Bacteriocins: evolution, ecology, and application

Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture

Several beneficial microbial strains inhibit the growth of different phytopathogens and commercialized worldwide as biocontrol agents (BCAs) for plant disease management. These BCAs employ different strategies for growth inhibition of pathogens, which includes production of antibiotics, siderophores, lytic enzymes, bacteriocins, hydrogen cyanide, volatile organic compounds, biosurfactants and induction of systemic resistance. The efficacy of antagonistic strains could be further improved through genetic engineering for better disease suppression in sustainable farming practices. Some antagonistic microbial strains also possess plant-growth-promoting activities and their inoculation improved plant growth in addition to disease suppression. This review discusses the characterization of antagonistic microbes and their antimicrobial metabolites, and the application of these BCAs for disease control. The present review also provides a comprehensive summary of the genetic organization and regulation of the biosynthesis of different antimicrobial metabolites in antagonistic strains. Use of molecular engineering to improve production of metabolites in BCAs and their efficacy in disease control is also discussed. The application of these biopesticides will reduce use of conventional pesticides in disease control and help in achieving sustainable and eco-friendly agricultural systems.

Preliminary Purification and Partial Characterization of a Functional Bacteriocin of Lacticaseibacillus paracasei Zhang and Mining for its Gene Cluster

Bacteriocins produced by lactic acid bacteria (LAB) have good potential for use as food biopreservatives. Lacticaseibacillus paracasei Zhang (L. paracasei Zhang) is both a food use and a probiotic bacterium. This study aimed to purify and preliminary characterize the active antibacterial metabolite of L. paracasei Zhang. The cell-free supernatant of L. paracasei Zhang was collected and purified by ultrafiltration and gel filtration chromatography. The 1-3 kDa active fraction could inhibit the growth of Staphylococcus aureus but not Escherichia coli. Further antibacterial activity assays revealed its capacity to suppress various foodborne and human opportunistic pathogens (including Staphylococcus aureus, Pseudomonas fluorescens, Pseudomonas aeruginosa, Listeria monocytogenes, and Bacillus cereus), but not fungi. The antibacterial activity showed good tolerance to heat (40 to 100 °C), acid-base (pH 2-3 and pH 6-10), and digestions by a number of industrial and animal/human enzymes (such as trypsin, pepsin, α-amylase, and protease K, except papain); these desired properties make it a suitable biopreservative to be used in harsh and complex industrial production processes. The high papain sensitivity suggested a proteinaceous/peptide nature of the bioactivity. Moreover, our genomic data mining for bacteriocin through BAGEL4 revealed an area of interest encoding a complete set of putative genes required for bacteriocin production. In conclusion, our study showed that L. paracasei Zhang can produce extracellular functional antibacterial metabolite, likely a class II bacteriocin. Our preliminary extraction and characterization of the active metabolite demonstrated that it has good potential to be used as a biopreservative or an agent for suppressing gastrointestinal infections.

Heterologous Expression of Bacteriocins from the Metagenome Mining of Cotija Cheese

Bacteriocins are a heterologous group of ribosomal peptides with antibacterial activity. They are of interest to the pharmaceutical and food industries due to their potential to fight antibiotic-resistant pathogens and improve microbial food safety, respectively. Metagenomic data mining for antibacterial activity is valuable for the information it provides from unstudied genomic sequences. Furthermore, the higher biosynthetic yield obtained by the heterologous expression of putative bacteriocins allows their subsequent purification and characterization. This work aimed to express antilisterial bacteriocins in Escherichia coli after obtaining their gene sequences by in silico mining the bacterial metagenome of Cotija cheese. This artisanal Mexican cheese is manufactured with unpasteurized milk and ripens for at least 3 months. Analyzing the Cotija cheese bacterial shotgun metagenome allowed us to select two sequences (QC1 and QC2) encoding novel Class IId bacteriocins belonging to the lactococcin family. These genes were expressed as (His)6-fusion proteins in E. coli BL21 (DE3) and showed high antimicrobial activity against Listeria monocytogenes, with a minimum inhibitory concentration of 78 µg/mL. QC1 and QC2 were tested against several pathogenic bacteria and showed activity exclusively against L. monocytogenes. QC2 has a novel sequence that showed no matches against the UniProt database. It was purified by Ni2+ affinity chromatography and retained its activity after heating at 70 °C for 30 min. As the sequences were obtained by genomic mining on a fermented food metagenome, QC1 and QC2 have potential applications as sanitizers in industrial food facilities where L. monocytogenes contamination is the most prevalent.

Acquired Bacterial Resistance to Antibiotics and Resistance Genes: From Past to Future

The discovery, commercialization, and regular administration of antimicrobial agents have revolutionized the therapeutic paradigm, making it possible to treat previously untreatable and fatal infections. However, the excessive use of antibiotics has led to develop resistance soon after their use in clinical practice, to the point of becoming a global emergency. The mechanisms of bacterial resistance to antibiotics are manifold, including mechanisms of destruction or inactivation, target site modification, or active efflux, and represent the main examples of evolutionary adaptation for the survival of bacterial species. The acquirement of new resistance mechanisms is a consequence of the great genetic plasticity of bacteria, which triggers specific responses that result in mutational adaptation, acquisition of genetic material, or alteration of gene expression, virtually producing resistance to all currently available antibiotics. Understanding resistance processes is critical to the development of new antimicrobial agents to counteract drug-resistant microorganisms. In this review, both the mechanisms of action of antibiotic resistance (AMR) and the antibiotic resistance genes (ARGs) mainly found in clinical and environmental bacteria will be reviewed. Furthermore, the evolutionary background of multidrug-resistant bacteria will be examined, and some promising elements to control or reduce the emergence and spread of AMR will be proposed.

Replicator dynamics with feedback-evolving games in heterogeneous populations

Understanding the dynamics of cooperation in public goods games is critical for enhancing collaborative efforts across various domains, yet existing literature often overlooks the complexities introduced by heterogeneous participants. In order to characterize the heterogeneity of populations, we divide individuals into knowledgeable individuals and ordinary individuals, and the games organized by different focal individuals may have different efficiency. In this study, we introduce feedback evolution games where strategies coevolve with the multiplication factor of the defector. Our results indicate that full cooperation is frequently unfeasible in crowdsourcing contexts, consistent with real-world observations. Moreover, for organizers, the increase in the proportion of knowledgeable individuals carries not only direct costs but also indirect costs that may arise from defectors. Importantly, we highlight that the speed of feedback updates plays a crucial role in fostering group cooperation, with a sufficiently high update speed being essential to overcoming social dilemmas. These insights not only advance our understanding of strategic decision-making in collaborative environments but also provide actionable implications for promoting cooperation in complex social systems.

Development of Synthetic Antimicrobial Peptides Based on Genomic Analysis of Streptococcus salivarius

BACKGROUND

In the oral environment, the production of bacteriocins or antimicrobial peptides (AMPs) plays a crucial role in maintaining ecological balance by impeding the proliferation of closely related microorganisms. This study aims to conduct in silico genome screening of Streptococcus salivarius to identify potential antimicrobial compounds existing as hypothetical peptides, with the goal of developing novel synthetic antimicrobial peptides.

