The microbiome-shaping roles of bacteriocins

Postbiotics in inflammatory bowel disease: efficacy, mechanism, and therapeutic implications

Inflammatory bowel disease (IBD) is one of the most challenging diseases in the 21st century, and more than 10 million people around the world suffer from IBD. Because of the limitations and adverse effects associated with conventional IBD therapies, there has been increased scientific interest in microbial-derived biomolecules, known as postbiotics. Postbiotics are defined as the preparation of inanimate microorganisms and/or their components that confer a health benefit on the host, comprising inactivated microbial cells, cell fractions, metabolites, etc. Postbiotics have shown potential in enhancing IBD treatment by reducing inflammation, modulating the immune system, stabilizing intestinal flora and maintaining the integrity of intestinal barriers. Consequently, they are considered promising adjunctive therapies for IBD. Recent studies indicate that postbiotics offer distinctive advantages, including spanning clinical (safe origin), technological (easy for storage and transportation) and economic (reduced production costs) dimensions, rendering them suitable for widespread applications in functional food/pharmaceutical. This review offers a comprehensive overview of the definition, classification and applications of postbiotics, with an emphasis on their biological activity in both the prevention and treatment of IBD. © 2024 Society of Chemical Industry.

Complete genome sequence of Staphylococcus epidermidis B273 and its epidermicin NI01 biosynthesis plasmid

The human skin commensal Staphylococcus epidermidis produces diverse, therapeutically relevant bacteriocins. We report the complete whole-genome sequence of the nasal isolate S. epidermidis B273, which contains a plasmid with the biosynthetic gene cluster for epidermicin NI01, a broad-spectrum type II antimicrobial peptide.

Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate

INTRODUCTION

Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.

OBJECTIVES

The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.

METHODS

We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.

RESULTS

The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.

CONCLUSION

This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.

Impact of pre-exposure stress on the growth and viability of Lactobacillus acidophilus in regular, buriti pulp and orange byproduct fermented milk products

The loss of probiotics viability in yogurts and fermented milk is a significant challenge in producing yogurt and fermented milk. Thus, pre-exposure of probiotics to stress conditions can be a viable alternative to increase the probiotic viability. Moreover, the use of fruit pulp and agro-industrial residues in these products has demonstrated promising results in promoting growth and improving the viability of probiotics. Thus, this study aimed to evaluate the effects of pre-exposure to acid, oxidative and osmotic stress on the growth and viability of Lactobacillus acidophilus in yogurts and naturally fermented milk containing buriti (Mauritia flexuosa Mart.) pulp or orange byproduct. L. acidophilus was individually pre-exposed to acid, oxidative, and osmotic stress and used in the production of yogurts and fermented milk to determine both the acidification profile and growth of the cultures. Furthermore, during cold storage, the post-acidification profiles and viability of microbial cultures added to the yogurts and fermented milk were monitored. Results showed that pre-exposure to stress conditions influenced the growth parameters as the growth rate (μ) and lag phase (λ) of L. acidophilus and the starter cultures of S. thermophilus and L. delbrueckii subsp. bulgaricus. Moreover, an increase in the viability of L. acidophilus - pre-exposed to acid stress - was observed on the 21st day of storage of natural yogurts containing orange byproduct compared with non-stressful conditions. This study reports new data on the growth of probiotic cultures pre-exposed to stress conditions in products added of pulps and agro-industrial residues, which have not yet been shown in the literature.

The Actinobacillus pleuropneumoniae apxIV operon encodes an antibacterial toxin-immunity pair

The ApxIVA protein belongs to a distinct class of a "clip and link" activity of Repeat-in-ToXin (RTX) exoproteins. Along with the three other pore-forming RTX toxins (ApxI, ApxII and ApxIII), ApxIVA serves as a major virulence factor of Actinobacillus pleuropneumoniae, the causative agent of porcine pneumonia. The gene encoding ApxIVA is located on a bicistronic operon downstream of the orf1 gene and is expressed exclusively under in vivo conditions. Both ApxIVA and ORF1 are essential for full virulence of A. pleuropneumoniae, but the molecular mechanisms by which they contribute to the pathogenicity are not yet understood. Here, we provide a comprehensive structural and functional analysis of ApxIVA and ORF1 proteins. Our findings reveal that the N-terminal segment of ApxIVA shares structural similarity with colicin M (ColM)-like bacteriocins and exhibits an antimicrobial activity. The ORF1 protein resembles the colicin M immunity protein (Cmi) and, like Cmi, is exported to the periplasm through its N-terminal signal peptide. Additionally, ORF1 can protect bacterial cells from the antimicrobial activity of ApxIVA, suggesting that ORF1 and ApxIVA function as an antibacterial toxin-immunity pair. Moreover, we demonstrate that fetal bovine serum could elicit ApxIVA and ORF1 production under in vitro conditions. These findings highlight the coordinated action of various RTX determinants, where the fine-tuned spatiotemporal production of ApxIVA may enhance the fitness of A. pleuropneumoniae, facilitating its invasion to a resident microbial community on the surface of airway mucosa.

