Functions and emerging applications of bacteriocins

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Assessment of Bacteriocin-Antibiotic Synergy for the Inhibition and Disruption of Biofilms of Listeria monocytogenes and Vancomycin-Resistant Enterococcus

In this study, we have evaluated the effects of previously characterized bacteriocins produced by E. faecium strains ST651ea, ST7119ea, and ST7319ea, against biofilm formation and biofilms formed by L. monocytogenes ATCC15313 and vancomycin-resistant E. faecium VRE19. The effects of bacteriocins on the biofilms formed by L. monocytogenes ATCC151313 were evaluated by crystal violet assay and further confirmed by quantifying viable cells and cell metabolic activities through flow cytometry and TTC assay, respectively, indicating that bacteriocin activities required to completely eradicate biofilms are at least 1600 AU mL−1, 3200 AU mL−1, and 6400 AU mL−1, respectively for each bacteriocin evaluated. Furthermore, bacteriocins ST651ea and ST7119ea require at least 6400 AU mL−1 to completely eradicate the viability of cells within the biofilms formed by E. faecium VRE19, while bacteriocin ST7319ea requires at least 12800 AU mL−1 to obtain the same observations. Assessment of synergistic activities between selected conventional antibiotics (ciprofloxacin and vancomycin) with these bacteriocins was carried out to evaluate their effects on biofilm formation and pre-formed biofilms of both test microorganisms. Results showed that higher concentrations are needed to completely eradicate metabolic activities of cells within pre-formed biofilms in contrast with the biofilm formation abilities of the strains. Furthermore, synergistic activities of bacteriocins with both ciprofloxacin and vancomycin are more evident against vancomycin-resistant E. faecium VRE19 rather than L. monocytogenes ATCC15313. These observations can be further explored for possible applications of these combinations of antibiotics as a possible treatment of clinically relevant pathogens.

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

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

Combined Action of Antibiotics and Bacteriocins against Vancomycin-Resistant Enterococci

Antibiotics have been one of the most important discoveries in the area of applied medical microbiology; however, as a result of various factors, we are currently facing a dramatic and relatively dangerous increase in the number of cases of antibiotic resistance, and the need for new types of antimicrobials continues to grow. New approaches are needed to combat antibiotic-resistant pathogens. Bacteriocins, as part of the group of antimicrobial peptides, can be considered as alternatives and/or complements to known antibiotics. Their narrow spectra of activity can be explored for the control of various pathogens, such as vancomycin-resistant enterococci (VRE), as single therapies or in combination with known antibiotics. In the present study, we isolated bacteriocins from different lactic acid bacteria (LAB) strains, including Enterococcus and Pediococcus, and explored the possible synergistic inhibition of growth by bacteriocins and vancomycin. It was observed in the growth dynamics with previously selected VRE strains that the bacteriocins had a high specificity and a promising inhibitory effect against the VRE strains, and these results were validated by a propidium iodide viability test using flow cytometry. The data obtained indicate that the selected bacteriocins can be used to control VRE in the food industry or even as an alternative treatment to combat infections with antibiotic-resistant bacteria.

Recent advances in antiviral effects of probiotics: potential mechanism study in prevention and treatment of SARS-CoV-2

SARS-CoV-2 is responsible for coronavirus disease 2019 (COVID-19), progressively extended worldwide countries on an epidemic scale. Along with all the drug treatments suggested to date, currently, there are no approved management protocols and treatment regimens for SARS-CoV-2. The unavailability of optimal medication and effective vaccines against SARS-CoV-2 indicates the requirement for alternative therapies. Probiotics are living organisms that deliberate beneficial effects on the host when used sufficiently and in adequate amounts, and fermented food is their rich source. Probiotics affect viruses by antiviral mechanisms and reduce diarrhea and respiratory tract infection. At this point, we comprehensively evaluated the antiviral effects of probiotics and their mechanism with a particular focus on SARS-CoV-2. In this review, we suggested the conceptual and potential mechanisms of probiotics by which they could exhibit antiviral properties against SARS-CoV-2, according to the previous evidence concerning the mechanism of antiviral effects of probiotics. This study reviewed recent studies that speculate about the role of probiotics in the prevention of the SARS-CoV-2-induced cytokine storm through the mechanisms such as induction of anti-inflammatory cytokines (IL-10), downregulation of pro-inflammatory cytokines (TNF-α, IL-2, IL-6), inhibition of JAK signaling pathway, and act as HDAC inhibitor. Also, the recent clinical trials and their outcome have been reviewed.

Food and gut originated bacteriocins involved in gut microbe-host interactions

The gut microbes interact with each other as well as host, influencing human health and some diseases. Many gut commensals and food originated bacteria produce bacteriocins which can inhibit pathogens and modulate gut microbiota. Bacteriocins have comparable narrow antimicrobial spectrum and are attractive potentials for precision therapy of gut disorders. In this review, the bacteriocins from food and gut microbiomes and their involvement in the interaction between producers and gut ecosystem, along with their characteristics, types, biosynthesis, and functions are described and discussed. Bacteriocins are produced by many intestinal commensals and food microbes among which lactic acid bacteria (many are probiotics) has been paid more attention. Bacteriocin production has been generally regarded as a probiotic trait. They give a competitive advantage to bacteria, enabling their colonization in human gut, and mediating the interaction between the producers and host ecosystem. They fight against unwanted bacteria and pathogens without significant impact on the composition of commensal microbiota. Bacteriocins assist the producers to survive and colonize in the gut microbial populations. There is a great need to evaluate and utilize the potential of bacteriocins for improved therapeutic implications for intestinal health.

