antibiotics. In this connection much interest has been focused on a group of antimicrobial peptides, so-called bacteriocins. These antagonising peptides, which are gene-encoded in contrast to those made by multi-enzyme-complexes, share some common physico-chemical properties, such as being small, cationic, amphiphilic and often being membrane active. However, they differ greatly from each other in their primary sequence and exhibit an impressively large inhibitory spectrum which covers almost all bacterial genera, including many important pathogens and food-spoilage bacteria. Many of these peptides are produced by lactic acid bacteria, organisms which have been used by man from ancient time in diverse fermentation processes, to improve and/or prolong self-life of many food and feed products. Numerous bacteriocins have been purified and characterised in great detail, both at biochemical and genetic levels. Still, novel bacteriocins with new properties are reported in an increasing number in recent years. In this review we will give a brief status quo of the present knowledge on bacteriocin research; thus different aspects such as their diversity in nature, biochemical properties, modes of action, biosynthesis and genetics will be treated.

Bacteriocins: safe, natural antimicrobials for food preservation

Bacteriocins are antibacterial proteins produced by bacteria that kill or inhibit the growth of other bacteria. Many lactic acid bacteria (LAB) produce a high diversity of different bacteriocins. Though these bacteriocins are produced by LAB found in numerous fermented and non-fermented foods, nisin is currently the only bacteriocin widely used as a food preservative. Many bacteriocins have been characterized biochemically and genetically, and though there is a basic understanding of their structure-function, biosynthesis, and mode of action, many aspects of these compounds are still unknown. This article gives an overview of bacteriocin applications, and differentiates bacteriocins from antibiotics. A comparison of the synthesis. mode of action, resistance and safety of the two types of molecules is covered. Toxicity data exist for only a few bacteriocins, but research and their long-time intentional use strongly suggest that bacteriocins can be safely used.

Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers

In this study, we succeeded in differentiating Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus paraplantarum by means of recA gene sequence comparison. Short homologous regions of about 360 bp were amplified by PCR with degenerate consensus primers, sequenced, and analyzed, and 322 bp were considered for the inference of phylogenetic trees. Phylograms, obtained by parsimony, maximum likelihood, and analysis of data matrices with the neighbor-joining model, were coherent and clearly separated the three species. The validity of the recA gene and RecA protein as phylogenetic markers is discussed. Based on the same sequences, species-specific primers were designed, and a multiplex PCR protocol for the simultaneous distinction of these bacteria was optimized. The sizes of the amplicons were 318 bp for L. plantarum, 218 bp for L. pentosus, and 107 bp for L. paraplantarum. This strategy permitted the unambiguous identification of strains belonging to L. plantarum, L. pentosus, and L. paraplantarum in a single reaction, indicating its applicability to the speciation of isolates of the L. plantarum group.

Classification and mode of action of membrane-active bacteriocins produced by gram-positive bacteria

Bacteriocins are ribosomally synthesized antimicrobial peptides produced by microorganisms belonging to different eubacterial taxonomic branches. Most of them are small cationic membrane-active compounds that form pores in the target cells, disrupting membrane potentials and causing cell death. The production of small cationic peptides with antibacterial activity is a defense strategy found not only in bacteria, but also in plants and animals. Bacteriocins are classified according to different criteria by different authors; in this review, we will summarize the principal bacteriocin classifications, highlight their main physical and chemical characteristics, and describe the mechanism of some selected bacteriocins that act at the membrane level.

Antimicrobial peptides of lactic acid bacteria: mode of action, genetics and biosynthesis

A survey is given of the main classes of bacteriocins, produced by lactic acid bacteria: I. lantibiotics II. small heat-stable non-lanthionine containing membrane-active peptides and III. large heat-labile proteins. First, their mode of action is detailed, with emphasis on pore formation in the cytoplasmatic membrane. Subsequently, the molecular genetics of several classes of bacteriocins are described in detail, with special attention to nisin as the most prominent example of the lantibiotic-class. Of the small non-lanthionine bacteriocin class, the Lactococcus lactococcins, and the Lactobacillus sakacin A and plantaricin A-bacteriocins are discussed. The principles and mechanisms of immunity and resistance towards bacteriocins are also briefly reported. The biosynthesis of bacteriocins is treated in depth with emphasis on response regulation, post-translational modification, secretion and proteolytic activation of bacteriocin precursors. To conclude, the role of the leader peptides is outlined and a conceptual model for bacteriocin maturation is proposed.

