Bacteriocins: nature, function and structure

Phenotyping the Chemical Communications of the Intestinal Microbiota and the Host: Secondary Bile Acids as Postbiotics

The current definition of a postbiotic is a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Postbiotics can be mainly classified as metabolites, derived from intestinal bacterial fermentation, or structural components, as intrinsic constituents of the microbial cell. Secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA) are bacterial metabolites generated by the enzymatic modifications of primary bile acids by microbial enzymes. Secondary bile acids function as receptor ligands modulating the activity of a family of bile-acid-regulated receptors (BARRs), including GPBAR1, Vitamin D (VDR) receptor and RORγT expressed by various cell types within the entire human body. Secondary bile acids integrate the definition of postbiotics, exerting potential beneficial effects on human health given their ability to regulate multiple biological processes such as glucose metabolism, energy expenditure and inflammation/immunity. Although there is evidence that bile acids might be harmful to the intestine, most of this evidence does not account for intestinal dysbiosis. This review examines this novel conceptual framework of secondary bile acids as postbiotics and how these mediators participate in maintaining host health.

Biosynthesis, classification, properties, and applications of Weissella bacteriocins

This review aims to comprehensively chronicle the biosynthesis, classification, properties, and applications of bacteriocins produced by Weissella genus strains, particularly emphasizing their potential benefits in food preservation, human health, and animal productivity. Lactic Acid Bacteria (LAB) are a class of microorganisms well-known for their beneficial role in food fermentation, probiotics, and human health. A notable property of LAB is that they can synthesize antimicrobial peptides known as bacteriocins that exhibit antimicrobial action against both closely related and other bacteria as well. Bacteriocins produced by Weissella spp. are known to exhibit antimicrobial activity against several pathogenic bacteria including food spoilage species, making them highly invaluable for potential application in food preservation and food safety. Importantly, they provide significant health benefits to humans, including combating infections, reducing inflammation, and modulating the gut microbiota. In addition to their applications in food fermentation and probiotics, Weissella bacteriocins show promising prospects in poultry production, processing, and improving animal productivity. Future research should explore the utilization of Weissella bacteriocins in innovative food safety measures and medical applications, emphasizing their potential to combat antibiotic-resistant pathogens, enhance gut microbiota composition and function, and synergize with existing antimicrobial therapies.

BaPreS: a software tool for predicting bacteriocins using an optimal set of features

BACKGROUND

Antibiotic resistance is a major public health concern around the globe. As a result, researchers always look for new compounds to develop new antibiotic drugs for combating antibiotic-resistant bacteria. Bacteriocin becomes a promising antimicrobial agent to fight against antibiotic resistance, due to cases of both broad and narrow killing spectra. Sequence matching methods are widely used to identify bacteriocins by comparing them with the known bacteriocin sequences; however, these methods often fail to detect new bacteriocin sequences due to their high diversity. The ability to use a machine learning approach can help find new highly dissimilar bacteriocins for developing highly effective antibiotic drugs. The aim of this work is to develop a machine learning-based software tool called BaPreS (Bacteriocin Prediction Software) using an optimal set of features for detecting bacteriocin protein sequences with high accuracy. We extracted potential features from known bacteriocin and non-bacteriocin sequences by considering the physicochemical and structural properties of the protein sequences. Then we reduced the feature set using statistical justifications and recursive feature elimination technique. Finally, we built support vector machine (SVM) and random forest (RF) models using the selected features and utilized the best machine learning model to implement the software tool.

RESULTS

We applied BaPreS to an established dataset and evaluated its prediction performance. Acquired results show that the software tool can achieve a prediction accuracy of 95.54% for testing protein sequences. This tool allows users to add new bacteriocin or non-bacteriocin sequences in the training dataset to further enhance the predictive power of the tool. We compared the prediction performance of the BaPreS with a popular sequence matching-based tool and a deep learning-based method, and our software tool outperformed both.

CONCLUSIONS

BaPreS is a bacteriocin prediction tool that can be used to discover new highly dissimilar bacteriocins for developing highly effective antibiotic drugs. This software tool can be used with Windows, Linux and macOS operating systems. The open-source software package and its user manual are available at https://github.com/suraiya14/BaPreS .

The current status, challenges, and future perspectives for managing diseases of brassicas

The Brassica genus comprises the greatest diversity of agriculturally important crops. Several species from this genus are grown as vegetable and oil crops for food, animal feed and industrial purposes. In particular, B. oleracea has been extensively bred to give rise to several familiar vegetables (cabbage, broccoli, cauliflower, kale and Brussels Sprouts, etc.) that are grouped under seven major cultivars. In 2020, 96.4 million tonnes of vegetable brassicas were produced globally with a 10.6% increase over the past decade. Yet, like other crops, the production of brassicas is challenged by diseases among which, black rot, clubroot, downy mildew and turnip yellows virus have been identified by growers as the most damaging to UK production. In some cases, yield losses can reach 90% depending upon the geographic location of cultivation. This review aims to provide an overview of the key diseases of brassicas and their management practices, with respect to the biology and lifecycle of the causal pathogens. In addition, the existing controls on the market as well as those that are currently in the research and development phases were critically reviewed. There is not one specific control method that is effective against all the diseases. Generally, cultural practices prevent disease rather than reduce or eliminate disease. Chemical controls are limited, have broad-spectrum activity, are damaging to the environment and are rapidly becoming ineffective due to the evolution of resistance mechanisms by the pathogens. It is therefore important to develop integrated pest management (IPM) strategies that are tailored to geographic locations. Several knowledge gaps have been identified and listed in this review along with the future recommendations to control these four major diseases of brassicas. As such, this review paper will act as a guide to sustainably tackle pre-harvest diseases in Brassica crops to reduce food loss.