Increasing prevalence of bacteriocin carriage in a 6-year hospital cohort of E. faecium

Vancomycin-resistant enterococci (VRE) are important pathogens in hospitalized patients; however, the factors involved in VRE colonization of hospitalized patients are not well characterized. Bacteriocins provide a competitive advantage to enterococci in experimental models of colonization, but little is known about bacteriocin content in samples derived from humans and even less is known about their dynamics in the clinical setting. To identify bacteriocins which may be relevant in the transmission of VRE, we present a systematic analysis of bacteriocin content in the genomes of 2,248 patient-derived E. faecium isolates collected over a 6-year period from a single hospital system. We used computational methods to broadly search for bacteriocin structural genes and a functional assay to look for phenotypes consistent with bacteriocin expression. We identified homology to 15 different bacteriocins, with 2 having a high presence in this clinical cohort. Bacteriocin 43 (bac43) was found in a total of 58% of isolates, increasing from 8% to 91% presence over the 6-year collection period. There was little genetic variation in the bac43 structural or immunity genes across isolates. The enterocin A structural gene was found in 98% of isolates, but only 0.3% of isolates had an intact enterocin A gene cluster and displayed a bacteriocin-producing phenotype. This study presents a wide survey of bacteriocins from hospital isolates and identified bac43 as highly conserved, increasing in prevalence, and phenotypically functional. This makes bac43 an interesting target for future investigation for a potential role in E. faecium transmission.IMPORTANCEWhile enterococci are a normal inhabitant of the human gut, vancomycin-resistant E. faecalis and E. faecium are urgent public health threats responsible for hospital-associated infections. Bacteriocins are ribosomally synthesized antimicrobial proteins and are commonly used by bacteria to provide a competitive advantage in polymicrobial environments. Bacteriocins have the potential to be used by E. faecium to invade and dominate the human gut leading to a greater propensity for transmission. In this work, we explore bacteriocin content in a defined clinically derived population of E. faecium using both genetic and phenotypic studies. We show that one highly active bacteriocin is increasing in prevalence over time and demonstrates great potential relevance to E. faecium transmission.

Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens

Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.

Impacts of Helicobacter pylori infection and eradication on gastrointestinal microbiota: An up-to-date critical review and future perspectives

ABSTRACT

Helicobacter pylori ( H. pylori ) infects approximately half of the population worldwide and causes chronic gastritis, peptic ulcers, and gastric cancer. Test-and-treat strategies have been recommended for the prevention of H. pylori -associated diseases. Advancements in high-throughput sequencing technologies have broadened our understanding of the complex gastrointestinal (GI) microbiota and its role in maintaining host homeostasis. Recently, an increasing number of studies have indicated that the colonization of H. pylori induces dramatic alterations in the gastric microbiota, with a predominance of H. pylori and a reduction in microbial diversity. Dysbiosis of the gut microbiome has also been observed after H. pylori infection, which may play a role in the development of colorectal cancer. However, there is concern regarding the impact of antibiotics on the gut microbiota during H. pylori eradication. In this review, we summarize the current literature concerning how H. pylori infection reshapes the GI microbiota and the underlying mechanisms, including changes in the gastric environment, immune responses, and persistent inflammation. Additionally, the impacts of H. pylori eradication on GI microbial homeostasis and the use of probiotics as adjuvant therapy are also discussed. The shifts in the GI microbiota and their crosstalk with H. pylori  may provide potential targets for H. pylori -related gastric diseases and extragastric manifestations.