Scientists’ Assessments of Research on Lactic Acid Bacterial Bacteriocins 1990–2010

The antimicrobial activity of bacteriocins from lactic acid bacteria has constituted a very active research field within the last 35 years. Here, we report the results of a questionnaire survey with assessments of progress within this field during the two decades of the 1990s and the 2000s by 48 scientists active at that time. The scientists had research positions at the time ranging from the levels of Master’s and Ph.D. students to principal investigators in 19 Asian, European, Oceanian and North American countries. This time period was evaluated by the respondents to have resulted in valuable progress regarding the basic science of bacteriocins, whereas this was not achieved to the same degree with regard to their applications. For the most important area of application, food biopreservation, there were some success stories, but overall the objectives had not been entirely met due to a number of issues, such as limited target spectrum, target resistance, poor yield as well as economic and regulatory challenges. Other applications of bacteriocins such as enhancers of the effects of probiotics or serving as antimicrobials in human clinical or veterinary microbiology, were not evaluated as having been implemented successfully to any large extent at the time. However, developments in genomic and chemical methodologies illustrate, together with an interest in combining bacteriocins with other antimicrobials, the current progress of the field regarding potential applications in human clinical microbiology and food biopreservation. In conclusion, this study illuminates parameters of importance not only for R&D of bacteriocins, but also for the broader field of antimicrobial research.

Gene Rearrangement and Modification of Immunity Factors Are Correlated with the Insertion of Bacteriocin Cassettes in Streptococcus mutans

Bacteriocins have been applied in the food industries and have become promising next-generation antibiotics. Some bacteria produce bacteriocins and possess immunity factors for self-protection. Nisin A, a bacteriocin produced by Lactococcus lactis, shows broad-spectrum activity. However, the evolution and cross-resistance ability of the immunity factors in some species results in reduced susceptibility to bacteriocins. Here, we investigated the elements responsible for nisin A resistance in Streptococcus mutans and their contribution to mutacins (bacteriocins produced by S. mutans) resistance. We classified the nisin A-resistance regions into six types based on the different combinations of 3 immunity factors, mutFEG, nsrX, and mutHIJ, and the presence of mutacin synthesis operon upstream of mutF. Data shows that NsrX effectively acts against nisin A but not mutacins, while the newly identified ABC transporter MutHIJ acts against three mutacins but not nisin A. Three types of MutFEG are identified based on their amino acid sequences: α (in Nsr-types C and D-I), β (in Nsr-types B and d-III), and γ (in Nsr-type E). MutFEG-α strongly contributes to mutacin I resistance, while MutFEG-β and MutFEG-γ strongly contribute to mutacin III, IIIb, and nisin A resistance. Additionally, mutFEG-like structures could be found in various streptococcal species isolated from the oral cavity of humans, chimpanzees, monkeys, bears, and hamsters. Our findings suggest that immunity factors rearrange and adapt in the presence of bacteriocins and could be transferred among closely related species, thus altering the bacterial competition within the microflora.

IMPORTANCEStreptococcus mutans is an important organism of oral microbiota and associated with dental caries and systemic diseases such as stroke and endocarditis. They produce bacteriocins known as mutacins to compete with other oral bacteria and possess immune factors for self-protection. We found that the nisin A and mutacins resistance patterns correlated with the immunity components and MutFEG variants, and the genetic difference was driven by the insertion of mutacin-synthesis cassettes. Our study provides an understanding of the development of bacteriocin resistance among streptococcal species, which may alter the bacterial interaction and ecology within the oral biofilm.

Listeria monocytogenes exposed to antimicrobial peptides displays differential regulation of lipids and proteins associated to stress response

With the onset of Listeria monocytogenes resistance to the bacteriocin nisin, the search for alternative antimicrobial treatments is of fundamental importance. In this work, we set out to investigate proteins and lipids involved in the resistance mechanisms of L. monocytogenes against the antimicrobial peptides (AMPs) nisin and fengycin. The effect of sub-lethal concentrations of nisin and lipopeptide fengycin secreted by Bacillus velezensis P34 on L. monocytogenes was investigated by mass spectrometry-based lipidomics and proteomics. Both AMPs caused a differential regulation of biofilm formation, confirming the promotion of cell attachment and biofilm assembling after treatment with nisin, whereas growth inhibition was observed after fengycin treatment. Anteiso branched-chain fatty acids were detected in higher amounts in fengycin-treated samples (46.6%) as compared to nisin-treated and control samples (39.4% and 43.4%, respectively). In addition, a higher relative abundance of 30:0, 31:0 and 32:0 phosphatidylglycerol species was detected in fengycin-treated samples. The lipidomics data suggest the inhibition of biofilm formation by the fengycin treatment, while the proteomics data revealed downregulation of important cell wall proteins involved in the building of biofilms, such as the lipoteichoic acid backbone synthesis (Lmo0927) and the flagella-related (Lmo0718) proteins among others. Together, these results provide new insights into the modification of lipid and protein profiles and biofilm formation in L. monocytogenes upon exposure to antimicrobial peptides.