A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments

Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.

Beneficial features of pediococcus: from starter cultures and inhibitory activities to probiotic benefits

Pediococci are lactic acid bacteria (LAB) which have been used for centuries in the production of traditional fermented foods. There fermentative abilities were explored by the modern food processing industry in use of pediococci as starter cultures, enabling the production of fermented foods with distinct characteristics. Furthermore, some pediococci strains can produce bacteriocins and other antimicrobial metabolites (AMM), such as pediocins, which are increasingly being explored as bio-preservatives in various food matrices. Due to their versatility and inhibitory spectrum, pediococci bacteriocins and AMM are being extensively researched not only in the food industry, but also in veterinary and human medicine. Some of the pediococci were evaluated as potential probiotics with different beneficial areas of application associated with human and other animals' health. The main taxonomic characteristics of pediococci species are presented here, as well as and their potential roles and applications as starter cultures, as bio-preservatives and as probiotic candidates.

An Overview of the Potentialities of Antimicrobial Peptides Derived from Natural Sources

Antimicrobial peptides (AMPs) are constituents of the innate immune system in every kind of living organism. They can act by disrupting the microbial membrane or without affecting membrane stability. Interest in these small peptides stems from the fear of antibiotics and the emergence of microorganisms resistant to antibiotics. Through membrane or metabolic disruption, they defend an organism against invading bacteria, viruses, protozoa, and fungi. High efficacy and specificity, low drug interaction and toxicity, thermostability, solubility in water, and biological diversity suggest their applications in food, medicine, agriculture, animal husbandry, and aquaculture. Nanocarriers can be used to protect, deliver, and improve their bioavailability effectiveness. High cost of production could limit their use. This review summarizes the natural sources, structures, modes of action, and applications of microbial peptides in the food and pharmaceutical industries. Any restrictions on AMPs' large-scale production are also taken into consideration.

Applications of Bacteriocins of Lactic Acid Bacteria in Biotechnology and Food Preservation: A Bibliometric Review

Introduction:

Due to the growing prevalence of antibiotic resistance in microorganisms and the demand for safe food, there is increasing interest in using natural bioproducts such as the antimicrobial peptides bacteriocins to extend the shelf-life of foods. This is because of their spectrum of activity, ease of synthesis and applicability. This study reports on the global trends in lactic acid bacteria (LAB) bacteriocins based research publications in the Web of Science core collections within the last 20 years (2000-2019), with specific focus to their applications in biotechnology and food science.

Methods:

Data analysis was undertaken using VOSviewer and HistCite software to evaluate relationships between articles and visualise research linkages amongst authors, institutions and countries.

Results:

In the 20 years under review, a total of 1741 bacteriocin related articles were published, with the most cited publication examining the anti-infective activity of Lactobacillus salivarius. The highest research output was recorded by the United States, followed by Spain and China. However, Europe as a continent had the highest research output with a higher inter-institution collaboration network and stronger food safety legislations.

Discussion:

The bibliometric analysis gave insights into the research areas, cooperation network of authors, co-citation maps and co-occurrence of keywords utilized in the research field and indicates that bacteriocin-based research is highly multidisciplinary with a global reach.

Conclusion:

Key focus is on the control of foodborne disease pathogens, search for new producer organisms and approaches to improve bacteriocin yield and application. This class of antimicrobial peptides has the potential to replace chemical food preservatives in the future.

Bacteriocins from lactic acid bacteria and their potential clinical applications

Bacteriocins are ribosomally synthesized antimicrobial peptides that have long been used in the food industry. Being a highly diverse and heterogeneous group of molecules the classification is ever-evolving. Their production is widespread among bacteria; nevertheless, their biosynthesis and mode of action remain fairly similar. With the advances in drug resistance mechanisms, it is important to look for alternatives to conventional approaches. Therefore, the advantages of bacteriocin over antibiotics need to be considered to provide a scientific basis for their use. Particularly in the last decade, intensive studies look at their potential as next-generation therapeutics against drug-resistant bacteria. Bacteriocins from lactic acid bacteria are being tested as controlling agents for bacterial and viral infections; they can inhibit biofilm synthesis and have potential as contraceptives. Bioengineered peptides have shown enhanced activity and thereby indicate the lack of knowledge we possess regarding these bacteriocins. In this review, we have listed various Gram-positive LAB bacteriocins with their synthesis and mechanism of action. Recent developments in screening and purification technologies have been analyzed with an emphasis on their potential clinical applications. Although extensive research has been done to identify multifunctional bacteriocins, it is important to focus on the mechanism of action of these peptides to get them from bench to bedside.