METHODS

Draft genomes of various oral Streptococcus salivarius strains were obtained from the NCBI database and subjected to analysis using bioinformatic tools, viz. Expert Protein-Analysis System (Expasy), UniProt Knowledgebase (UniProtKB), European Molecular Biology Open Software Suite (EMBOSS), Pepwheel, and PEP-FOLD Peptide Structure Prediction Server. The antimicrobial potential of peptides was assessed through the Antimicrobial Peptide Database (AMP) and Bactibase. Two short peptides, viz. synthetic antimicrobial peptides (SAMPs), were designed based on current knowledge of hydrophobic and cationic residues, synthesized, and their efficacy against biofilm formation was evaluated with standard microbiological methods.

RESULTS

The synthesized short peptides reduced the growth and effectively inhibited biofilm formation by specific oral microbial strains, demonstrating their potential as antimicrobial peptides. Furthermore, the alignment of bacteriocin biosynthetic clusters among streptococcus strains revealed variations in putative bacteriocin amino acid sequences across different strains of the same organism.

CONCLUSION

Streptococcus salivarius emerges as a promising bioresource for the development of novel antimicrobial agents, particularly for combating biofilm-associated oral infections.

Biofilm formation mechanisms of mixed antibiotic-resistant bacteria in water: Bacterial interactions and horizontal transfer of antibiotic-resistant plasmids

Over 95 % of bacteria on water supply pipeline surfaces exist in biofilms, which are hotspots for antibiotic resistance gene (ARG) transmission. This study established mixed biofilm culture systems on a metal iron substrate using Escherichia coli: antibiotic-sensitive bacteria (ASB) and antibiotic-resistant bacteria (ARB). The growth rate and extracellular polymeric substances (EPS) content of mixed biofilm surpassed single-species biofilms due to synergistic interactions among different bacteria. However, the composition of mixed biofilms formed by ASB and ARB became unstable after 72 h, linked to reduced polysaccharide proportions in EPS and inter-bacterial competition. The bacterial composition and conjugative transfer frequency of ARGs in mixed biofilms indicate that biofilm formation significantly enhances horizontal transfer of ARGs. Notably, the conjugative transfer frequency of the mixed biofilm formed by two ARB increased 100-fold within five days. In contrast, the conjugative transfer frequency in the mixed biofilm formed by ASB and ARB was unstable; inter-bacterial competition led to plasmid loss associated with horizontal transfer of ARGs, ultimately resulting in biofilm shedding. Furthermore, genes associated with ARG transfer and biofilm growth up-regulated by 1.5 - 6 and 2 - 7 times, respectively, in mixed biofilm. These findings highlight a mutually reinforcing relationship between biofilm formation and horizontal ARG transmission, with significant environmental implications.

Gut Microbiota Secondary Metabolites: Key Roles in GI Tract Cancers and Infectious Diseases

The gut microbiota, a dynamic ecosystem of trillions of microorganisms, produces secondary metabolites that profoundly influence host health. Recent research has highlighted the significant role of these metabolites, particularly short-chain fatty acids, indoles, and bile acids, in modulating immune responses, impacting epigenetic mechanisms, and contributing to disease processes. In gastrointestinal (GI) cancers such as colorectal, liver, and gastric cancer, microbial metabolites can drive tumorigenesis by promoting inflammation, DNA damage, and immune evasion. Conversely, these same metabolites hold therapeutic promise, potentially enhancing responses to chemotherapy and immunotherapy and even directly suppressing tumor growth. In addition, gut microbial metabolites play crucial roles in infectious disease susceptibility and resilience, mediating immune pathways that impact pathogen resistance. By consolidating recent insights into the gut microbiota's role in shaping disease and health, this review underscores the therapeutic potential of targeting microbiome-derived metabolites for treating GI cancers and infectious diseases and calls for further research into microbiome-based interventions.

Nesting hoopoes cultivate in their uropygial gland the microbial symbionts with the highest antimicrobial capacity

The European hoopoe (Upupa epops) conforms a paradigmatic example of animals cultivating bacteria in their uropygial gland that protect them against pathogenic infections. We here explore the hypothesis that enterococci are the responsible bacteria of such beneficial effect. We did so by comparing the antimicrobial activity against three indicator bacteria of colonies isolated from cultures of enterococci and mesophilic bacteria from the uropygial skin or secretion of nestlings, brooding or non-brooding females, and males of the subspecies longirostris in Hainan (China). In accordance with the hypothesis, enterococci isolated from nesting birds are more active than those from non-nesting birds. Moreover, enterococci from the uropygial secretion were more active than those isolated from the skin or than mesophilic bacteria isolates. These results therefore support the hypothesis that, during the nesting phase, hoopoe females and nestlings cultivate enterococci in their uropygial gland with relatively high antimicrobial activity.

Presence of lactic acid bacteria in hydrogen production by dark fermentation: competition or synergy

Dark fermentation in mixed cultures has been extensively studied due to its great potential for sustainable hydrogen production from organic wastes. However, microbial composition, substrate competition, and inhibition by fermentation products can affect hydrogen yield and production rates. Lactic acid bacteria have been identified as the key organisms in this process. On one hand, lactic acid bacteria can efficiently compete for carbohydrate rich substrates, producing lactic acid and secreting bacteriocins that inhibit the growth of hydrogen-producing bacteria, thereby decreasing hydrogen production. On the other hand, due to their metabolic capacity and synergistic interactions with certain hydrogen-producing bacteria, they contribute positively in several ways, for example by providing lactic acid as a substrate for hydrogen generation. Analyzing different perspectives about the role of lactic acid bacteria in hydrogen production by dark fermentation, a literature review was done on this topic. This review article shows a comprehensive view to understand better the role of these bacteria and their influence on the process efficiency, either as competitors or as contributors to hydrogen production by dark fermentation.

Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.

Disentangling the Factors Selecting for Unicellular Programmed Cell Death

AbstractThe widespread occurrence of genetically programmed cell death (PCD) in unicellular species poses an evolutionary puzzle. While kin selection theory predicts that the fitness benefits of cell suicide must be preferentially directed toward genetic relatives, it does not predict the nature of these benefits. Furthermore, cell suicide must be conditionally expressed, leaving open the question of what conditions optimally regulate expression. Here we formalize several verbal hypotheses for the ecological function of unicellular PCD. We show that self-sacrifice by healthy cells cannot evolve. Instead, PCD evolution requires that damaged cells sense impending death and then (1) expedite this death to spare resources for groupmates, (2) prepare cellular contents so that necrotic toxins are not released upon death, or initiate autolysis in order to (3) release beneficial compounds or (4) release anticompetitior toxins. The prerequisite ability to predict death is a severe cell biological constraint as well as an ecological constraint that restricts PCD evolution to species with specific sources of mortality. We show that the specific type of PCD that will evolve, though, differs on the basis of a species' ecology, life history, and genetic structure.