Bradyrhizobium japonicum FN1 produces an inhibitory substance that affects competition for nodule occupancy

Bacteriocins are narrow-spectrum antibiotics of bacterial origin that can affect competition in resource-limited environments, such as the rhizosphere. Therefore, bacteriocins may be good candidates for manipulation to generate more competitive inocula for soybean. In this study, Bradyrhizobium japonicum FN1, along with other Bradyrhizobia in our culture collection, was screened for bacteriocin-like activity. Five distinct inhibitory effects were observed. FN1 genes putatively involved in bacteriocin production were computationally identified. These genes were mutagenized, and the subsequent strains were screened for loss of inhibitory activity. Mutant strain BRJ-48, with an insert in bjfn1_01204, displayed a loss of ability to inhibit an indicator strain. This loss can be complemented by the introduction of a plasmid expressing bjfn1_01204 in trans. The strain carrying the mutation did not affect competition in broth cultures but was less competitive for nodule occupancy. Annotation suggests that bjfn1_01204 encodes a carboxymuconolactone decarboxylase; however, the direct contribution of how this enzyme contributes to inhibiting the tester strain remains unknown.

Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development

Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.

Enterocin: Promising Biopreservative Produced by Enterococcus sp

Food preservation is a method used to handle and treat food products to slow down food spoilage and subsequently reduce the risk of foodborne illness. Nowadays, the demand for natural preservatives over chemical preservatives in food is increasing due to the awareness of consuming healthy food products without the risk of harmful side effects. Thus, the research and development of preservation techniques, referred to as biopreservation, is growing rapidly. In biopreservation methods, microorganisms that are known as lactic acid bacteria (LAB) and their antimicrobial substances are used to extend shelf life and maintain the nutritional value of foods. Among the most studied LAB are from the genus Enterococcus, which produces a bacteriocin called enterocin. Bacteriocins are ribosomal-synthesized antimicrobial peptides that are capable of inhibiting the growth of pathogenic bacteria that cause spoilage in food. LAB is generally regarded as safe (GRAS) for human consumption. The current application of LAB, notably Enterococcus sp. in the biopreservation of meat and meat-based products was highlighted in this review. This report also includes information on the effects of enzymes, temperature, and pH on the stability of bacteriocin produced by Enterococcus sp. An extensive compilation of numerous industry procedures for preserving meat has also been emphasized, highlighting the benefits and drawbacks of each method.

In vitro assessment of skin sensitization, irritability and toxicity of bacteriocins and reuterin for possible topical applications

Bacteriocins and reuterin are promising antimicrobials for application in food, veterinary, and medical sectors. In the light of their high potential for application in hand sanitizer, we investigated the skin toxicity of reuterin, microcin J25, pediocin PA-1, bactofencin A, and nisin Z in vitro using neutral red and LDH release assays on NHEK cells. We determined their skin sensitization potential using the human cell line activation test (h-CLAT). Their skin irritation potential was measured on human epidermal model EpiDerm™. We showed that the viability and membrane integrity of NHEK cells remained unaltered after exposure to bacteriocins and reuterin at concentrations up to 400 µg/mL and 80 mg/mL, respectively. Furthermore, microcin J25 and reuterin showed no skin sensitization at concentrations up to 100 µg/mL and 40 mg/mL, respectively, while pediocin PA-1, bactofencin A, and nisin Z caused sensitization at concentrations higher than 100 µg/mL. Tissue viability was unaffected in presence of bacteriocins and reuterin at concentrations up to 200 µg/mL and 40 mg/mL, respectively, which was confirmed by measuring cytokine IL-1α and IL-8 levels and by histological analysis. In conclusion, the current study provides scientific evidence that some bacteriocins and reuterin, could be safely applied topically as sanitizers at recommended concentrations.

Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability

The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.

Nisin Induces Cell-Cycle Arrest in Free-Living Amoebae Acanthamoeba castellanii

PURPOSE

Acanthamoeba spp. are free-living amoebas with worldwide distribution and play an important role as disease-causing agents in humans. Drug inability to completely eradicate these parasites along with their toxic effects suggest urgent need for new antimicrobials. Nisin is a natural antimicrobial peptide produced by Lactococcus lactis. Nisin is also the only bacteriocin approved for use in food preservation. In this work, we analyzed the effect of nisin on the growth of Acanthamoeba castellanii trophozoites.

METHODS

A total of 8 × 10⁴ trophozoites were exposed to increasing concentrations of nisin to determine its activity. Changes in cell membrane and cellular cycle of trophozoites were investigated by flow cytometry, and nisin cytotoxicity in mammalian cells was evaluated in L929 cells by MTT method.

RESULTS

After 24 h exposure to increasing nisin concentrations, an IC₅₀ of 4493.2 IU mL^-1 was obtained for A. castellanii trophozoites. However, after 72 h a recovery in amoebic growth was observed, and it was no longer possible to determine IC₅₀. Flow cytometry analysis showed that nisin has no effect on the membrane integrity. Treatment with nisin induced cell-cycle arrest during G1 and S phases in A. castellanii trophozoites, which recovered their growth after 72 h.