Unraveling the Uncharacterized Domain of Carocin S2: A Ribonuclease Pectobacterium carotovorum subsp. carotovorum Bacteriocin

Carocin S2 is a bacteriocin with a low molecular weight generated by Pectobacterium carotovorum subsp. carotovorum 3F3 strain. The caroS2K gene, which is found in the genomic DNA alongside the caroS2I gene, which codes for an immunity protein, encodes this bacteriocin. We explored the residues responsible for Carocin S2’s cytotoxic or RNA-se activity using a structure-based mutagenesis approach. The minimal antibiotic functional region starts at Lys691 and ends at Arg783, according to mutational research. Two residues in the identified region, Phe760 and Ser762, however, are unable to demonstrate this activity, suggesting that these sites may interact with another domain. Small modifications in the secondary structure of mutant caroS2K were revealed by circular dichroism (CD) spectroscopy and intrinsic tryptophan fluorescence (ITF), showing ribosomal RNA cleavage in the active site. A co-immunoprecipitation test indicated that the immunity protein CaroS2I binds to CaroS2K’s C-terminus, while a region under the uncharacterized Domain III inhibits association of N-terminally truncated CaroS2K from interacting with CaroS2I. Carocin S2, a ribosomal ribonuclease bacteriocin, is the first to be identified with a domain III that encodes the cytotoxic residues as well as the binding sites between its immunity and killer proteins.

Antimicrobial Peptides: An Update on Classifications and Databases

Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.

Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context

Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.

Bacteriocins Produced by LAB Isolated from Cheeses within the Period 2009-2021: a Review

A survey is presented concerning original research articles published in well-reputed scientific journals on the isolation of lactic acid bacteria (LAB) from cheeses worldwide, where researchers evaluated the bacteriocin production by such isolates in searching for novel functional peptides that can exhibit potential for biotechnological applications. Seventy-one articles were published in the period of study, with contributions being American (45%), Asiatic (28%), and European (21%), being Brazil-USA-Mexico, Turkey-China, and France-Italy the countries that contributed the most for each said continent, respectively. Most of the isolated LAB belong to the genera Enterococcus (35%), Lactobacillus (30%), Lactococcus (14%), and Pediococcus (10%), coming from soft (64%), hard (27%), and semi-hard (9%) cheeses, predominantly. Also, scholars focused mainly on the food biopreservation (81%) and pharmaceutical field (18%) potential applications.

Bacteriocins, A Natural Weapon Against Bacterial Contamination for Greater Safety and Preservation of Food: A Review

Nowadays, consumers have become increasingly attentive to human health and the use of more natural products. Consequently, the demand for natural preservatives in the food industry is more frequent. This has led to intense research to discover new antimicrobial compounds of natural origin that could effectively fight foodborne pathogens. This research aims to safeguard the health of consumers and, above all, to avoid potentially harmful chemical compounds. Lactobacillus is a bacterial genus belonging to the Lactic Acid Bacteria and many strains are defined GRAS, generally recognized as safe. These strains are able to produce substances with antibacterial activity against food spoilage bacteria and contaminating pathogens: the bacteriocins. The aim of this review was to focus on this genus and its capability to produce antibacterial peptides. The review collected all the information from the last few years about bacteriocins produced by Lactobacillus strains, isolated from clinical or food samples, with remarkable antimicrobial activities useful for being exploited in the food field. In addition, the advantages and disadvantages of their use and the possible ways of improvement for industrial applications were described.

Thuricin17 Production and Proteome Differences in Bacillus thuringiensis NEB17 Cell-Free Supernatant Under NaCl Stress

Bacillus thuringiensis strain NEB17, produces a bacteriocin, thuricin17 (Th17) and is known to promote the growth more effectively under salt stress conditions. In this study, bacterial salt stress tolerance screening and the possible changes in its secretome under two levels of NaCl stress was evaluated. The salt tolerance screening suggested that the bacterium is able to grow and survive in up to 900 mM NaCl. Thuricin17 production at salt levels from 100 to 500 mM NaCl was quantified using High Performance Liquid Chromatography (HPLC). Salt stress adversely affected the production of Th17 at levels as low as 100 mM NaCl; and the production stopped at 500 mM NaCl, despite the bacterium thriving at these salt levels. Hence, a comparative proteomic study was conducted on the supernatant of the bacterium after 42 h of growth, when Th17 production peaked in the control culture, as determined by Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS). Optimal (salt free) bacterial culture served as a control and 200 and 500 mM NaCl as stress conditions. As salt levels increased, the major enzyme classes, transferases, hydrolases, lyases, and ligases showed increased abundance as compared to the control, mostly related to molecular function mechanisms. Some of the notable up-regulated proteins in 500 mM NaCl stress conditions included an S-layer protein, chitin binding domain 3 protein, enterotoxins, phosphopentomutase, glucose 6-phosphate isomerase and bacterial translation initiation factor; while notable down-regulated proteins included hemolytic enterotoxin, phospholipase, sphingomyelinase C, cold shock DNA-binding protein family and alcohol dehydrogenase. These results indicate that, as the salt stress levels increase, the bacterium probably shuts down the production of Th17 and regulates its molecular functional mechanisms to overcome stress. This study indicates that end users have the option of using Th17 as a biostimulant or the live bacterial inoculum depending on the soil salt characteristics, for crop production. The mass spectrometry proteomics data have been deposited to Mass Spectrometry Interactive Virtual Environment (MassIVE) with the dataset identifier PXD024069, and doi: 10.25345/C5RB8T.