BglaTNB6, a tailocin produced by a plant-associated nonpathogenic bacterium, prevents rice seed-borne bacterial diseases

Rice seed-borne diseases caused by the bacterial pathogens Burkholderia glumae and B. plantarii pose a major threat to rice production worldwide. To manage these diseases in a sustainable manner, a biocontrol strategy is crucial. In this study, we showed that B. gladioli NB6 (NB6), a nonpathogenic bacterium, strongly protects rice from infection caused by the above-mentioned pathogens. NB6 was isolated from the indica rice cultivar Nona Bokra seedlings, which possesses genetic resistance to B. glumae. We discovered that cell suspensions of NB6 and its culture filtrate suppressed the disease symptoms caused by B. glumae and B. plantarii in rice seedlings, which indicated that NB6 secretes a plant-protective substance extracellularly. Through purification and mass spectrometry analysis of the culture filtrate, combined with transmission electron microscopy and mutant analysis, the substance was identified as a tailocin and named BglaTNB6. Tailocins are bacteriotoxic multiprotein structures morphologically similar to headless phage tails. BglaTNB6 exhibited antibacterial activity against several Burkholderia species, including B. glumae, B. plantarii, and B. gladioli, suggesting it can prevent pathogen infection. Interestingly, BglaTNB6 greatly contributed only to the biocontrol activity of NB6 cell suspensions against B. plantarii, and not against B. glumae. BglaTNB6 was shown to be encoded by a prophage locus lacking genes for phage head proteins, and a B. gladioli strain with the coded BglaTNB6-like locus equipped with phage head proteins failed to prevent rice seedlings from being infected with B. plantarii. These results suggested that BglaTNB6 may enhance the competitiveness of NB6 against a specific range of bacteria. Our study also highlights the potential of tailocin-producing endophytes for managing crop bacterial diseases.

Evolutionary stability of developmental commitment

Evolution of unicellular to multicellular organisms must resolve conflicts in reproductive interests between individual cells and the group. The social amoeba Dictyostelium discoideum is a soil-living eukaryote with facultative sociality. While cells grow in the presence of nutrients, cells aggregate under starvation to form fruiting bodies containing spores and altruistic stalk cells. Once cells socially committed, they complete formation of fruiting bodies, even if a new source of nutrients becomes available. The persistence of this social commitment raises questions as it inhibits individual cells from swiftly returning to solitary growth. I hypothesize that traits enabling premature de-commitment are hindered from being selected. Recent work has revealed outcomes of the premature de-commitment through forced refeeding; The de-committed cells take an altruistic prestalk-like position due to their reduced cohesiveness through interactions with socially committed cells. I constructed an evolutionary model assuming their division of labor. The results revealed a valley in the fitness landscape that prevented invasion of de-committing mutants, indicating evolutionary stability of the social commitment. The findings provide a general scheme that maintains multicellularity by evolving a specific division of labor, in which less cohesive individuals become altruists.

Plant growth-promoting rhizobacterial secondary metabolites in augmenting heavy metal(loid) phytoremediation: An integrated green in situ ecorestorative technology

In recent times, increased geogenic and human-centric activities have caused significant heavy metal(loid) (HM) contamination of soil, adversely impacting environmental, plant, and human health. Phytoremediation is an evolving, cost-effective, environment-friendly, in situ technology that employs indigenous/exotic plant species as natural purifiers to remove toxic HM(s) from deteriorated ambient soil. Interestingly, the plant's rhizomicrobiome is pivotal in promoting overall plant nutrition, health, and phytoremediation. Certain secondary metabolites produced by plant growth-promoting rhizobacteria (PGPR) directly participate in HM bioremediation through chelation/mobilization/sequestration/bioadsorption/bioaccumulation, thus altering metal(loid) bioavailability for their uptake, accumulation, and translocation by plants. Moreover, the metallotolerance of the PGPR and the host plant is another critical factor for the successful phytoremediation of metal(loid)-polluted soil. Among the phytotechniques available for HM remediation, phytoextraction/phytoaccumulation (HM mobilization, uptake, and accumulation within the different plant tissues) and phytosequestration/phytostabilization (HM immobilization within the soil) have gained momentum in recent years. Natural metal(loid)-hyperaccumulating plants have the potential to assimilate increased levels of metal(loid)s, and several such species have already been identified as potential candidates for HM phytoremediation. Furthermore, the development of transgenic rhizobacterial and/or plant strains with enhanced environmental adaptability and metal(loid) uptake ability using genetic engineering might open new avenues in PGPR-assisted phytoremediation technologies. With the use of the Geographic Information System (GIS) for identifying metal(loid)-impacted lands and an appropriate combination of normal/transgenic (hyper)accumulator plant(s) and rhizobacterial inoculant(s), it is possible to develop efficient integrated phytobial remediation strategies in boosting the clean-up process over vast regions of HM-contaminated sites and eventually restore ecosystem health.

Exploring pathological link between antimicrobial and amyloid peptides

Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.

Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds

BACKGROUND

Animal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies (Pica pica) and great spotted cuckoos (Clamator glandarius) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin.

RESULTS

We demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies.

CONCLUSIONS

Our findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite-host system.

Overcoming toxicity: why boom-and-bust cycles are good for non-antagonistic microbes

Antagonistic interactions are critical determinants of microbial community stability and composition, offering host benefits such as pathogen protection and providing avenues for antimicrobial control. While the ability to eliminate competitors confers an advantage to antagonistic microbes, it often incurs a fitness cost. Consequently, many microbes only produce toxins or engage in antagonistic behavior in response to specific cues like population density or environmental stress. In laboratory settings, antagonistic microbes typically dominate over sensitive ones, raising the question of why both antagonistic and non-antagonistic microbes are found in natural environments and host microbiomes. Here, using both theoretical models and experiments with killer strains of Saccharomyces cerevisiae , we show that boom-and-bust dynamics caused by temporal environmental fluctuations can favor non-antagonistic microbes that do not incur the growth rate cost of toxin production. Additionally, using control theory, we derive bounds on the competitive performance and identify optimal regulatory toxin-production strategies in various boom-and-bust environments where population dilutions occur either deterministically or stochastically over time. Our findings offer a new perspective on how both antagonistic and non-antagonistic microbes can thrive under varying environmental conditions.

Escherichia coli removal in down-flow hanging sponge reactors: insights from laboratory reactor studies

Down-flow hanging sponge (DHS) reactors, employed in domestic wastewater treatment, have demonstrated efficacy in eliminating Escherichia coli and other potentially pathogenic bacteria. The aim of this study was to elucidate the mechanism of removal of E. coli by employing a cube-shaped polyurethane sponge carrier within a compact hanging reactor. An E. coli removal experiment was conducted on this prepared sponge. Escherichia. coli level was found to decrease by more than 2 logs after passing through five nutrient-restricted DHS sponges. Conversely, a newly introduced sponge did not exhibit a comparable reduction in E. coli level. Furthermore, under conditions of optimal nutritional status, the reduction in E. coli level was limited to 0.5 logs, underscoring the crucial role of nutrient restriction in achieving effective elimination. Analysis of the sponge-associated bacterial community revealed the presence of a type VI secretion system (T6SS), a competitive mechanism observed in bacteria. This finding suggests that T6SS might play a pivotal role in contributing to the observed decline in E. coli level.

MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?

Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.

High-throughput detection of potential bacteriocin producers in a large strain library using live fluorescent biosensors

The global increase in antibiotic resistances demands for additional efforts to identify novel antimicrobials such as bacteriocins. These antimicrobial peptides of bacterial origin are already used widely in food preservation and promising alternatives for antibiotics in animal feed and some clinical setting. Identification of novel antimicrobials is facilitated by appropriate high throughput screening (HTS) methods. Previously, we have described a rapid, simple and cost-efficient assay based on live biosensor bacteria for detection of antimicrobial compounds that act on membrane integrity using the ratiometric pH-dependent fluorescent protein pHluorin2 (pHin2). Here, we use these biosensors to develop an integrated pipeline for high-throughput identification of bacteriocin producers and their biosynthetic gene clusters. We extend the existing portfolio of biosensors by generating pHin2 expressing strains of Escherichia coli, Bacillus cereus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus. These strains were characterized, and control experiments were performed to assess heterogeneity of these biosensors in response to known bacteriocins and develop a robust HTS system. To allow detection of compounds that inhibit target bacteria by inhibiting growth without disturbing membrane integrity, the HTS system was extended with a growth-dependent readout. Using this HTS system, we screened supernatants of a total of 395 strains of a collection of lactic acid bacteria. After two rounds of screening 19 strains of the collection were identified that produced antimicrobial activity against Listeria innocua and Listeria monocytogenes. Genomes of confirmed hits were sequenced and annotated. In silico analysis revealed that the identified strains encode between one and six biosynthetic gene clusters (BGCs) for bacteriocins. Our results suggest that pHin2 biosensors provides a flexible, cheap, fast, robust and easy to handle HTS system for identification of potential bacteriocins and their BGCs in large strain collections.

Biochemical characterisation and production kinetics of high molecular-weight (HMW) putative antibacterial proteins of insect pathogenic Brevibacillus laterosporus isolates

BACKGROUND

Bacterial genomes often encode structures similar to phage capsids (encapsulins) and phage tails which can be induced spontaneously or using genotoxic compounds such as mitomycin C. These high molecular-weight (HMW) putative antibacterial proteins (ABPs) are used against the competitive strains under natural environment. Previously, it was unknown whether these HMW putative ABPs originating from the insect pathogenic Gram-positive, spore-forming bacterium Brevibacillus laterosporus (Bl) isolates (1821L, 1951) are spontaneously induced during the growth and pose a detrimental effect on their own survival. Furthermore, no prior work has been undertaken to determine their biochemical characteristics.

RESULTS

Using a soft agar overlay method with polyethylene glycol precipitation, a narrow spectrum of bioactivity was found from the precipitated lysate of Bl 1951. Electron micrographs of mitomycin C- induced filtrates showed structures similar to phage capsids and contractile tails. Bioactivity assays of cell free supernatants (CFS) extracted during the growth of Bl 1821L and Bl 1951 suggested spontaneous induction of these HMW putative ABPs with an autocidal activity. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of spontaneously induced putative ABPs showed appearance of ~ 30 kDa and ~ 48 kDa bands of varying intensity across all the time intervals during the bacterial growth except in the initial hours. Statistically, spontaneously induced HMW putative ABPs of Bl 1951 exhibited a significant decrease in the number of viable cells of its producer strain after 18 h of growth in liquid. In addition, a significant change in pH and prominent bioactivity of the CFS of this particular time period was noted. Biochemically, the filtered supernatant derived from either Bl 1821L or Bl 1951 maintained bioactivity over a wide range of pH and temperature.

CONCLUSION

This study reports the spontaneous induction of HMW putative ABPs (bacteriocins) of Bl 1821L and Bl 1951 isolates during the course of growth with potential autocidal activity which is critically important during production as a potential biopesticide. A narrow spectrum of putative antibacterial activity of Bl 1951 precipitate was found. The stability of HMW putative ABPs of Bl 1821L and Bl 1951 over a wide range of pH and temperature can be useful in expanding the potential of this useful bacterium beyond the insecticidal value.

Microcin C7 as a Potential Antibacterial-Immunomodulatory Agent in the Postantibiotic Era: Overview of Its Bioactivity Aspects and Applications

In the postantibiotic era, the pathogenicity and resistance of pathogens have increased, leading to an increase in intestinal inflammatory disease. Bacterial infections remain the leading cause of animal mortality. With increasing resistance to antibiotics, there has been a significant decrease in resistance to both inflammation and disease in animals, thus decreasing production efficiency and increasing production costs. These side effects have serious consequences and have detracted from the development of China's pig industry. Microcin C7 (McC7) demonstrates potent antibacterial activity against a broad spectrum of pathogens, stable physicochemical properties, and low toxicity, reducing the likelihood of resistance development. Thus, McC7 has received increasing attention as a potential clinical antibacterial and immunomodulatory agent. McC7 has the potential to serve as a new generation of antibiotic substitutes; however, its commercial applications in the livestock and poultry industry have been limited. In this review, we summarize and discuss the biosynthesis, biochemical properties, structural characteristics, mechanism of action, and immune strategies of McC7. We also describe the ability of McC7 to improve intestinal health. Our aim in this study was to provide a theoretical basis for the application of McC7 as a new feed additive or new veterinary drug in the livestock and poultry breeding industry, thus providing a new strategy for alleviating resistance through feed and mitigating drug resistance. Furthermore, this review provides insight into the new functions and anti-infection mechanisms of bacteriocin peptides and proposes crucial ideas for the research, product development, and application of bacteriocin peptides in different fields, such as the food and medical industries.

Nisin Inhibition of Gram-Negative Bacteria

Aims: This study investigates the activity of the broad-spectrum bacteriocin nisin against a large panel of Gram-negative bacterial isolates, including relevant plant, animal, and human pathogens. The aim is to generate supportive evidence towards the use/inclusion of bacteriocin-based therapeutics and open avenues for their continued development. Methods and Results: Nisin inhibitory activity was screened against a panel of 575 strains of Gram-negative bacteria, encompassing 17 genera. Nisin inhibition was observed in 309 out of 575 strains, challenging the prevailing belief that nisin lacks effectiveness against Gram-negative bacteria. The genera Acinetobacter, Helicobacter, Erwinia, and Xanthomonas exhibited particularly high nisin sensitivity. Conclusions: The findings of this study highlight the promising potential of nisin as a therapeutic agent for several key Gram-negative plant, animal, and human pathogens. These results challenge the prevailing notion that nisin is less effective or ineffective against Gram-negative pathogens when compared to Gram-positive pathogens and support future pursuits of nisin as a complementary therapy to existing antibiotics. Significance and Impact of Study: This research supports further exploration of nisin as a promising therapeutic agent for numerous human, animal, and plant health applications, offering a complementary tool for infection control in the face of multidrug-resistant bacteria.