CONCLUSION

This is one of the first studies showing the effect of internationally approved nisin against A. castellanii trophozoites. Nisin caused cell-cycle arrest in trophozoites, momentarily interfering with the DNA replication process. The data highlight the amoebostatic activity of nisin, and suggest its use as an adjuvant for the treatment of infections caused by Acanthamoeba spp.

Prophylactic Application of Tailocins Prevents Infection by Pseudomonas syringae

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability. Our group has categorized and characterized tailocins produced by and tailocin sensitivities of the phytopathogen Pseudomonas syringae, and here we extend these experiments to test whether prophylactic tailocin application can prevent infection of Nicotiana benthamiana by P. syringae pv. syringae B728a. Specifically, we demonstrate that multiple strains can produce tailocins that prevent infection by strain B728a and engineer a deletion mutant to prove that tailocin targeting is responsible for this protective effect. Lastly, we provide evidence that heritable resistance mutations do not explain the minority of cases in which tailocins fail to prevent infection. Our results extend previous reports of prophylactic use of tailocins against phytopathogens, and establish a model system with which to test and optimize tailocin application for prophylactic treatment to prevent phytopathogen infection.

Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages

In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.

Horses as a source of bioactive fecal strains Enterococcus mundtii

Bacteriocin-producing bacteria with probiotic character are known as nutritional supplements mainly for livestock. Among those beneficial bacteria we also found enterococci. Because the species strains Enterococcus mundtii also can produce bacteriocins, this study was focused on fecal strains E. mundtii from horses and their bioactivity with a view to their possible future use in breeding. Rectal removal from 47 horses (40 mares and 7 stallions), the Norik breed from Muráň were sampled in eastern Slovakia during November 2019 year. Horses age ranged from five months up to 23 years. Using MALDI-TOF mass spectrometry and 16S rRNA sequences analysis, 14 strains were allotted to the species E. mundtii. Bacteriocin substances produced by the strains EMKD 38/1, EMKD 40/2, EMKD 34/2 and EMKD 41/3 showed inhibitory activity against the most susceptible (principal) indicator strain Enterococcus avium EA5 and against listeriae as well (inhibitory activity from 100 up to 1 600 AU/mL). Only strain EMKD 41/3 possess Ent P and Mundticin KS genes and showed the broadest inhibitory activity. Ent B gene possessing strain EMKD 24/1 inhibited a growth of only indicator strain EA5. Identified E. mundtii tolerate low pH 3 and oxgall/bile. They were hemolysis, gelatinase and DNase negative and mostly susceptible to clinical antibiotics which are properties requested for application potential of strain. Substance from the strain with the broadest antimicrobial spectrum showed its practical/application potential, e.g. for optimizing the host microbiota which is important regarding the maintenance of animal`s health status.

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.

Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products

Microbes host a huge variety of biosynthetic gene clusters that produce an immeasurable array of secondary metabolites with many different biological activities such as antimicrobial, anticarcinogenic and antiviral. Despite the complex task of isolating and characterizing novel natural products, microbial genomic strategies can be useful for carrying out these types of studies. However, although genomic-based research on secondary metabolism is on the increase, there is still a lack of reports focusing specifically on the genus Pseudomonas. In this work, we aimed (i) to unveil the main biosynthetic systems related to secondary metabolism in Pseudomonas type strains, (ii) to study the evolutionary processes that drive the diversification of their coding regions and (iii) to select Pseudomonas strains showing promising results in the search for useful natural products. We performed a comparative genomic study on 194 Pseudomonas species, paying special attention to the evolution and distribution of different classes of biosynthetic gene clusters and the coding features of antimicrobial peptides. Using EvoMining, a bioinformatic approach for studying evolutionary processes related to secondary metabolism, we sought to decipher the protein expansion of enzymes related to the lipid metabolism, which may have evolved toward the biosynthesis of novel secondary metabolites in Pseudomonas. The types of metabolites encoded in Pseudomonas type strains were predominantly non-ribosomal peptide synthetases, bacteriocins, N-acetylglutaminylglutamine amides and ß-lactones. Also, the evolution of genes related to secondary metabolites was found to coincide with Pseudomonas species diversification. Interestingly, only a few Pseudomonas species encode polyketide synthases, which are related to the lipid metabolism broadly distributed among bacteria. Thus, our EvoMining-based search may help to discover new types of secondary metabolite gene clusters in which lipid-related enzymes are involved. This work provides information about uncharacterized metabolites produced by Pseudomonas type strains, whose gene clusters have evolved in a species-specific way. Our results provide novel insight into the secondary metabolism of Pseudomonas and will serve as a basis for the prioritization of the isolated strains. This article contains data hosted by Microreact.