Identification and characterization of the bacteriocin Carocin S3 from the multiple bacteriocin producing strain of Pectobacterium carotovorum subsp. carotovorum

Background

Pectobacterium carotovorum subsp. carotovorum belongs to the Enterobacteriaceae family, which causes soft-rot disease in numerous plants worldwide resulting in significant economic losses. Results from our previous studies showed that the strain H-rif-8-6 produces low-molecular-weight bacteriocin (LMWB) Carocin S1. Interestingly, TH22–10, the caroS1K:Tn5 insertional mutant in H-rif-8-6, loses Carocin S1 producing ability, but still produces other LMWBs which the indicator strain SP33 can detect. The SP33 is one of the many strains that are sensitive toward the cytotoxic effects of Carocin S3K, but not Carocin S1. The result revealed that H-rif-8-6 is a multiple-bacteriocin producing strain.

Results

In this study, a 4.1-kb DNA fragment was isolated from the chromosomal DNA of Pcc strain, H-rif-8-6, by a DNA probe using the caroS1K gene as the template. DNA sequencing and analysis by GenBank revealed two complete open reading frames (ORFs), designated ORF1 and ORF2, which were identified within the sequence fragment. ORF1 and ORF2, similar to the identified carocin S2 genes, encode the killer (Carocin S3K) and the immunity (Carocin S3I) proteins, respectively, which were homologous to the colicin E3 gene. Carocin S3K and Carocin S3I were expressed, isolated, and purified in Escherichia coli BL21 after subcloning of the expression plasmid pGS3KI or pGSK3I. SDS-PAGE analysis showed that the relative masses of Carocin S3K and Carocin S3I were 95.6 kDa and 10.2 kDa, respectively. The results reveal that Carocin S3K has higher antimicrobial and specific antimicrobial activities for Pcc along with a nuclease activity than Carocin S3I. However, Carocin S3I inhibits the activity of Carocin S3K. Interestingly, a high concentration of Carocin S3I protein is also a DNA nuclease, and Carocin S3K also inhibits its activity.

Conclusion

This study showed that another type of bacteriocin was found in Pectobacterium carotovorum. This new type of bacteriocin, Carocin S3, has the killer protein, Carocin S3K, and the immunity protein, Carocin S3I.

In Vitro Evaluation of Potential Probiotic Strain Lactococcus lactis Gh1 and Its Bacteriocin-Like Inhibitory Substances for Potential Use in the Food Industry

Determination of a microbial strain for the joining into sustenance items requires both in vitro and in vivo assessment. A newly isolated bacteriocin-like inhibitory substance (BLIS) producing lactic acid bacterium, Lactococcus lactis Gh1, was isolated from a traditional flavour enhancer and evaluated in vitro for its potential applications in the food industry. Results from this study showed that L. lactis was tolerant to NaCl (≤ 4.0%, w/v), phenol (≤ 0.4%, w/v), 0.3% (w/v) bile salt, and pH 3. BLIS from L. lactis showed antimicrobial activity against Listeria monocytogenes ATCC 15313 and was susceptible to 10 types of antibiotics. The absence of haemolytic activity and the presence of acid phosphatase and naphthol-AS-BI-phosphohydrolase were observed in L. lactis. L. lactis could coagulate milk and showed a negative response to amylolytic and proteolytic activities and did not secrete β-galactosidase. The antimicrobial activity of BLIS was completely abolished at 121 °C. The BLIS was conserved at 4 °C in BHI and MRS medium up to 6-4 months, respectively. BLIS activity was more stable in BHI as compared to MRS after four freeze-thaw cycles and was not affected by a wide range of pH (pH 4-8). BLIS was sensitive to proteinase k and resistant to catalase and trypsin. The antimicrobial activity was slightly reduced by acetone, ethanol, methanol, and acetonitrile at 10% (v/v) and also towards Tween-80, urea, and NaCl 1% (v/v). Results from this study have demonstrated that L. lactis has a vast potential to be applied in the food industry, such as for the preparation of starter culture, functional foods, and probiotic products.

Bacteriocins, Antimicrobial Peptides from Bacterial Origin: Overview of Their Biology and Their Impact against Multidrug-Resistant Bacteria

Currently, the emergence and ongoing dissemination of antimicrobial resistance among bacteria are critical health and economic issue, leading to increased rates of morbidity and mortality related to bacterial infections. Research and development for new antimicrobial agents is currently needed to overcome this problem. Among the different approaches studied, bacteriocins seem to be a promising possibility. These molecules are peptides naturally synthesized by ribosomes, produced by both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB), which will allow these bacteriocin producers to survive in highly competitive polymicrobial environment. Bacteriocins exhibit antimicrobial activity with variable spectrum depending on the peptide, which may target several bacteria. Already used in some areas such as agro-food, bacteriocins may be considered as interesting candidates for further development as antimicrobial agents used in health contexts, particularly considering the issue of antimicrobial resistance. The aim of this review is to present an updated global report on the biology of bacteriocins produced by GPB and GNB, as well as their antibacterial activity against relevant bacterial pathogens, and especially against multidrug-resistant bacteria.

Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity

Social cellular aggregation or multicellular organization pose increased risk of transmission of infections through the system upon infection of a single cell. The generality of the evolutionary responses to this outside of Metazoa remains unclear. We report the discovery of several thematically unified, remarkable biological conflict systems preponderantly present in multicellular prokaryotes. These combine thresholding mechanisms utilizing NTPase chaperones (the MoxR-vWA couple), GTPases and proteolytic cascades with hypervariable effectors, which vary either by using a reverse transcriptase-dependent diversity-generating system or through a system of acquisition of diverse protein modules, typically in inactive form, from various cellular subsystems. Conciliant lines of evidence indicate their deployment against invasive entities, like viruses, to limit their spread in multicellular/social contexts via physical containment, dominant-negative interactions or apoptosis. These findings argue for both a similar operational 'grammar' and shared protein domains in the sensing and limiting of infections during the multiple emergences of multicellularity.

Bacterial Proteinaceous Compounds With Multiple Activities Toward Cancers and Microbial Infection

In recent decades, cancer and multidrug resistance have become a worldwide problem, resulting in high morbidity and mortality. Some infectious agents like Streptococcus pneumoniae, Stomatococcus mucilaginous, Staphylococcus spp., E. coli. Klebsiella spp., Pseudomonas aeruginosa, Candida spp., Helicobacter pylori, hepatitis B and C, and human papillomaviruses (HPV) have been associated with the development of cancer. Chemotherapy, radiotherapy and antibiotics are the conventional treatment for cancer and infectious disease. This treatment causes damage in healthy cells and tissues, and usually triggers systemic side-effects, as well as drug resistance. Therefore, the search for new treatments is urgent, in order to improve efficacy and also reduce side-effects. Proteins and peptides originating from bacteria can thus be a promising alternative to conventional treatments used nowadays against cancer and infectious disease. These molecules have demonstrated specific activity against cancer cells and bacterial infection; indeed, proteins and peptides can be considered as future antimicrobial and anticancer drugs. In this context, this review will focus on the desirable characteristics of proteins and peptides from bacterial sources that demonstrated activity against microbial infections and cancer, as well as their efficacy in vitro and in vivo.

Partial purification, characterization and mode of action of bacteriocins produced by three strains of Pediococcus sp

The main objective of the study is to assess a comparative antibacterial potential of three new bacteriocins produced by Pediococcus sp. through partial characterization and mode of action against some food spoilage bacteria. The bacteriocins from three different Pediococcus sp. viz. Pediococcus sp. LAB 33 (HQ185406), Pediococcus sp. LAB 41 (HQ185407), and Pediococcus sp. LAB 51 (HQ184064) were partially purified by adsorption-desorption method and tested for autoclave heat, pH, detergent and enzymes stability. A comparative analysis by Tricin-SDS PAGE with MALDI-TOF MS was done to estimate their molecular weight. The mode of action studies were done by cell viability and lactate dehydrogenase assay against two food associated pathogens, viz. Listeria monocytogenes and Pseudomonas aeruginosa using standard protocols. The bacteriocins produced by the strains were resistant to autoclave heat, detergent, wide range of pH and were active against different food borne pathogens at a minimum dose of ~ 100 AU/ml. The mode of action studies showed bactericidal action with lysis of the targeted cells. Therefore, the selective low dose efficacy, heat and detergent stability of the bacteriocins produced by the three strains could be considered as potent bacteriocins for use as food preservatives.

Novel natural food preservatives and applications in seafood preservation: a review

Food preservative additives are natural or synthetic substances which delay degradation in foods caused by microbial growth, enzyme activity, and oxidation. Until recently, the use of synthetic additives in food was more common. However, synthetic additives have not been widely accepted by consumers in recent years due to their assumed adverse effects on their health. Therefore, the tendency of consumers to natural additives is increasing day-by-day. Seafood is an easily perishable food due to its chemical composition. Immediately after harvest, changes in odor, taste, and texture in fishery products can be noticed. For this reason, measures to protect the product must be taken immediately after harvest or catching. Various preservation methods have been developed. In addition to various technological methods, preservative additives are used in fresh or processed seafood as well as in other foods. This review focuses on novel natural preservatives from different sources such as plants, bacteria, fungi, animals and algae, and their use in seafood to protect quality and prolong shelf life. © 2018 Society of Chemical Industry.

In Vitro Cytotoxic Activity of a Lactococcus lactis Antimicrobial Peptide Against Breast Cancer Cells

BACKGROUND

Nisin, an effective natural food preservative, is an antimicrobial peptide produced by Lactococcus lactis. Although it has been mainly studied and developed as a potential alternative for antibiotics, other pharmacological effects of the nisin including cytotoxic and anti-tumor activity have been attracted many attentions.

OBJECTIVES

Here, we aimed to evaluate in vitro cytotoxic activity of the nisin against breast cancer cells.

MATERIALS AND METHODS

The effect of temperature, pH, and chemical composition of the medium on the yield of nisin production was evaluated. As well, the anti-proliferative effect of nisin against a breast cancer cell line (i. e., MCF-7) and a non-cancerous cell line (i.e, HUVEC) was determined using MTT assay. Furthermore, the potential of the synergistic effect of the nisin on the doxorubicin cytotoxicity was evaluated.

RESULTS

The optimum culture condition for the nisin production by L. lactis was found to be MRS medium (pH 6.3) supplemented with the tryptone and incubation at 30 °C. MTT assay results indicate that nisin exhibits a high and selective cytotoxicity against MCF-7 cell line with IC50 value of 5 μM. Furthermore, a combination of nisin and doxorubicin at sub-inhibitory concentrations were more cytotoxic compared to either of drugs alone.