Characterization of recurrent and sporadic Listeria monocytogenes isolates from raw milk and nondairy foods by pulsed-field gel electrophoresis, monocin typing, plasmid profiling, and cadmium and antibiotic resistance determination

Following previous surveys to assess the incidence of Listeria monocytogenes in raw milk and nondairy foods processed in Northern Ireland, isolates were characterized as recurrent or sporadic on the basis of multilocus enzyme electrophoresis (MEE) analysis and restriction fragment length polymorphism typing. In the present study, 45 representative recurrent and sporadic electrophoretic types (ETs) previously identified by MEE were subjected to pulsed-field gel electrophoresis (PFGE) of genomic DNA macrorestriction fragments, monocin typing, plasmid profiling, and an examination of resistance to cadmium and nine different antibiotics. Although PFGE proved to be capable of subdividing a number of recurrent and sporadic ETs, the grouping of strains arrived at by PFGE and MEE were in broad agreement, and previous conclusions regarding the designation of L. monocytogenes strains as recurrent or sporadic remained unaltered. It is considered that PFGE was able to detect minor genetic changes in recurrent ETs which occurred during the time period in which food surveys were carried out. Production of type E monocin (Types A to E were found among the 45 strains), plasmid carriage, and resistance to cadmium occurred more frequently in recurrent than in sporadic strains and may be important with regard to the ability of L. monocytogenes to persist in food and food-processing environments. Only 2 of 45 strains showed resistance to any of the nine antibiotics tested: two sporadic strains were resistant to tetracycline (MIC, 64 microg x ml(-1)).

Characterization and purification of a bacteriocin produced by a potential probiotic culture, Lactobacillus acidophilus 30SC

Lactobacillus acidophilus 30SC was tested for its potential as a probiotic culture. The strain exhibited good acid tolerance in an artificial gastric solution as well as bile resistance in media containing 0.3% bile acids. The strain produced a heat-stable antimicrobial compound that was shown to be proteinaceous in nature and, therefore, referred to as a bacteriocin. The bacteriocin was active over a wide pH range and inhibited a number of gram-positive bacteria including Listeria ivanovii and pathogenic strains. The bacteriocin was purified by 50% ammonium sulfate precipitation followed by hydrophobic interaction column chromatography. The SDS-PAGE of the active fractions resulted in a single band with estimated molecular mass of 3.5 kDa. These results demonstrate the potential of L. acidophilus 30SC as a probiotic culture that can be utilized in the manufacturing of dairy foods and dietary supplements.

The rpoN gene of Enterococcus faecalis directs sensitivity to subclass IIa bacteriocins

The final sigma 54 factor has been previously described to be involved in Listeria monocytogenes sensitivity to mesentericin Y105, a subclass IIa bacteriocin. Here, we identified the rpoN gene, encoding final sigma 54, of Enterococcus faecalis JH2-2 and showed that its interruption leads to E. faecalis resistance to different subclass IIa bacteriocins. Moreover, this rpoN mutant remained sensitive to nisin, a class I bacteriocin, suggesting that final sigma 54 is especially involved in sensitivity to subclass IIa bacteriocins.

Similarity of bacteriocin activity profiles of mutans streptococci within the family when the children acquire the strains after the age of 5

It has been shown that there is a window of infectivity for mutans streptococci between the ages of 19 and 31 months, when many children acquire mutans streptococci transmitted from their mothers. Part of the children that escape this window acquire mutans streptococci at a later age. In this group, maternal transmission is expected to be less prevalent. The present study compared the bacteriocin activity profiles of mutans streptococci isolated from mothers, fathers and children when the children acquired the mutans streptococci between the ages of 5 and 11. Twelve families were randomly selected from a group of 11-year-old children who were known to have acquired mutans streptococci during this age period. From the saliva of the mothers (n = 12), fathers (n = 8) and children (n = 12) approximately 30 mutans streptococci strains were isolated. All isolates were tested twice for bacteriocin activity against 21 indicator strains with a double-layer technique. Bacteriocin activity of strains was considered to be different when the number of strains against which bacteriocin was produced differed >1 or when the width of one or more inhibition zones differed > or =4 mm. In 7/12 mother-child pairs similar profiles were found. In the 8 father-child pairs similar profiles were only found on 2 occasions. In these 2 families, all 3 ( mother, father and child) harboured strains with a similar profile. In 4/8 father-mother pairs similar profiles were found. There was no correlation between the prevalence of mutans streptococci strains, the number of indicator strains against which the strains made bacteriocin, nor the mean size of the inhibition zones and the presence of similarity of bacteriocin activity profiles of mutans streptococci within the family members. The results show that even when a child acquires mutans streptococci after the age of 5, there may be similarity between mutans streptococci in mother, father and child, indicating that transmission between the family members occurs.