Intraspecific Diversity of Microbial Anti-Inflammatory Molecule (MAM) from Faecalibacterium prausnitzii

The commensal bacterium Faecalibacterium prausnitzii has unique anti-inflammatory properties, at least some of which have been attributed to its production of MAM, the Microbial Anti-inflammatory Molecule. Previous phylogenetic studies of F. prausnitzii strains have revealed the existence of various phylogroups. In this work, we address the question of whether MAMs from different phylogroups display distinct anti-inflammatory properties. We first performed wide-scale identification, classification, and phylogenetic analysis of MAM-like proteins encoded in different genomes of F. prausnitzii. When combined with a gene context analysis, this approach distinguished at least 10 distinct clusters of MAMs, providing evidence for functional diversity within this protein. We then selected 11 MAMs from various clusters and evaluated their anti-inflammatory capacities in vitro. A wide range of anti-inflammatory activity was detected. MAM from the M21/2 strain had the highest inhibitory effect (96% inhibition), while MAM from reference strain A2-165 demonstrated only 56% inhibition, and MAM from strain CNCM4541 was almost inactive. These results were confirmed in vivo in murine models of acute and chronic colitis. This study provides insights into the family of MAM proteins and generates clues regarding the choice of F. prausnitzii strains as probiotics for use in targeting chronic inflammatory diseases.

Antibacterial effect of bacteriocin XJS01 and its application as antibiofilm agents to treat multidrug-resistant Staphylococcus aureus infection

Multidrug-resistant (MDR) Staphylococcus aureus biofilms have emerged as a serious threat to human health. Recently, the development of antibiotic replacement therapy has gained much attention due to the potential application of bacteriocin. The present study sought to evaluate the antibacterial effect of bacteriocin XJS01 against MDR S. aureus, a previously reported bacteriocin against S. aureus strain 2612:1606BL1486 (S. aureus_26, an MDR strain demonstrated here), and its potential application as an antibiofilm agent. The minimum bactericide concentration of XJS01 against MDR S. aureus_26 was 33.18 μg/mL. XJS01 exhibited excellent storage stability and resistance against acid and reduced the density of established MDR S. aureus_26 biofilm. The hemolytic and HEK293T cytotoxicity activities of XJS01 and the histological analyses in mice confirmed its safety. Moreover, XJS01 effectively disrupted the MDR S. aureus_26 biofilm established on the skin wound surface and reduced the biofilm-isolated bacteria, thereby decreasing the release of pro-inflammatory cytokines and the proliferation of alternatively activated macrophages. Compared to mupirocin, XJS01 exhibited an excellent therapeutic effect on mice skin wounds, confirming it to be a potential alternative to antibiotics.

Genomic and functional characterization of bacteriocinogenic lactic acid bacteria isolated from Boza, a traditional cereal-based beverage

Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0-10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage β-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.

Susceptibility to Bacteriocins of Multiresistant, mecA Gene Possessing Staphylococcus pseudintermedius Strains from Lesions on Dogs in Vojvodina (Serbia)

Aims: Staphylococci are considered commensal organisms; however, they can also cause diseases in animals. The species Staphylococcus pseudintermedius was originally isolated from the nares and anal mucosa of healthy dogs; nowadays, the incidence of methicillin-resistant S. pseudintermedius strains in dogs has increased, and this species has also become the most common cause of canine skin lesions. S. pseudintermedius were tested for their susceptibility to bacteriocins to show the potential of bacteriocins to eliminate/reduce S. pseudintermedius as a causative agent. Material and Methods: In this study, S. pseudintermedius were isolated from skin lesions on dogs of various breeds and ages in the Vojvodina region (Serbia) in the framework of our international co-operation. Results: S. pseudintermedius strains were identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, and the species allocation was confirmed by genotypization and corroborated using phenotyping tests. The strains were multiresistant, involving methicillin-resistance. In addition, the mecA gene was detected in S. pseudintermedius strains, confirming the presence of a genetic feature for methicillin resistance. S. pseudintermedius strains produced large amounts of the enzymes alkaline phosphatase and acid phosphatase; they were low-grade biofilm forming (0.1 ≤ A₅₇₀ < 1.0), except S. pseudintermedius SPs1. All strains were susceptible to gallidermin (inhibition activity up to 204,800 arbitrary unit [AU]/mL); however, they were mostly resistant to enterocins. However, biofilm-forming S. pseudintermedius SPs1 was susceptible to enterocins (200 AU/mL). Conclusion: Establishing the susceptibility of multiresistant and mecA gene-possessing S. pseudintermedius strains to gallidermin is an innovative, original result; it provides a new opportunity for preventing/eliminating infection caused by those agents.

An oxidation resistant pediocin PA-1 derivative and penocin A display effective anti-Listeria activity in a model human gut environment

Pediocin PA-1 is a class IIa bacteriocin that is particularly effective against the foodborne pathogen Listeria monocytogenes. The loss of activity of PA-1 pediocin due to methionine oxidation is one of the challenges that limit the wider application of the bacteriocin. In this study, we heterologously expressed an oxidation resistant form of pediocin PA-1, i.e., pediocin M31L, and compared its activity to that of native pediocin PA-1 and to penocin A, a pediocin-like bacteriocin that displays a narrower antimicrobial spectrum. Minimal inhibitory concentration assays revealed that pediocin M31L was as effective as PA-1 and more effective than synthetic penocin A against Listeria with negligible activity against a range of obligate anaerobic commensal gut bacterial species. The anti-Listeria activity of these pediocins was also assessed in a simulated human distal colon model assay using the L. monocytogenes, spiked at 6.5 ±   0.13 Log CFU/mL, as a bioindicator. At 24 h, pediocin M31L and penocin A (2.6 μM) reduced Listeria counts to 3.5 ± 0.4 and 3.64 ± 0.62 Log CFU/mL, respectively, whereas Listeria counts were considerably higher, i.e. 7.75 ±   0.43 Log CFU/mL, in the non-bacteriocin-containing control. Ultimately, it was established that synthetic penocin A and the stable pediocin M31L derivative, heterologously produced, display effective anti-Listeria activity in a human gut environment.