CONCLUSION

It could be suggested that nisin, either alone or in combination with other chemotherapeutic agents, could be a potential therapeutic for the breast cancer cells.

Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors

Enzymatic effectors targeting nucleic acids, proteins and other cellular components are the mainstay of conflicts across life forms. Using comparative genomics we identify a large class of eukaryotic proteins, which include effectors from oomycetes, fungi and other parasites. The majority of these proteins have a characteristic domain architecture with one of several N-terminal 'Header' domains, which are predicted to play a role in trafficking of these effectors, including a novel version of the Ubiquitin fold. The Headers are followed by one or more diverse C-terminal domains, such as restriction endonuclease (REase), protein kinase, HNH endonuclease, LK-nuclease (a RNase) and multiple distinct peptidase domains, which are predicted to carry their toxicity determinants. The most common types of these proteins appear to have originated from prokaryotic transposases (e.g. TN7 and Mu) and combine a CDC6/ORC1-STAND clade NTPase domain with a C-terminal REase domain. Other than the so-called Crinkler effectors of oomycetes and fungi, these effectors are encoded by other eukaryotic parasites such as trypanosomatids (the RHS proteins) and the rhizarian Plasmodiophora, and symbionts like Capsaspora Remarkably, we also find these proteins in free-living eukaryotes, including several viridiplantae, fungi, amoebozoans and animals. These versions might either still be transposons or function in other poorly understood eukaryote-specific inter-organismal and inter-genomic conflicts. These include the Medea1 selfish element of Tribolium that spreads via post-zygotic killing. We present a unified mechanism for the recombination-dependent diversification and action of this widespread class of molecular weaponry deployed across diverse conflicts ranging from parasitic to free-living forms.

Differential Susceptibility of Bacteria to Mouse Paneth Cell α-Defensins under Anaerobic Conditions

Small intestinal Paneth cells secrete α-defensin peptides, termed cryptdins (Crps) in mice, into the intestinal lumen, where they confer immunity to oral infections and define the composition of the ileal microbiota. In these studies, facultative bacteria maintained under aerobic or anaerobic conditions displayed differential sensitivities to mouse α-defensins under in vitro assay conditions. Regardless of oxygenation, Crps 2 and 3 had robust and similar bactericidal activities against S. typhimurium and S. flexneri, but Crp4 activity against S. flexneri was attenuated in the absence of oxygen. Anaerobic bacteria varied in their susceptibility to Crps 2-4, with Crp4 showing less activity than Crps 2 and 3 against Enterococcus faecalis, and Bacteroides fragilis in anaerobic assays, but Fusobacterium necrophorum was killed only by Crp4 and not by Crps 2 and 3. The influence of anaerobiosis in modulating Crp bactericidal activities in vitro suggests that α-defensin effects on the enteric microbiota may be subject to regulation by local oxygen tension.

Antagonistic activity expressed by Shigella sonnei: identification of a putative new bacteriocin

Bacteriocins are antibacterial, proteinaceous substances that mediate microbial dynamics. Bacteriocin production is a highly disseminated property among all major lineages of bacteria, including Shigella. In this paper, we addressed the purification and characterisation of a bacteriocin produced by a Shigella sonnei strain (SS9) isolated from a child with acute diarrhoea. The substance was purified through ammonium-sulphate precipitation and sequential steps of chromatography. The intracellular fraction obtained at 75% ammonium sulphate maintained activity following exposure to pH values from 1-11 and storage at -80ºC for more than two years and was inactivated by high temperatures and proteases. The molecular mass of the purified bacteriocin was determined by mass spectrometry to be 18.56 kDa. The N-terminal sequence of the bacteriocin did not match any other antibacterial proteins described. A putative new bacteriocin produced by S. sonnei has been detected. This bacteriocin may represent a newly described protein or a previously described protein with a newly detected function. Considering that SS9 expresses antagonism against other diarrhoeagenic bacteria, the bacteriocin may contribute to S. sonnei virulence and is potentially applicable to either preventing or controlling diarrhoeal disease.

The effects of antimicrobials and exposure to smoking on bacterial interference in the upper respiratory tract of children

Interactions between micro-organisms that include antagonism (interference) and synergism maintain balance between members of the normal endogenous flora, and play a role in preventing colonization by potential pathogens. Bacteria with interference capability of potential respiratory tract pathogens include alpha-hemolytic streptococci, non-hemolytic streptococci, Prevotella spp. and Peptostreptococcus spp. The role of bacterial interference in the occurrence of upper respiratory tract infections and its effect on their eradication is discussed. The infections include otitis media, sinusitis and pharyngo-tonsillitis. Treatment with antimicrobial agents and direct and indirect exposure to smoking, can affect the balance between the interfering organisms and potential pathogens. Introduction into the indigenous microflora of low virulence bacterial strains that are capable of interfering with colonization and infection with virulent organisms has been used to prevent the failure of antimicrobials in the treatment of pharyngo-tonsillitis and otitis media.