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.

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

Campylobacter is a leading cause of food-borne gastroenteritis worldwide, linked to the consumption of contaminated poultry meat. Targeting this pathogen at source, vaccines for poultry can provide short-term caecal reductions in Campylobacter numbers in the chicken intestine. However, this approach is unlikely to reduce Campylobacter in the food chain or human incidence. This is likely as vaccines typically target only a subset of the high genomic strain diversity circulating among chicken flocks, and rapid evolution diminishes vaccine efficacy over time. To address this, we used a genomic approach to develop a whole-cell autogenous vaccine targeting isolates harbouring genes linked to survival outside of the host. We hyper-immunised a whole major UK breeder farm to passively target offspring colonisation using maternally-derived antibody. Monitoring progeny, broiler flocks revealed a near-complete shift in the post-vaccination Campylobacter population with an ~50% reduction in isolates harbouring extra-intestinal survival genes and a significant reduction of Campylobacter cells surviving on the surface of meat. Based on these findings, we developed a logistic regression model that predicted that vaccine efficacy could be extended to target 65% of a population of clinically relevant strains. Immuno-manipulation of poultry microbiomes towards less harmful commensal isolates by competitive exclusion, has major potential for reducing pathogens in the food production chain.

PLGA nanoparticle-encapsulated lysostaphin for the treatment of Staphylococcus aureus infections

Staphylococcus aureus possesses the ability to become pathogenic, leading to severe and life-threatening infections. Its methicillin-resistant variant MRSA has garnered high-priority status due to its increased morbidity and associated mortality. This emphasizes the urgency for novel anti-staphylococcal agents. The bacteriocin lysostaphin stands out for its remarkable bactericidal activity against S. aureus, including MRSA, outperforming conventional antibiotics. However, the clinical application of lysostaphin faces challenges, including enzymatic activity loss under physiological conditions and potential immunogenicity. This study introduces a novel approach by encapsulating lysostaphin within polylactic-co-glycolic acid (PLGA) nanoparticles, a biodegradable copolymer known for its biocompatibility and sustained drug release ability. The study assesses the antimicrobial activity of lysostaphin-loaded PLGA nanoparticles against different S. aureus strains, and we also used GFP-expressing S. aureus for facilitating its traceability in planktonic, biofilm, and intracellular infection models. The results showed the significant reduction in bacteria viability both in planktonic and biofilm states. The in vitro intracellular infection model demonstrated the significantly enhanced efficiency of the developed nanoparticles compared to the treatment with the free bacteriocin. This research presents lysostaphin encapsulation within PLGA nanoparticles and offers promising avenues for enhancing lysostaphin's therapeutic efficacy against S. aureus infections.

Turbidimetric bioassays: A solution to antimicrobial activity detection in asymptomatic bacteriuria isolates against uropathogenic Escherichia coli

Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and SK-106-1). The inhibition of the CFS by proteinase K suggested that the antimicrobial activity was proteinaceous in nature, potentially bacteriocins. The activity of E. coli PUTS 58 and SK-106-1 was enhanced in an artificial urine medium, with both inhibiting all eight UPECs. A putative microcin H47 operon was identified in E. coli SK-106-1, along with a previously identified microcin V and colicin E7 in E. coli PUTS 37 and PUTS 58, respectively. These findings indicate that ABU bacteriocin-producers could serve as viable prophylactics and therapeutics in the face of increasing antibiotic resistance among uropathogens.

In Vitro and In Silico Characterization of N-Formylated Two-Peptide Bacteriocin from Enterococcus faecalis CAUM157 with Anti-Listeria Activity

Enterococcus faecalis CAUM157 (KACC 81148BP), a Gram-positive bacteria isolated from raw cow's milk, was studied for its bacteriocin production. The antimicrobial activity of CAUM157 was attributed to a two-peptide class IIb bacteriocin with potent activity against food-borne pathogen Listeria monocytogenes and periodontal disease-causing pathogens (Prevotella intermedia KCTC 15693 T and Fusobacterium nucleatum KCTC 2488 T). M157 bacteriocins exhibit high temperature and pH stability and resist hydrolytic enzyme degradation and detergent denaturation, potentially due to their structural conformation. Based on amino acid sequence, M157A and M157B were predicted to be 5.176 kDa and 5.182 kDa in size, respectively. However, purified bacteriocins and chemically synthesized N-formylated M157 peptides both showed 5.204 kDa (M157A) and 5.209 kDa (M157B) molecular mass, confirming the formylation of the N-terminal methionine of both peptides produced by strain CAUM157. Furthermore, the strain demonstrated favorable growth and fermentation with minimal bacteriocin production when cultured in whey-based media, whereas a 1.0% tryptone or soytone supplementation resulted in higher bacteriocin production. Although Ent. faecalis CAUM157 innately harbors genes for virulence factors and antimicrobial resistance (e.g., tetracycline and erythromycin), its bacteriocin production is valuable in circumventing the need for live microorganisms, particularly in food applications for pathogen control.

Improved production of RNA-inhibiting antimicrobial peptide by Bacillus licheniformis MCC 2514 facilitated by a genetic algorithm optimized medium

One of the significant challenges during the purification and characterization of antimicrobial peptides (AMPs) from Bacillus sp. is the interference of unutilized peptides from complex medium components during analytical procedures. In this study, a semi-synthetic medium was devised to overcome this challenge. Using a genetic algorithm, the production medium of AMP is optimized. The parent organism, Bacillus licheniformis MCC2514, produces AMP in very small quantities. This AMP is known to inhibit RNA biosynthesis. The findings revealed that lactose, NH4Cl and NaNO3 were crucial medium constituents for enhanced AMP synthesis. The potency of the AMP produced was studied using bacterium, Kocuria rhizophila ATCC 9341. The AMP produced from the optimized medium was eightfold higher than that produced from the unoptimized medium. Furthermore, activity was increased by 1.5-fold when cultivation conditions were standardized using the optimized medium. Later, AMP was produced in a 5 L bioreactor under controlled conditions, which led to similar results as those of shake-flask production. The mode of action of optimally produced AMP was confirmed to be inhibition of RNA biosynthesis. Here, we demonstrate that improved production of AMP is possible with the developed semi-synthetic medium recipe and could help further AMP production in an industrial setup.

Greenbeards in plants?

Greenbeards are selfish genetic elements that make their bearers behave either altruistically towards individuals bearing similar greenbeard copies or harmfully towards individuals bearing different copies. They were first proposed by W. D. Hamilton over 50 yr ago, to illustrate that kin selection may operate at the level of single genes. Examples of greenbeards have now been reported in a wide range of taxa, but they remain undocumented in plants. In this paper, we discuss the theoretical likelihood of greenbeard existence in plants. We then question why the greenbeard concept has never been applied to plants and speculate on how hypothetical greenbeards could affect plant-plant interactions. Finally, we point to different research directions to improve our knowledge of greenbeards in plants.