Disorders of the skin microbiome in atopic dermatitis and psoriasis

The notion of skin microbiome encompasses a heterogeneous group of microorganisms that belong to various taxonomic units, such as bacteria, archaea, viruses, and fungi. The impact of these microbial community constituents upon the epidermal barrier condition, and upon the immune system functioning, is being intensely scrutinized. There is a particular interest in studying the role that the microorganisms of genus Staphylococcus spp. play in the course of physiological and pathological processes occurring in the skin. This review examines in detail the interaction of the microorganisms of genus Staphylococcus spp. with the microbial community constituents, as well as with the skin immune system in normal condition and in the condition associated with inflammatory dermatoses. There are also the data given on S. aureus pathogenicity factors, the data on the impact of this microorganism upon the course of atopic dermatitis, and upon the course of psoriasis. The review examines the role that coagulase-negative staphylococci, S. epidermidis in particular, play in maintaining the microbiome homeostasis. The review as well examines the impact of the skin microbiome upon the development and activity of the skin immune system, and upon maintaining the integrity of the epidermal barrier.

Lacticaseicin 30 and Colistin as a Promising Antibiotic Formulation against Gram-Negative β-Lactamase-Producing Strains and Colistin-Resistant Strains

Antimicrobial resistance is a global health concern across the world and it is foreseen to swell if no actions are taken now. To help curbing this well announced crisis different strategies are announced, and these include the use of antimicrobial peptides (AMP), which are remarkable molecules known for their killing activities towards pathogenic bacteria. Bacteriocins are ribosomally synthesized AMP produced by almost all prokaryotic lineages. Bacteriocins, unlike antibiotics, offer a set of advantages in terms of cytotoxicity towards eukaryotic cells, their mode of action, cross-resistance and impact of microbiota content. Most known bacteriocins are produced by Gram-positive bacteria, and specifically by lactic acid bacteria (LAB). LAB-bacteriocins were steadily reported and characterized for their activity against genetically related Gram-positive bacteria, and seldom against Gram-negative bacteria. The aim of this study is to show that lacticaseicin 30, which is one of the bacteriocins produced by Lacticaseibacillus paracasei CNCM I-5369, is active against Gram-negative clinical strains (Salmonella enterica Enteritidis H10, S. enterica Typhimurium H97, Enterobacter cloacae H51, Escherichia coli H45, E. coli H51, E. coli H66, Klebsiella oxytoca H40, K. pneumoniae H71, K. variicola H77, K. pneumoniae H79, K. pneumoniae H79), whereas antibiotics failed. In addition, lacticaseicin 30 and colistin enabled synergistic interactions towards the aforementioned target Gram-negative clinical strains. Further, the combinations of lacticaseicin 30 and colistin prompted a drastic downregulation of mcr-1 and mcr-9 genes, which are associated with the colistin resistance phenotypes of these clinical strains. This report shows that lacticaseicin 30 is active against Gram-negative clinical strains carrying a rainbow of mcr genes, and the combination of these antimicrobials constitutes a promising therapeutic option that needs to be further exploited.

Angicin, a novel bacteriocin of Streptococcus anginosus

As a conserved defense mechanism, many bacteria produce antimicrobial peptides, called bacteriocins, which provide a colonization advantage in a multispecies environment. Here the first bacteriocin of Streptococcus anginosus, designated Angicin, is described. S. anginosus is commonly described as a commensal, however it also possesses a high pathogenic potential. Therefore, understanding factors contributing to its host colonization and persistence are important. A radial diffusion assay was used to identify S. anginosus BSU 1211 as a potent bacteriocin producer. By genetic mutagenesis the background of bacteriocin production and the bacteriocin gene itself were identified. Synthetic Angicin shows high activity against closely related streptococci, listeria and vancomycin resistant enterococci. It has a fast mechanism of action and causes a membrane disruption in target cells. Angicin, present in cell free supernatant, is insensitive to changes in temperature from - 70 to 90 °C and pH values from 2 to 10, suggesting that it represents an interesting compound for potential applications in food preservation or clinical settings.

Lactic Acid Bacteria as Antimicrobial Agents: Food Safety and Microbial Food Spoilage Prevention

In the wake of continual foodborne disease outbreaks in recent years, it is critical to focus on strategies that protect public health and reduce the incidence of foodborne pathogens and spoilage microorganisms. Currently, there are limitations associated with conventional microbial control methods, such as the use of chemical preservatives and heat treatments. For example, such conventional treatments adversely impact the sensorial properties of food, resulting in undesirable organoleptic characteristics. Moreover, the growing consumer advocacy for safe and healthy food products, and the resultant paradigm shift toward clean labels, have caused an increased interest in natural and effective antimicrobial alternatives. For instance, natural antimicrobial elements synthesized by lactic acid bacteria (LAB) are generally inhibitory to pathogens and significantly impede the action of food spoilage organisms. Bacteriocins and other LAB metabolites have been commercially exploited for their antimicrobial properties and used in many applications in the dairy industry to prevent the growth of undesirable microorganisms. In this review, we summarized the natural antimicrobial compounds produced by LAB, with a specific focus on the mechanisms of action and applications for microbial food spoilage prevention and disease control. In addition, we provide support in the review for our recommendation for the application of LAB as a potential alternative antimicrobial strategy for addressing the challenges posed by antibiotic resistance among pathogens.