Microbiota in tumors: new factor influencing cancer development

Tumor microbiota research is a new field in oncology. With the advancement of high-throughput sequencing, there is growing evidence that a microbial community exists within tumor tissue. How these bacteria access tumor cells varies, including through the invasion of mucous membranes, the bloodstream, or the gut-organ axis. Previous literature has shown that microbes promote the development and progression of cancer through various mechanisms, such as affecting the host's immune system, promoting inflammation, regulating metabolism, and activating invasion and transfer. The study of the tumor microbiota offers a new perspective for the diagnosis and treatment of cancer, and it holds the potential for the development of new diagnostic tools and therapies. The role of the tumor microbiota in the pathogenesis of cancer is becoming increasingly evident, and future research will continue to uncover the specific mechanisms of action of these microbes, potentially shedding light on new strategies and methods for cancer prevention and therapy. This article reviews the latest advancements in this field, including how intratumor microbes migrate, their carcinogenic mechanisms, and the characteristics of different types of tumor microbes as well as the application of relevant methods in tumor microbiota research and the clinical values of targeting tumor microbes in cancer therapy.

Bacteriocin Mining in Lactiplantibacillus pentosus PCZ4 with Broad-Spectrum Antibacterial Activity and Its Biopreservative Effects on Snakehead Fish

Some lactic acid bacteria (LAB) produce antibacterial substances such as bacteriocins, making them promising candidates for food preservation. In our study, Lactiplantibacillus pentosus PCZ4-a strain with broad-spectrum antibacterial activity-was isolated from traditional fermented kimchi in Sichuan. Whole-genome sequencing of PCZ4 revealed one chromosome and three plasmids. Through BAGEL4 mining, classes IIa and IIb bacteriocin plantaricin S were identified. Additionally, two new antibacterial peptides, Bac1109 and Bac2485, were predicted from scratch by limiting open reading frames. Furthermore, during refrigerated storage of snakehead fish, PCZ4 crude extract reduced the total bacterial count, slowed the increase in TVB-N and pH values, improved the sensory quality of the snakehead, and extended its shelf life by 2 days. Meanwhile, PCZ4 effectively inhibited the growth of artificially contaminated Aeromonas hydrophila in snakehead fish. These findings indicate that Lp. pentosus PCZ4 can produce multiple antibacterial substances with strong potential for food preservation applications.

Synthetic translational coupling element for multiplexed signal processing and cellular control

Repurposing natural systems to develop customized functions in biological systems is one of the main thrusts of synthetic biology. Translational coupling is a common phenomenon in diverse polycistronic operons for efficient allocation of limited genetic space and cellular resources. These beneficial features of translation coupling can provide exciting opportunities for creating novel synthetic biological devices. Here, we introduce a modular synthetic translational coupling element (synTCE) and integrate this design with de novo designed riboregulators, toehold switches. A systematic exploration of sequence domain variants for synTCEs led to the identification of critical design considerations for improving the system performance. Next, this design approach was seamlessly integrated into logic computations and applied to construct multi-output transcripts with well-defined stoichiometric control. This module was further applied to signaling cascades for combined signal transduction and multi-input/multi-output synthetic devices. Further, the synTCEs can precisely manipulate the N-terminal ends of output proteins, facilitating effective protein localization and cellular population control. Therefore, the synTCEs could enhance computational capability and applicability of riboregulators for reprogramming biological systems, leading to future applications in synthetic biology, metabolic engineering and biotechnology.

Cell-Free Supernatant of Vaginal Viridans Streptococcus Induces Membrane Permeabilization and Transcriptional Regulation in Methicillin-Resistant Staphylococcus aureus

The genus Streptococcus is a heterogenous group of commensal and pathogenic bacteria that are normal inhabitants of the human body, including the female genital tract (FGT). In the FGT microbiome, streptococci represent two major groups: the pathogenic group B Streptococci (GBS) and the commensal viridans group streptococci (VGS). Though members of the VGS are frequently detected from the FGT, their role in the FGT microbiome remains underexplored. Here, we report the characterization of Streptococcus sp. K0074, isolated from the vaginal swab of an endometrial cancer patient admitted to the hospital, with no evidence of bacterial vaginosis. Phylogenetic analysis revealed that the strain is a member of the commensal VGS and possibly represents a novel species in the mitis subgroup. The strain demonstrated the production of low molecular weight bacteriocin-like substance with narrow-spectrum antagonistic activity, affecting the growth, biofilm formation, and colonization of aerobic vaginitis (AV)-causing bacterium methicillin-resistant Staphylococcus aureus (MRSA). The putative bacteriocin exhibited cell membrane-permeabilizing activity and exerted negative regulatory effect on the accessory gene regulator and SaeRS two-component systems of MRSA. Collectively, our results suggest that the isolate may modulate the FGT microbiome by inhibiting or displacing specific pathogen. Furthermore, the results presented here highlight new perspectives regarding the existence of VGS in the FGT microbiome and in particular pinpoint the potential clinical significance of the isolated VGS strain Streptococcus sp. K0074 for the treatment of AV caused by MRSA.