Bacteriocins: potentials and prospects in health and agrifood systems

Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.

Peptide Dendrimer-Based Antibacterial Agents: Synthesis and Applications

Pathogenic bacteria cause the deaths of millions of people every year. With the development of antibiotics, hundreds and thousands of people's lives have been saved. Nevertheless, bacteria can develop resistance to antibiotics, rendering them insensitive to antibiotics over time. Peptides containing specific amino acids can be used as antibacterial agents; however, they can be easily degraded by proteases in vivo. To address these issues, branched peptide dendrimers are now being considered as good antibacterial agents due to their high efficacy, resistance to protease degradation, and low cytotoxicity. The ease with which peptide dendrimers can be synthesized and modified makes them accessible for use in various biological and nonbiological fields. That is, peptide dendrimers hold a promising future as antibacterial agents with prolonged efficacy without bacterial resistance development. Their in vivo stability and multivalence allow them to effectively target multi-drug-resistant strains and prevent biofilm formation. Thus, it is interesting to have an overview of the development and applications of peptide dendrimers in antibacterial research, including the possibility of employing machine learning approaches for the design of AMPs and dendrimers. This review summarizes the synthesis and applications of peptide dendrimers as antibacterial agents. The challenges and perspectives of using peptide dendrimers as the antibacterial agents are also discussed.

Blue Biotechnology: Marine Bacteria Bioproducts

The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.

An exploratory in silico analysis of bacteriocin gene clusters in the urobiome

Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production. Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7. Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins. Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.

Gonorrhea caused due to antimicrobial-resistant bacteria Neisseria gonorrhoeae treated using probiotic peptide

Neisseria gonorrhea is a sexually transmitted disease from gonorrhea that lacks treatment; despite the urgency, the absence of adequate drugs, lack of human correlates of protection, and inadequate animal models of infection have delayed progress toward the prevention of gonococcal infection. Lactobacillus crispatus is a lactic acid bacterium typically found in the human vaginal microbiota. Peptides from L. crispatus have shown a potential therapeutic option for targetting N. gonorrhea. Bioinformatics analysis is important for speeding up drug target acquisition, screening refinement, and evaluating adverse effects and drug resistance prediction. Therefore, this study identified an antimicrobial peptide from the bacteriocin immunity protein (BIP) of L. crispatus using the bioinformatics tool and Collection of Antimicrobial Peptide (CAMPR3). Based on the AMP score and highest ADMET properties, the peptide SM20 was chosen for docking analysis. SM20 was docked against multiple proteins from the genome of the AMR bacterium N. gonorrhea using an online tool; protein-peptide interactions were established and visualized using the PyMol visualizing tool. Molecular docking was carried out using the CABSdock tool, and multiple conformations were obtained against the membrane proteins of N. gonorrhoea. The peptide SM20 exhibited higher docking scores and ADMET properties. Therefore, SM20 could be further encapsulated with cellulose; it can be applied topically to the genital tract to target N. gonorrhea infection. The controlled release of the antimicrobial peptide from the gel can provide sustained delivery of the treatment, increasing its efficacy and reducing the risk of resistance development.

The role of proteinaceous toxins secreted by Staphylococcus aureus in interbacterial competition

Staphylococcus aureus is highly adapted to colonization of the mammalian host. In humans the primary site of colonization is the epithelium of the nasal cavity. A major barrier to colonization is the resident microbiota, which have mechanisms to exclude S. aureus. As such, S. aureus has evolved mechanisms to compete with other bacteria, one of which is through secretion of proteinaceous toxins. S. aureus strains collectively produce a number of well-characterized Class I, II, and IV bacteriocins as well as several bacteriocin-like substances, about which less is known. These bacteriocins have potent antibacterial activity against several Gram-positive organisms, with some also active against Gram-negative species. S. aureus bacteriocins characterized to date are sporadically produced, and often encoded on plasmids. More recently the type VII secretion system (T7SS) of S. aureus has also been shown to play a role in interbacterial competition. The T7SS is encoded by all S. aureus isolates and so may represent a more widespread mechanism of competition used by this species. T7SS antagonism is mediated by the secretion of large protein toxins, three of which have been characterized to date: a nuclease toxin, EsaD; a membrane depolarizing toxin, TspA; and a phospholipase toxin, TslA. Further study is required to decipher the role that these different types of secreted toxins play in interbacterial competition and colonization of the host.

BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier

The use of bacteriocins has emerged as a propitious strategy in the development of new drugs to combat antibiotic resistance, given their ability to kill bacteria with both broad and narrow natural spectra. Hence, a compelling requirement arises for a precise and efficient computational model that can accurately predict novel bacteriocins. Machine learning's ability to learn patterns and features from bacteriocin sequences that are difficult to capture using sequence matching-based methods makes it a potentially superior choice for accurate prediction. A web application for predicting bacteriocin was created in this study, utilizing a machine learning approach. The feature sets employed in the application were chosen using alternating decision tree (ADTree), genetic algorithm (GA), and linear support vector classifier (linear SVC)-based feature evaluation methods. Initially, potential features were extracted from the physicochemical, structural, and sequence-profile attributes of both bacteriocin and non-bacteriocin protein sequences. We assessed the candidate features first using the Pearson correlation coefficient, followed by separate evaluations with ADTree, GA, and linear SVC to eliminate unnecessary features. Finally, we constructed random forest (RF), support vector machine (SVM), decision tree (DT), logistic regression (LR), k-nearest neighbors (KNN), and Gaussian naïve Bayes (GNB) models using reduced feature sets. We obtained the overall top performing model using SVM with ADTree-reduced features, achieving an accuracy of 99.11% and an AUC value of 0.9984 on the testing dataset. We also assessed the predictive capabilities of our best-performing models for each reduced feature set relative to our previously developed software solution, a sequence alignment-based tool, and a deep-learning approach. A web application, titled BPAGS (Bacteriocin Prediction based on ADTree, GA, and linear SVC), was developed to incorporate the predictive models built using ADTree, GA, and linear SVC-based feature sets. Currently, the web-based tool provides classification results with associated probability values and has options to add new samples in the training data to improve the predictive efficacy. BPAGS is freely accessible at https://shiny.tricities.wsu.edu/bacteriocin-prediction/.

The Role of Probiotics in Improving Food Safety: Inactivation of Pathogens and Biological Toxins

Currently, many advances have been made in avoiding food contamination by numerous pathogenic and toxigenic microorganisms. Many studies have shown that different probiotics, in addition to having beneficial effects on the host's health, have a very good ability to eliminate and neutralize pathogens and their toxins in foods which leads to enhanced food safety. The present review purposes to comprehensively discuss the role of probiotics in improving food safety by inactivating pathogens (bacterial, fungal, viral, and parasite agents) and neutralizing their toxins in food products. Some recent examples in terms of the anti-microbial activities of probiotics in the body after consuming contaminated food have also been mentioned. This review shows that different probiotics have the potential to inactivate pathogens and neutralize and detoxify various biological agents in foods, as well as in the host body after consumption.