Reprogramming microbial populations using a programmed lysis system to improve chemical production

Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.

Characterization and safety evaluation of two beneficial, enterocin-producing Enterococcus faecium strains isolated from kimchi, a Korean fermented cabbage

Enterococcus faecium ST20Kc and ST41Kc were isolated from kimchi, a traditional Korean fermented cabbage. Bacteriocins produced by both strains exhibited strong activity against Listeria monocytogenes and various Enterococcus spp., including 30 vancomycin-resistant enterococcal strains, but not against other lactic acid bacteria (LAB) on the evaluated test panel. The antimicrobials produced by the strains were found to be proteinaceous and stable even after exposure to varying pH, temperature, and chemicals used in the industry and laboratory processes. Antimicrobial activity of both strains was evaluated as bactericidal against exponentially growing cultures of L. monocytogenes ATCC® 15313™ and Enterococcus faecalis 200A. Based on tricine-SDS-PAGE, the molecular weights of the bacteriocins produced by the strains were between 4 and 6 kDa. Additionally, both strains were susceptible to antibiotics, including vancomycin, kanamycin, gentamycin, ampicillin, streptomycin, tylosin, chloramphenicol, clindamycin, and tetracycline. Adhesion genes, map, mub, and EF-Tu, were also detected in the genomes of both strains. With gastrointestinal stress induction, both strains showed high individual survival rates, and capability to reduce viable counts of L. monocytogenes ATCC® 15313™ and Enterococcus faecalis 200A in mixed cultures. Based on the metabolomics analysis, both strains were found to produce additional antimicrobial compounds, particularly, lactic acid, phenyllactic acid, and phenethylamine, which can be potentially involved in the antimicrobial interaction with pathogenic microorganisms.

The urobiome, urinary tract infections, and the need for alternative therapeutics

Improvements in bacterial culturing and DNA sequencing techniques have revealed a diverse, and hitherto unknown, urinary tract microbiome (urobiome). The potential role of this microbial community in contributing to health and disease, particularly in the context of urinary tract infections (UTIs) is of significant clinical importance. However, while several studies have confirmed the existence of a core urobiome, the role of its constituent microbes is not yet fully understood, particularly in the context of health and disease. Herein, we review the current state of the art, concluding that the urobiome represents an important component of the body's innate immune defences, and a potentially rich resource for the development of alternative treatment and control strategies for UTIs.

Selection of Bacteriocinogenic Bacillus spp. from Traditional Fermented Korean Food Products with Additional Beneficial Properties

Two Bacillus spp. isolated from kimchi, Bacillus tequilensis ST816CD and Bacillus subtilis ST830CD, were characterized for their antimicrobial properties and safety. The proteinaceous nature of their inhibitory metabolites was confirmed after exposure to proteolytic enzymes, resulting in partial loss of the antimicrobial effect. This indicated that different non-proteinaceous antimicrobial substances may also be produced by these strains. This hypothesis was later confirmed when genes associated with the production of surfactants were detected in their DNA. The expressed antimicrobial metabolites were not affected by treatment at different temperatures and pH levels, including exposure to selected chemicals. Their strong adherence to susceptible pathogens was not significantly affected by different temperatures, chemicals, or pH values. Both Bacillus strains showed inhibitory activity against clinical and food-associated pathogens, including Listeria monocytogenes ATCC 15313, and some Staphylococcus species. Several genes associated with the production of antimicrobial metabolites were detected, but key virulence and beneficial genes were not present in these strains. Even though only B. tequilensis ST816CD displayed γ-hemolysin production, both selected strains were found to produce gelatinase and biogenic amines, which are considered as either potential virulence- or health-related factors. Moreover, the strains were susceptible to a variety of antibiotics except for the penicillin G [1 IU/disc] resistance of B. tequilensis ST816CD. Both strains showed proteolytic activity. Additionally, both strains showed low hydrophobicity based on bacterial adherence measured by hydrocarbons (n-hexadecane).

[Regulatory role of small RNA srn821978 in mutacin IV expression in Streptococcus mutans]

OBJECTIVE

To analyze the role of small RNA srn821798 in posttranscriptional regulation of mutacin IV expression in Streptococcus mutans.

METHODS

The potential target genes of srn821978 were predicted using RNAhybrid, RNAPredator and IntaRNA. We collected 10 Streptococcus mutans (S.muans) strains with high expression of mutacin IV and another 10 S.muans strains that did not express mutacin IV screened by inhibition zone test, and the expression levels of srn821798 and the candidate target genes in these strains were detected by qPCR. Using synthesized mimics and inhibitors of srn821798, we constructed S.muans strains with high or low srn821798 expression via electroporation based on the standard strain of S.muans UA159, and analyzed the expression levels of srn821798 and its candidate target genes in these strains. We also examined the binding ability of srn821798 to its target gene sepM using electrophoresis and a dual- luciferase reporter system.