Characterization of maltocin P28, a novel phage tail-like bacteriocin from Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an important global opportunistic pathogen for which limited therapeutics are available because of the emergence of multidrug-resistant strains. A novel bacteriocin, maltocin P28, which is produced by S. maltophilia strain P28, may be the first identified phage tail-like bacteriocin from S. maltophilia. Maltocin P28 resembles a contractile but nonflexible phage tail structure based on electron microscopy, and it is sensitive to trypsin, proteinase K, and heat. SDS-PAGE analysis of maltocin P28 revealed two major protein bands of approximately 43 and 20 kDa. The N-terminal amino acid residues of these two major subunits were sequenced, and the maltocin P28 gene cluster was located on the S. maltophilia P28 chromosome. Our sequence analysis results indicate that this maltocin gene cluster consists of 23 open reading frames (ORFs), and that its gene organization is similar to that of the P2 phage genome and R2 pyocin gene cluster. ORF17 and ORF18 encode the two major structural proteins, which correspond to gpFI (tail sheath) and gpFII (tail tube) of P2 phage, respectively. We found that maltocin P28 had bactericidal activity against 38 of 81 tested S. maltophilia strains. Therefore, maltocin P28 is a promising therapeutic substitute for antibiotics for S. maltophilia infections.

Identification of commensal Escherichia coli genes involved in biofilm resistance to pathogen colonization

Protection provided by host bacterial microbiota against microbial pathogens is a well known but ill-understood property referred to as the barrier effect, or colonization resistance. Despite recent genome-wide analyses of host microbiota and increasing therapeutic interest, molecular analysis of colonization resistance is hampered by the complexity of direct in vivo experiments. Here we developed an in vitro-to-in vivo approach to identification of genes involved in resistance of commensal bacteria to exogenous pathogens. We analyzed genetic responses induced in commensal Escherichia coli upon entry of a diarrheagenic enteroaggregative E. coli or an unrelated Klebsiella pneumoniae pathogen into a biofilm community. We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm. We tested the in vivo relevance of our findings by comparing the extent of intestinal colonization by enteroaggregative E. coli and K. pneumoniae pathogens in mice pre-colonized with E. coli wild type commensal strain, or mutants corresponding to identified colonization resistance genes. We demonstrated that the absence of yiaF and bssS (yceP) differentially alters pathogen colonization in the mouse gut. This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.

Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010^T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.

Leptospirosis is one of the most common diseases transmitted by animals worldwide and is important because it is a major cause of febrile illness in tropical areas and also occurs in epidemic form associated with natural disasters and flooding. The mechanisms through which Leptospira cause disease are not well understood. In this study we have sequenced the genomes of two strains of Leptospira licerasiae isolated from a person and a marsupial in the Peruvian Amazon. These strains were thought to be able to cause only mild disease in humans. We have compared these genomes with other leptospires that can cause severe illness and death and another leptospire that does not infect humans or animals. These comparisons have allowed us to demonstrate similarities among the disease-causing Leptospira. Studying genes that are common among infectious strains will allow us to identify genetic factors necessary for infecting, causing disease and determining the severity of disease. We have also found that L. licerasiae seems to be able to uptake and incorporate genetic information from other bacteria found in the environment. This information will allow us to begin to understand how Leptospira species have evolved.

Probing individual environmental bacteria for viruses by using microfluidic digital PCR

Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.

Cloning, purification, and functional characterization of Carocin S2, a ribonuclease bacteriocin produced by Pectobacterium carotovorum

Background

Most isolates of Pectobacterium carotovorum subsp. carotovorum (Pcc) produce bacteriocins. In this study, we have determined that Pcc strain F-rif-18 has a chromosomal gene encoding the low-molecular-weight bacteriocin, Carocin S2, and that this bacteriocin inhibits the growth of a closely related strain. Carocin S2 is inducible by ultraviolet radiation but not by mutagenic agents such as mitomycin C.

Results

A carocin S2-defective mutant, TF1-2, was obtained by Tn5 insertional mutagenesis using F-rif-18. A 5706-bp DNA fragment was detected by Southern blotting, selected from a genomic DNA library, and cloned to the vector, pMS2KI. Two adjacent complete open reading frames within pMS2KI were sequenced, characterized, and identified as caroS2K and caroS2I, which respectively encode the killing protein and immunity protein. Notably, carocin S2 could be expressed not only in the mutant TF1-2 but also in Escherichia coli DH5α after entry of the plasmid pMS2KI. Furthermore, the C-terminal domain of CaroS2K was homologous to the nuclease domains of colicin D and klebicin D. Moreover, SDS-PAGE analysis showed that the relative mass of CaroS2K was 85 kDa and that of CaroS2I was 10 kDa.

Conclusion

This study shown that another nuclease type of bacteriocin was found in Pectobacterium carotovorum. This new type of bacteriocin, Carocin S2, has the ribonuclease activity of CaroS2K and the immunity protein activity of CaroS2I.

Structural study of the Serratia entomophila antifeeding prophage: three-dimensional structure of the helical sheath

The sheath of the Serratia entomophila antifeeding prophage, which is pathogenic to the New Zealand grass grub Costelytra zealandica, is a 3-fold helix formed by a 4-fold symmetric repeating motif disposed around a helical inner tube. This structure, determined by electron microscopy and image processing, is distinct from that of the other known morphologically similar bacteriophage sheaths.