Biopreservation strategies using bacteriocins to control meat spoilage and foodborne outbreaks

Fresh meat is highly perishable, presenting challenges in spoilage mitigation and waste reduction globally. Despite the efforts, foodborne outbreaks from meat consumption persist. Biopreservation offers a natural solution to extend shelf life by managing microbial communities. However, challenges include the effective diffusion of bacteriocins through the meat matrix and the potential inhibition of starter cultures by bacteriocins targeting closely related lactic acid bacteria (LAB). LAB, predominant in meat, produce bacteriocins - small, stable peptides with broad antimicrobial properties effective across varying pH and temperature conditions. This review highlights the recent advances in the optimization of bacteriocin use, considering its structure and mode of action. Moreover, the strengths and weaknesses of different techniques for bacteriocin screening, including novel bioengineering methods, are described. Finally, we discuss the advantages and limitations of the modes of application of bacteriocins toward the preservation of fresh, cured, and novel meat products.

Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine

Recent studies have shown a growing interest in the complex relationship between the human gut microbiota, metabolism, and overall health. This review aims to explore the gut microbiota-host association, focusing on its implications for precision nutrition and personalized medicine. The objective is to highlight how gut microbiota modulate metabolic and immune functions, contributing to disease susceptibility and wellbeing. The review synthesizes recent research findings, analyzing key studies on the influence of gut microbiota on lipid and carbohydrate metabolism, intestinal health, neurobehavioral regulation, and endocrine signaling. Data were drawn from both experimental and clinical trials examining microbiota-host interactions relevant to precision nutrition. Our findings highlight the essential role of gut microbiota-derived metabolites in regulating host metabolism, including lipid and glucose pathways. These metabolites have been found to influence immune responses and gut barrier integrity. Additionally, the microbiota impacts broader physiological processes, including neuroendocrine regulation, which could be crucial for dietary interventions. Therefore, understanding the molecular mechanisms of dietary-microbiota-host interactions is pivotal for advancing personalized nutrition strategies. Tailored dietary recommendations based on individual gut microbiota compositions hold promise for improving health outcomes, potentially revolutionizing future healthcare approaches across diverse populations.

Living Engineered Bacterial Therapeutics: Emerging Affordable Precision Interventions

Live biotherapeutic products (LBPs), including engineered bacteria, are rapidly emerging as potential therapeutic interventions. These innovative therapies can serve as live in situ drug delivery platforms for the direct deposition of therapeutic payloads, including complex biologics, at sites of disease. This approach offers a platform likely to enhance therapeutic efficacy and decrease off-target side effects. LBPs also can likely be distributed at a relatively low price point, as their production can be economically scaled up. LBPs represent an exciting new means for ensuring healthy lives and promoting well-being for all ages, aligning with the World Health Organization's sustainable development goal 3.

The Core-Shell Microneedle with Probiotic Extracellular Vesicles for Infected Wound Healing and Microbial Homeostasis Restoration

Wound healing is a dynamic process involving the timely transition of organized phases. However, infected wounds often experience prolonged inflammation due to microbial overload. Thus, addressing the viable treatment needs across different healing stages is a critical challenge in wound management. Herein, a novel core-shell microneedle (CSMN) patch is designed for the sequential delivery of tannic acid-magnesium (TA-Mg) complexes and extracellular vesicles from Lactobacillus druckerii (LDEVs). Upon application to infected sites, CSMN@TA-Mg/LDEV releases TA-Mg first to counteract pathogenic overload and reduce reactive oxygen species (ROS), aiding the transition to proliferative phase. Subsequently, the sustained release of LDEVs enhances the activities of keratinocytes and fibroblasts, promotes vascularization, and modulates the collagen deposition. Notably, dynamic track of microbial composition demonstrates that CSMN@TA-Mg/LDEV can both inhibit the aggressive pathogen and increase the microbial diversity at wound sites. Functional analysis further highlights the potential of CSMN@TA-Mg/LDEV in facilitating wound healing and skin barrier restoration. Moreover, it is confirmed that CSMN@TA-Mg/LDEV can accelerate wound closure and improve post-recovery skin quality in the murine infected wound. Conclusively, this innovative CSMN patch offers a rapid and high-quality alternative treatment for infected wounds and emphasizes the significance of microbial homeostasis.