Class II antimicrobial peptides from lactic acid bacteria

Strains of lactic acid bacteria (LAB) produce a wide variety of antibacterial peptides. More than fifty of these so-called peptide bacteriocins have been isolated in the last few years. They contain 20-60 amino acids, and are cationic and hydrophobic in nature. Several of these bacteriocins consist of two complementary peptides. The peptide bacteriocins of LAB are inhibitory at concentrations in the nanomolar range, and cause membrane permeabilization and leakage of intracellular components in sensitive cells. The inhibitory spectrum is limited to gram-positive bacteria, and in many cases to bacteria closely related to the producing strain. Among the target organisms are food spoilage bacteria and pathogens such as Listeria, so that many of these antimicrobial peptides could have a potential as food preservatives as well as in medical applications.

[Analysis of bacteriocinogenic properties of Yersinia enterocolitica strains]

The aim of the study was the investigation of bacteriocinogenic properties of 102 Yersinia enterocolitica strains. The influence of selected factors on the production of bacteriocins by Y. enterocolitica and properties of jersiniacin 44JPSBKOH were also investigated. Bacteriocinogenic properties of Y. enterocolitica strains were tested by using the delayed cross-streaking method. It was found that the production of bacteriocins by Y. enterocolitica depended on the type of media on which the producer and indicator strains were grown. It turned out that some strains of Y. enterocolitica showed bacteriocinogenic properties at 25 degrees C, 30 degrees C and 37 degrees C irrespective of the presence of manganese ions in medium. In the presence of iron ions these strains showed bacteriocinogenic properties only at 25 degrees C. Y. enterocolitica strains which required Mn2+ or Mn7+ ions for bacteriocins production showed this activity only at 25 degrees C but in presence of Fe3+ ions they had no bacteriocinogenic properties. The partially purified jersiniacin 44JPSBKOH is a protein, its molecular weight was estimated to be 40 kDa. Yersiniacin 44JPSBKOH was active in the pH range of 3 to 9. Its bactericidal activity was rapidly lost when heated to 100 degrees C and treated with proteolytic enzymes. Yersiniacin 44JPSBKOH showed bactericidal activity against other Y. enterocolitica strains and some strains of Pseudomonas aeruginosa isolated from humans.

Characterization and mechanism of action of cerein 7, a bacteriocin produced by Bacillus cereus Bc7

Cerein 7 is a peptidic antibiotic produced by Bacillus cereus Bc7 (CECT 5148) at the end of exponential growth but before sporulation onset. Cerein 7 has a broad spectrum of antibacterial activity against Gram-positive bacteria, but it is inactive against Gram-negative bacteria. The sequence of its amino-terminal end and its characteristics of hydrophobicity and molecular mass make cerein 7 unique among the bacteriocins produced by the soil bacterium B. cereus. In this paper a further characterization of cerein 7 is presented, it is shown that it can be classified as a Klaenhammer's class II bacteriocin and that its mode of action corresponds to that of a membrane-active compound.

Identification and nucleotide sequence of genes involved in the synthesis of lactocin 705, a two-peptide bacteriocin from Lactobacillus casei CRL 705

The structural gene determinants of lactocin 705, a bacteriocin produced by Lactobacillus casei CRL 705, have been amplified from a plasmid of approximately 35 kb and sequenced. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705alpha and 705beta) of 33 amino acid residues each. These peptides are synthesized as precursors with signal sequences of the double-glycine type, which exhibited high identities with the leader peptides of plantaricin S and J from Lactobacillus plantarum, brochocin C from Brochotrix campestris, sakacin P from Lactobacillus sake, and the competence stimulating peptides from Streptococcus gordonii and Streptococcus mitis. However, the two mature bacteriocins 705alpha and 705beta do not show significant similarity to other sequences in the databases.