Inhibitors targeting BamA in gram-negative bacteria

Antibiotic resistance has led to an increase in the number of patient hospitalizations and deaths. The situation for gram-negative bacteria is especially dire as the last new class of antibiotics active against these bacteria was introduced to the clinic over 60 years ago, thus there is an immediate unmet need for new antibiotic classes able to overcome resistance. The outer membrane, a unique and essential structure in gram-negative bacteria, contains multiple potential antibacterial targets including BamA, an outer membrane protein that folds and inserts transmembrane β-barrel proteins. BamA is essential and conserved, and its outer membrane location eliminates a barrier that molecules must overcome to access this target. Recently, antibacterial small molecules, natural products, peptides, and antibodies that inhibit BamA activity have been reported, validating the druggability of this target and generating potential leads for antibiotic development. This review will describe these BamA inhibitors, highlight their key attributes, and identify challenges with this potential target.

Searching for Antimicrobial-Producing Bacteria from Soils through an Educational Project and Their Evaluation as Potential Biocontrol Agents

Antimicrobial resistance (AMR) is a serious threat to public health due to the lack of effective drugs to combat infectious diseases, which generates the need to search for new antimicrobial substances. In this study, the potential of soil as a source of antimicrobial-producing bacteria (APB) was investigated and the importance of the connection between education and science was emphasized, using service-learning methodologies. Sixty-one soil samples were collected, and 1220 bacterial isolates were recovered. Eighteen of these isolates showed antimicrobial activity against at least 1 of the 12 indicator bacteria tested (including multidrug-resistant and relevant pathogens). The 18 APB were identified by MALDI-TOF and 6 different genera (Bacillus, Brevibacillus, Lysinobacillus, Peribacillus, Streptomyces, and Advenella) and 10 species were identified. The 18 APB were tested for antifungal activity against four phytopathogenic fungi (Botritis cynerea, Lecanicillium fungicola, Trichoderma harzianum, and Cladobotryum mycophilum). Moreover, the antibiotic susceptibility of APB was tested using the disk-diffusion method as well as their β-hemolytic activity (important safety criteria for potential future applications). A total of 10 of the 18 APB were able to inhibit at least 50% of indicator bacteria tested, including methicillin-resistant Staphylococcus aureus (MRSA), among others. A total of 4 of the 18 APB (3 Bacillus pumilus and 1 Bacillus altitudinis) showed inhibitory activity against two of the four fungal pathogens tested (B. cinerea and L. fungicola), as well as against 5-7 of the 12 bacterial pathogen indicators; these 4 isolates showed susceptibility to the antibiotics tested and lacked β-hemolytic activity and were considered promising APB for use as potential biocontrol agents. In addition, one Brevibacillus laterosporus strain had activity against 83% of indicator bacteria tested including Escherichia coli, MRSA and other methicillin-resistant staphylococci, as well as vancomycin-resistant enterococci (but not against fungi). These results show that soil is a source of APB with relevant antibacterial and antifungal activities, and also emphasize the importance of education and science to raise public awareness of the AMR problem and the strategies to control it.

Reduced social function in experimentally evolved Dictyostelium discoideum implies selection for social conflict in nature

Many microbes interact with one another, but the difficulty of directly observing these interactions in nature makes interpreting their adaptive value complicated. The social amoeba Dictyostelium discoideum forms aggregates wherein some cells are sacrificed for the benefit of others. Within chimaeric aggregates containing multiple unrelated lineages, cheaters can gain an advantage by undercontributing, but the extent to which wild D. discoideum has adapted to cheat is not fully clear. In this study, we experimentally evolved D. discoideum in an environment where there were no selective pressures to cheat or resist cheating in chimaeras. Dictyostelium discoideum lines grown in this environment evolved reduced competitiveness within chimaeric aggregates and reduced ability to migrate during the slug stage. By contrast, we did not observe a reduction in cell number, a trait for which selection was not relaxed. The observed loss of traits that our laboratory conditions had made irrelevant suggests that these traits were adaptations driven and maintained by selective pressures D. discoideum faces in its natural environment. Our results suggest that D. discoideum faces social conflict in nature, and illustrate a general approach that could be applied to searching for social or non-social adaptations in other microbes.

Lack of PNPase activity in Enterococcus faecalis 14 increases the stability of EntDD14 bacteriocin transcripts

A mutant deficient in polynucleotide phosphorylase (PNPase) activity was previously constructed in Enterococcus faecalis 14; a strain producing a leaderless two-peptide enterocin DD14 (EntDD14). Here, we examined the impact of the absence of PNPase on the expression and synthesis of EntDD14, at the transcriptional and functional levels. As result, EntDD14 synthesis augmented in line with the growth curve, reaching a two- to fourfold increase in the ΔpnpA mutant compared to the E. faecalis 14 wild-type strain (WT). EntDD14 synthesis has reached its highest level after 9 h of growth in both strains. Notably, high expression level of the ddABCDEFGHIJ cluster was registered in ΔpnpA mutant. Transcriptional and in silico analyses support the existence of ddAB and ddCDEFGHIJ independent transcripts, and analysis of the fate of ddAB and ddCDEFGHIJ mRNAs indicated that the differences in mRNA levels and the high EntDD14 activity are likely due to a better stability of the two transcripts in the ΔpnpA mutant, which should result in a higher translation efficiency of the ddAB EntDD14 structural genes and their other protein determinants. Consequently, this study shows a potential link between the mRNA stability and EntDD14 synthesis, secretion and immunity in a genetic background lacking PNPase.

On the De Novo Emergence of Ecological Interactions during Evolutionary Diversification: A Conceptual Framework and Experimental Test

AbstractEcological interactions are crucial to the structure and function of biological communities, but we lack a causal understanding of the forces shaping their emergence during evolutionary diversification. Here we provide a conceptual framework linking different modes of diversification (e.g., ecological diversification), which depend on environmental characteristics, to the evolution of different forms of ecological interactions (e.g., resource partitioning) in asexual lineages. We tested the framework by examining the net interactions in communities of Pseudomonas aeruginosa produced via experimental evolution in nutritionally simple (SIM) or complex (COM) environments by contrasting the productivity and competitive fitness of whole evolved communities relative to their component isolates. As expected, we found that nutritional complexity drove the evolution of communities with net positive interactions whereas SIM communities had similar performance as their component isolates. A follow-up experiment revealed that high fitness in two COM communities was driven by rare variants (frequency <0.1%) that antagonized PA14, the ancestral strain and common competitor used in fitness assays. Our study suggests that the evolution of de novo ecological interactions in asexual lineages is predictable at a broad scale from environmental conditions. Further, our work demonstrates that rare variants can disproportionately impact the function of relatively simple microbial communities.