Bacteriocin production by Shigella sonnei isolated from faeces of children with acute diarrhoea

Shigella is a common agent of diarrhoea, a worldwide major health problem. The bacterium produces bacteriocins; however, the role of these substances as a virulence factor is completely unknown. With the aim to search for colicin production by Shigella sonnei, to evaluate the influence of culture conditions on bacteriocin expression, and to characterize the substance partially, 16 S. sonnei strains isolated from children with diarrhoea were tested for antagonism against members of the intestinal microbiota or agents of diarrhoea. Nine strains exhibited isoantagonism and heteroantagonism against S. flexneri and diarrhoeagenic Escherichia coli. Autoantagonism and antagonism against the intestinal microbiota were not detected. Culture medium and incubation conditions influenced antagonism expression. Antagonism resulting from bacteriophages, low pH, fatty acids, hydrogen peroxide, and chloroform was excluded. The activity of the intracellular fraction obtained with 75% ammonium sulphate was preserved at pH 1.0-11.0, and was found to be reduced by organic solvents and affected by high temperatures and proteases. The antagonistic spectrum and the in vitro conditions for better antagonism expression suggest that the role of colicin in S. sonnei virulence, if any, would be expressed prior to infection, and may regulate population density of enteropathogens by helping in organism transmission.

Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico

Eleven Bacillus isolates from the surface and subsurface waters of the Gulf of Mexico were examined for their capacity to sporulate and harbor prophages. Occurrence of sporulation in each isolate was assessed through decoyinine induction, and putative lysogens were identified by prophage induction by mitomycin C treatment. No obvious correlation between ability to sporulate and prophage induction was found. Four strains that contained inducible virus-like particles (VLPs) were shown to sporulate. Four strains did not produce spores upon induction by decoyinine but contained inducible VLPs. Two of the strains did not produce virus-like particles or sporulate significantly upon induction. Isolate B14905 had a high level of virus-like particle production and a high occurrence of sporulation and was further examined by genomic sequencing in an attempt to shed light on the relationship between sporulation and lysogeny. In silico analysis of the B14905 genome revealed four prophage-like regions, one of which was independently sequenced from a mitomycin C-induced lysate. Based on PCR and transmission electron microscopy (TEM) analysis of an induced phage lysate, one is a noninducible phage remnant, one may be a defective phage-like bacteriocin, and two were inducible prophages. One of the inducible phages contained four putative transcriptional regulators, one of which was a SinR-like regulator that may be involved in the regulation of host sporulation. Isolates that both possess the capacity to sporulate and contain temperate phage may be well adapted for survival in the oligotrophic ocean.

Genome sequence comparison and superinfection between two related Pseudomonas aeruginosa phages, D3112 and MP22

A temperate transposable bacteriophage (MP22) was isolated from a Korean clinical isolate of Pseudomonas aeruginosa. It has a coliphage lambda-like morphology and a double-stranded DNA genome. The complete nucleotide sequence and annotation of the MP22 genome and its characteristics are presented. The MP22 genome is 36 409 bp long with a G+C content of 64.2 mol%. The genome contains 51 proposed ORFs, of which 48 (94 %) display synteny and significant nucleotide and protein sequence similarity to the corresponding ORFs of the closely related phage, D3112. Three of the predicted ORFs are unique proteins, whose functions are yet to be revealed. The phage c repressors exhibit striking dissimilarities and, when present as a single gene, did not show cross-immunity. In contrast, although an MP22 lysogen could be productively infected with D3112, MP22 could not grow on a D3112 lysogen, indicating a role of other D3112 genes in superinfection exclusion.

The bacterial flora in the teat duct of ewes can protect against and can cause mastitis

We studied the possible effects of bacterial populations within the teat duct, in the pathogenesis of ovine mastitis. In experiment I, 32 ewes were allocated into group A (ewes from which we isolated (+++ growth) coagulase-negative staphylococci), B (ewes from whose duct we isolated (+ growth) coagulase-negative staphylococci) or C (ewes from which we isolated Bacillus spp.) and subdivided into A1, B1, C1 (n=4; challenged by deposition of 1.250 cfu of Mannheimia haemolytica into the teat duct) or A2, B2, C2 (n=4; used as uninoculated controls); group D (n=8) contained ewes with no bacteria in their teat ducts and were challenged as above. There were less bacteriological isolations of flora (P = 0.018) and challenge (P<0.05) organisms from A1 than from A2 and D ewes; the severity of pathological findings in A1 (summed up score: 27) ewes was smaller than in D (summed up score: 36) ewes (P = 0.038). No such findings were evident with B1 or C1 ewes (P>0.4). In experiment II, ewes (groups E and F, n=6) from whose duct we isolated coagulase-negative staphylococci (+ growth) were used; in group G (n=6) ewes with no bacteria in their teat ducts were included. Teat chapping was applied in E and G ewes. All E ewes developed acute clinical mastitis within 24 h after teat chapping, although we had carried out no challenge; there were more bacteriological isolations of flora organisms from E than from F and G ewes (P < 0.001); the severity of pathological findings in E (score: 28) was greater than in F (score: 3) or G (score: 14) ewes. In experiment III, eight ewes with no bacteria in their teat ducts were allocated into group H or I (n=4) and challenged into the teat (group H) or into the gland (group I) with 10(6) cfu of a Staphylococcus simulans recovered from the teat duct of a group E ewe. Group H ewes developed transiently clinical followed by subclinical mastitis (based on bacteriological and cytological evidence), whilst group I ewes developed severe clinical disease. We conclude that staphylococcal flora present in high numbers within the teat duct of ewes can afford some protection against invading microorganisms. However with impeded defence mechanisms of the teat, the same flora may invade the mammary parenchyma and cause clinical mastitis.