Addressing the surge of infections by multidrug-resistant Enterobacterales in hematopoietic cell transplantation

Patients undergoing hematopoietic cell transplantation (HCT) have an increased risk of developing severe infections. In recent years, bloodstream infections caused by Gram-negative bacteria have been increasingly reported among HCT recipients, and many of these infections are caused by bacterial strains of the Enterobacterales order. Among these pathogens, particularly concerning are the multidrug-resistant Enterobacterales (MDRE), such as Extended Spectrum β-lactamase-producing Enterobacterales and Carbapenem-resistant Enterobacterales, since infections caused by these pathogens are difficult to treat due to the limited antimicrobial options and are associated with worse transplant outcomes. We summarized the evidence from studies published in PubMed and Scopus on the burden of MDRE infections in HCT recipients, and strategies for the management and prevention of these infections, including strict adherence to recommended infection control practices and multidisciplinary antimicrobial stewardship, the use of probiotics, and fecal microbiota transplantation, are also discussed.

The Role of Iron in Intestinal Mucus: Perspectives from Both the Host and Gut Microbiota

Although research on the role of iron in host immunity has a history spanning decades, it is only relatively recently that attention has been directed toward the biological effects of iron on the intestinal mucus layer, prompted by an evolving understanding of the role of this material in immune defense. The mucus layer, secreted by intestinal goblet cells, covers the intestinal epithelium, and given its unique location, interactions between the host and gut microbiota, as well as among constituent microbiota, occur frequently within the mucus layer. Iron, as an essential nutrient for the vast majority of life forms, regulates immune responses from both the host and microbial perspectives. In this review, we summarize the iron metabolism of both the host and gut microbiota and describe how iron contributes to intestinal mucosal homeostasis via the intestinal mucus layer with respect to both host and constituent gut microbiota. The findings described herein offer a new perspective on iron-mediated intestinal mucosal barrier function.

The Impact of Bioactive Molecules from Probiotics on Child Health: A Comprehensive Review

Background: This review investigates the impact of bioactive molecules produced by probiotics on child health, focusing on their roles in modulating gut microbiota, enhancing immune function, and supporting overall development. Key metabolites, including short-chain fatty acids (SCFAs), bacteriocins, exopolysaccharides (EPSs), vitamins, and gamma-aminobutyric acid (GABA), are highlighted for their ability to maintain gut health, regulate inflammation, and support neurodevelopment. Objectives: The aim of this review is to examine the mechanisms of action and clinical evidence supporting the use of probiotics and postbiotics in pediatric healthcare, with a focus on promoting optimal growth, development, and overall health in children. Methods: The review synthesizes findings from clinical studies that investigate the effects of probiotics and their metabolites on pediatric health. The focus is on specific probiotics and their ability to influence gut health, immune responses, and developmental outcomes. Results: Clinical studies demonstrate that specific probiotics and their metabolites can reduce gastrointestinal disorders, enhance immune responses, and decrease the incidence of allergies and respiratory infections in pediatric populations. Additionally, postbiotics-bioactive compounds from probiotic fermentation-offer promising benefits, such as improved gut barrier function, reduced inflammation, and enhanced nutrient absorption, while presenting fewer safety concerns compared to live probiotics. Conclusions: By examining the mechanisms of action and clinical evidence, this review underscores the potential of integrating probiotics and postbiotics into pediatric healthcare strategies to promote optimal growth, development, and overall health in children.

Engineering Probiotics for Diabetes Management: Advances, Challenges, and Future Directions in Translational Microbiology

Background

Diabetes Mellitus (DM) is a substantial health concern worldwide, and its incidence is progressively escalating. Conventional pharmacological interventions frequently entail undesirable side effects, and while probiotics offer benefits, they are hindered by constraints such as diminished stability and effectiveness within the gastrointestinal milieu. Given these complications, the advent of bioengineered probiotics is a promising alternative for DM management.