RESULTS

The expression levels of the candidate target genes of srn821798 including sepM, comD, comE, nlmA and nlmB were significantly higher while the expression level of srn821798 was significantly lower in clinical S.muans strains with high expression of mutacin IV than in those without mutacin IV expression (P < 0.05). Although the expression levels of the candidate target genes in strains with up- regulated or down- regulated srn821798 expression did not differ significantly from those in the standard strain, the expression level of sepM showed a trend of differential distribution, and srn821798 was predicted to have a strong binding ability to sepM action site.

CONCLUSION

srn821798 may play a regulatory role in the expression of mutacin IV in S.muans, but the underlying mechanism remains to be explored.

Susceptibility to Nisin, Bactofencin, Pediocin and Reuterin of Multidrug Resistant Staphylococcus aureus, Streptococcus dysgalactiae and Streptococcus uberis Causing Bovine Mastitis

Antibiotics are the most effective strategy to prevent and treat intramammary infections. However, their misuse has led to the dissemination of multidrug resistant bacteria (MDR) for both animals and humans. Efforts to develop new alternative strategies to control bacterial infections related to MDR are continuously on the rise. The objective of this study was to evaluate the antimicrobial activity of different bacteriocins and reuterin against MDR Staphylococcus and Streptococcus clinical isolates involved in bovine mastitis. A bacterial collection including S. aureus (n = 19), S. dysgalactiae (n = 17) and S. uberis (n = 19) was assembled for this study. Antibiotic resistance profiles were determined by the disk diffusion method. In addition, sensitivity to bacteriocins and reuterin was evaluated by determining minimum inhibitory concentrations (MIC). A total of 21 strains (37.5%) were MDR. MICs ranged from ≤1.0 μg/mL to ≥100 μg/mL for nisin and 2.0 to ≥250 μg/mL for bactofencin. Reuterin was active against all tested bacteria, and MICs vary between 70 and 560 μg/mL. Interestingly, 20 MDR strains were inhibited by bactofencin at a concentration of ≤250 μg/mL, while 14 were inhibited by nisin at an MIC of ≤100 μg/mL. Pediocin did not show an inhibitory effect.

Bioevaluation and Targeted Modification of Temporin-FL From the Skin Secretion of Dark-Spotted Frog (Pelophylax nigromaculatus)

Bioactive proteins secreted by the granular glands of amphibian skin play a self-defensive role, and exhibit various bioactivities in vitro and in vivo. In light of the severity of the problem of antibiotic resistance for treating infections, many antimicrobial peptides (AMPs) have been developed and applied in clinical microbial treatments. We identified a naturally derived and potent antimicrobial peptide, temporin-FL, obtained from the skin secretion of Pelophylax nigromaculatus via “shotgun” cloning. Two truncated analogues of this peptide were chemically synthesized to explore their structural-functional relationships. The results of a functional evaluation showed that all of the tested AMPs were active against Gram-positive bacteria and fungi and demonstrated antibiofilm activity against methicillin-resistant Staphylococcus aureus (MRSA) but did not have an effect on Gram-negative bacteria. Moreover, temporin-FLa demonstrated a higher level of hydrophobicity and enhanced antimicrobial efficiency, as well as hemolytic activity and cell cytotoxicity than the parent peptide. Temporin-FLb, which evidenced significantly less α-helicity, was less potent against various microbes but exhibited lower cytotoxicity relating to mammalian cells. Both of the synthesized analogues possessed a higher therapeutic index than the original peptide. Moreover, the membrane permeability assay and the measuring membrane depolarization assay declared that temporin-FL and its analogues induced membrane fracture and depolarization; the quantitative biofilm formation assay and the observations of MRSA biofilms using scanning electron microscopy revealed that the AMPs caused biofilm disruption and blocked biofilm formation, the former experiments all confirming their antimicrobial and antibiofilm properties. Hence, the optimization of temporin-FL offers insights for the discovery of new drugs for treating MRSA infections.

Characterization of the antimicrobial activity produced by Bacillus sp. isolated from wetland sediment

Bacteria of the genus Bacillus sp. present the potential for inhibiting various pathogens, making them a promising starting point in the search for new antimicrobial substances. In this study, bacteria were isolated from sediment samples from humid areas of a Natural Conservation Unit in the state of Rio Grande do Sul, Brazil. The isolate Bacillus sp. sed 1.4 was selected for production of antimicrobial activity, and was characterized by MALDI-TOF and 16S rDNA sequencing. Phylogenetic analysis showed that Bacillus sed 1.4 was closely related to Bacillus altitudinis and Bacillus pumilus. The cell-free supernatant was partially purified using ammonium sulfate precipitation, gel filtration chromatography (Sephadex G-200) and an ultrafiltration membrane. Partial purification resulted in specific activity of 769.23 AU/mg, with a molecular mass of approximately 148 kDa. This antimicrobial substance showed stability at 100°C for 5 min, and was inactivated by proteolytic enzymes. An antimicrobial effect against Listeria species was observed. Considering the importance of the Listeria genus in the area of food safety, this antimicrobial activity should be further explored, specifically in the field of dairy products and with a focus on food biopreservation studies.