Systemic application of bone-targeting peptidoglycan hydrolases as a novel treatment approach for staphylococcal bone infection

IMPORTANCE

The rising prevalence of antimicrobial resistance in S. aureus has rendered treatment of staphylococcal infections increasingly difficult, making the discovery of alternative treatment options a high priority. Peptidoglycan hydrolases, a diverse group of bacteriolytic enzymes, show high promise as such alternatives due to their rapid and specific lysis of bacterial cells, independent of antibiotic resistance profiles. However, using these enzymes for the systemic treatment of local infections, such as osteomyelitis foci, needs improvement, as the therapeutic distributes throughout the whole host, resulting in low concentrations at the actual infection site. In addition, the occurrence of intracellularly persisting bacteria can lead to relapsing infections. Here, we describe an approach using tissue-targeting to increase the local concentration of therapeutic enzymes in the infected bone. The enzymes were modified with a short targeting moiety that mediated accumulation of the therapeutic in osteoblasts and additionally enables targeting of intracellularly surviving bacteria.

Circular and L50-like leaderless enterocins share a common ABC-transporter immunity gene

Microbes live within complex communities of interacting populations, either free-living in waters and soils or symbionts of animals and plants. Their interactions include the production of antimicrobial peptides (bacteriocins) to antagonize competitors, and these producers must carry their own immunity gene for self-protection. Whether other coexisting populations are sensitive or resistant to the bacteriocin producer will be key for the population dynamics within the microbial community. The immunity gene frequently consists of an ABC transporter to repel its own bacteriocin but rarely protects against a nonrelated bacteriocin. A case where this cross-resistance occurs mediated by a shared ABC transporter has been shown between enterocins MR10A/B and AS-48. The first is an L50-like leaderless enterocin, while AS-48 is a circular enterocin. In addition, L50-like enterocins such as MR10A/B have been found in E. faecalis and E. faecium, but AS-48 appears only in E. faecalis. Thus, using the ABC transporter of the enterocin MR10A/B gene cluster of Enterococcus faecalis MRR10-3 as a cross-resistance model, we aimed to unravel to what extent a particular ABC transporter can be shared across multiple bacteriocinogenic bacterial populations. To this end, we screened the MR10A/B-ABC transporters in available microbial genomes and analyzed their sequence homologies and distribution. Overall, our main findings are as follows: (i) the MR10A/B-ABC transporter is associated with multiple enterocin gene clusters; (ii) the different enterocins associated with this transporter have a saposin-like fold in common; (iii) the Mr10E component of the transporter is more conserved within its associated enterocin, while the Mr10FGH components are more conserved within the carrying species. This is the least known component of the transporter, but it has shown the greatest specificity to its corresponding enterocin. Bacteriocins are now being investigated as an alternative to antibiotics; hence, the wider or narrower distribution of the particular immunity gene should be taken into account for clinical applications to avoid the selection of resistant strains. Further research will be needed to investigate the mechanistic interactions between the Mr10E transporter component and the bacteriocin as well as the specific ecological and evolutionary mechanisms involved in the spread of the immunity transporter across multiple bacteriocins.

Antimicrobial Peptide Synergies for Fighting Infectious Diseases

Antimicrobial peptides (AMPs) are essential elements of thehost defense system. Characterized by heterogenous structures and broad-spectrumaction, they are promising candidates for combating multidrug resistance. Thecombined use of AMPs with other antimicrobial agents provides a new arsenal ofdrugs with synergistic action, thereby overcoming the drawback of monotherapiesduring infections. AMPs kill microbes via pore formation, thus inhibitingintracellular functions. This mechanism of action by AMPs is an advantage overantibiotics as it hinders the development of drug resistance. The synergisticeffect of AMPs will allow the repurposing of conventional antimicrobials andenhance their clinical outcomes, reduce toxicity, and, most significantly,prevent the development of resistance. In this review, various synergies ofAMPs with antimicrobials and miscellaneous agents are discussed. The effect ofstructural diversity and chemical modification on AMP properties is firstaddressed and then different combinations that can lead to synergistic action,whether this combination is between AMPs and antimicrobials, or AMPs andmiscellaneous compounds, are attended. This review can serve as guidance whenredesigning and repurposing the use of AMPs in combination with other antimicrobialagents for enhanced clinical outcomes.

Diversity of the bacteriocins, their classification and potential applications in combat of antibiotic resistant and clinically relevant pathogens

There is almost a century since discovery of penicillin by Alexander Fleming, a century of enthusiasm, abuse, facing development of antibiotic-resistance and clear conclusion that the modern medicine needs a new type of antimicrobials. Bacteriocins produced by Gram-positive and Gram-negative bacteria, Archaea and Eukaryotes were widely explored as potential antimicrobials with several applications in food industry. In last two decades bacteriocins showed their potential as promising alternative therapeutic for the treatment of antibiotic-resistant pathogens. Bacteriocins can be characterised as highly selective antimicrobials and therapeutics with low cytotoxicity. Most probably in order to solve the problems associated with the increasing number of antibiotic-resistant bacteria, the application of natural or bioengineered bacteriocins in addition to synergistically acting preparations of bacteriocins and conventional antibiotics, can be the next step in combat versus drug-resistant pathogens. In this overview we focussed on diversity of specific lactic acid bacteria and their bacteriocins. Moreover, some additional examples of bacteriocins from non-lactic acid, Gram-positive and Gram-negative bacteria, Archaea and eukaryotic organisms are presented and discussed. Therapeutic properties of bacteriocins, their bioengineering and combined applications, together with conventional antibiotics, were evaluated with the scope of application in human and veterinary medicine for combating (multi-)drug-resistant pathogens.

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 .

Immunomodulation, Bioavailability and Safety of Bacteriocins

The rise of antibiotic-resistant bacteria and the emergence of new pathogens have created a need for new strategies to fight against infectious diseases. One promising approach is the use of antimicrobial peptides produced by a certain species of bacteria, known as bacteriocins, which are active against other strains of the same or related species. Bacteriocins can help in the treatment and prevention of infectious diseases. Moreover, bacteriocins can be obtained in prokaryotic organisms, and contribute s to their widespread use. While the use of bacteriocins is currently limited to the food industry (for example, nisin is used as a preservative, E234), a large number of studies on their microbicidal properties suggest that their use in medicine may increase in the foreseeable future. However, for the successful use of bacteriocins in medicine, it is necessary to understand their effect on the immune system, especially in cases where immunity is weakened due to infectious processes, oncological, allergic, or autoimmune diseases. Studies on the immuno-modulatory activity of bacteriocins in animal models and human cells have revealed their ability to induce both pro-inflammatory and anti-inflammatory factors involved in the implementation of innate immunity. The influence of bacteriocins on acquired immunity is revealed by an increase in the number of T-lymphocytes with a simultaneous decrease in B-lymphocyte levels, which makes them attractive substances for reducing inflammation. The widespread use of bacteriocins in the food industry, their low toxicity, and their broad and narrow specificity are reasons for researchers to pay attention to their immunomodulatory properties and explore their medical applications. Inflammation regulation by bacteriocins can be used in the treatment of various pathologies. The aim of the review was to analyze scientific publications on the immunomodulatory activity, bioavailability, and safety of bacteriocins in order to use the data obtained to organize preclinical and clinical studies.