Typing of Listeria monocytogenes by monocin and phage receptors

One hundred strains of Listeria monocytogenes from both sporadic and epidemic cases were typed by monocin production combined with phage receptor and reverse phage receptor methods. The monocin-phage combination gave 72 types with 100% typability and 97% reproducibility. The results were compared to those of serotyping, phage typing, ribotyping, multilocus enzyme electrophoresis, restriction enzyme analysis and RAPD (random amplification of polymorphic DNA). The monocin/phage types were comparable in terms of discrimination with other methods for epidemiological investigations. The index of discrimination of using the monocin typing and phage receptor/reverse phage receptor method combination (0.99) for both the 87 epidemiologically unrelated strains and the epidemiologically important serogroup 4 strains was the highest of the seven different methods analysed. This combination of methods was simple, highly discriminatory and reproducible and can be carried out in a non-specialized laboratory. However, like most of the other Listeria typing methods, both the method and the indicator test strains need to be standardized.

Novel lantibiotics and their pre-peptides

In recent years there has been a considerable increase in studies of bactericidal peptides produced by Gram-positive bacteria, with particular emphasis upon their potential application as food preservatives. A number of these peptides contain lanthionine and other post-translationally modified amino acid residues. The lanthionine-containing molecules (lantibiotic) appear to have evolved in two quite different lineages, type A and type B. This mini-review introduces the reader to several of the more recently described type A lantibiotics for which relatively detailed biochemical and/or genetic data has already been gathered. A wider diversity of compounds of type A lantibiotics has been described in the recent years. Novel features of some of the more recently described type A lantibiotics to be reported in this review include: a) New modifications such as D-Ala and 2-hydroxypropionyl residues, both derived from serine. b) Different types of pre-lantibiotic leader sequences. c) The apparent requirement for different numbers and types of genes for synthesis of some active type A lantibiotics. d) Cytolysin functions as both a hemolysin and a bacteriocin. e) One of the newly-described lantibiotics (lactocin S) does not have any net charge at neutral pH another (carnocin UI49) is the largest of the lantibiotics discovered and the killing action of another (cytolysin) has been shown to be depend on the interaction of two peptides.

Bacteriocins: modes of action and potentials in food preservation and control of food poisoning

Lactic acid bacteria (LAB) play an essential role in the majority of food fermentations, and a wide variety of strains are routinely employed as starter cultures in the manufacture of dairy, meat, vegetable and bakery products. One of the most important contributions of these microorganisms is the extended shelf life of the fermented product by comparison to that of the raw substrate. Growth of spoilage and pathogenic bacteria in these foods is inhibited due to competition for nutrients and the presence of starter-derived inhibitors such as lactic acid, hydrogen peroxide and bacteriocins (Ray and Daeschel, 1992). Bacteriocins, are a heterogenous group of anti-bacterial proteins that vary in spectrum of activity, mode of action, molecular weight, genetic origin and biochemical properties. Currently, artificial chemical preservatives are employed to limit the number of microorganisms capable of growing within foods, but increasing consumer awareness of potential health risks associated with some of these substances has led researchers to examine the possibility of using bacteriocins produced by LAB as biopreservatives. The major classes of bacteriocins produced by LAB include: (I) lantibiotics, (II) small heat stable peptides, (III) large heat labile proteins, and (IV) complex proteins whose activity requires the association of carbohydrate or lipid moieties (Klaenhammer, 1993). Significantly however, the inhibitory activity of these substances is confined to Gram-positive bacteria and inhibition of Gram-negatives by these bacteriocins has not been demonstrated, an observation which can be explained by a detailed analysis and comparison of the composition of Gram-positive and Gram-negative bacterial cell walls (Fig. 1). In both types the cytoplasmic membrane which forms the border between the cytoplasm and the external environment, is surrounded by a layer of peptidoglycan which is significantly thinner in Gram-negative bacteria than in Gram-positive bacteria. Gram-negative bacteria possess an additional layer, the so-called outer membrane which is composed of phospholipids, proteins and lipopolysaccharides (LPS), and this membrane is impermeable to most molecules. Nevertheless, the presence of porins in this layer will allow the free diffusion of molecules with a molecular mass below 600 Da. The smallest bacteriocins produced by lactic acid bacteria are approximately 3 kDa and are thus too large to reach their target, the cytoplasmic membrane (Klaenhammer, 1993; Stiles and Hastings, 1991). However, Stevens et al. (1991) and Ray (1993) have demonstrated that Salmonella species and other Gram-negative bacteria become sensitive to nisin after exposure to treatments that change the permeability barrier properties of the outer membrane (see below). This review will focus on the mode of action of lantibiotics (class I) and class II LAB bacteriocins and their potentials in food preservation and control of food poisoning.