Aim of Review

The objective of this review is to provide an exhaustive synthesis of the most recent studies on the use of engineered probiotics in the management of DM. This study aimed to clarify the mechanisms through which these probiotics function, evaluate their clinical effectiveness, and enhance public awareness of their prospective advantages in the treatment of DM.

Key Scientific Concepts of Review

Scholarly critiques have explored diverse methodologies of probiotic engineering, including physical alteration, bioenrichment, and genetic manipulation. These techniques augment the therapeutic potency of probiotics by ameliorating gut microbiota, fortifying the intestinal barrier, modulating metabolic pathways, and regulating immune responses. Such advancements have established engineered probiotics as a credible therapeutic strategy for DM, potentially providing enhanced results compared to conventional treatments.

Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework

Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.

IMPORTANCE

This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.

The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy

BACKGROUND

Bacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes. Beneficial commensal bacteria can often prevent the invasion and persistence of such pathogens by using molecular strategies that are only superficially understood. We recently reported that the commensal bacterium Staphylococcus lugdunensis produces the novel antibiotic lugdunin, which eradicates S. aureus from the nasal microbiomes of hospitalized patients. However, it has remained unclear if S. lugdunensis may affect S. aureus carriage in the general population and which external factors might promote S. lugdunensis carriage to enhance its S. aureus-eliminating capacity.

RESULTS

We could cultivate S. lugdunensis from the noses of 6.3% of healthy human volunteers. In addition, S. lugdunensis DNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. Healthy S. lugdunensis carriers had a 5.2-fold lower propensity to be colonized by S. aureus indicating that lugdunin can eliminate S. aureus also in healthy humans. S. lugdunensis-positive microbiomes were dominated by either Staphylococcus epidermidis, Corynebacterium species, or Dolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated with S. lugdunensis, promoted S. lugdunensis growth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supportive commensals and on the capacity of S. lugdunensis to import siderophores. Video Abstract CONCLUSIONS: These findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.

The Gut Microbiome in Sepsis: From Dysbiosis to Personalized Therapy

Sepsis is a complex clinical syndrome characterized by an uncontrolled inflammatory response to an infection that may result in septic shock and death. Recent research has revealed a crucial link between sepsis and alterations in the gut microbiota, showing that the microbiome could serve an essential function in its pathogenesis and prognosis. In sepsis, the gut microbiota undergoes significant dysbiosis, transitioning from a beneficial commensal flora to a predominance of pathobionts. This transformation can lead to a dysfunction of the intestinal barrier, compromising the host's immune response, which contributes to the severity of the disease. The gut microbiota is an intricate system of protozoa, fungi, bacteria, and viruses that are essential for maintaining immunity and metabolic balance. In sepsis, there is a reduction in microbial heterogeneity and a predominance of pathogenic bacteria, such as proteobacteria, which can exacerbate inflammation and negatively influence clinical outcomes. Microbial compounds, such as short-chain fatty acids (SCFAs), perform a crucial task in modulating the inflammatory response and maintaining intestinal barrier function. However, the role of other microbiota components, such as viruses and fungi, in sepsis remains unclear. Innovative therapeutic strategies aim to modulate the gut microbiota to improve the management of sepsis. These include selective digestive decontamination (SDD), probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT), all of which have shown potential, although variable, results. The future of sepsis management could benefit greatly from personalized treatment based on the microbiota. Rapid and easy-to-implement tests to assess microbiome profiles and metabolites associated with sepsis could revolutionize the disease's diagnosis and management. These approaches could not only improve patient prognosis but also reduce dependence on antibiotic therapies and promote more targeted and sustainable treatment strategies. Nevertheless, there is still limited clarity regarding the ideal composition of the microbiota, which should be further characterized in the near future. Similarly, the benefits of therapeutic approaches should be validated through additional studies.

Targeting the gut microbiota: a new strategy for colorectal cancer treatment

BACKGROUND

How to reduce the high incidence rate and mortality of colorectal cancer (CRC) effectively is the focus of current research. Endoscopic treatment of early-stage CRC and colorectal adenomas (CAC) has a high success rate, but although several treatments are available for advanced CRC, such as surgery, radiotherapy, chemotherapy, and immunotherapy, the 5-year survival rate remains low. In view of the high incidence rate and mortality of CRC, early rational drug prevention for high-risk groups and exploration of alternative treatment modalities are particularly warranted. Gut microbiota is the target of and interacts with probiotics, prebiotics, aspirin, metformin, and various Chinese herbal medicines (CHMs) for the prevention of CRC. In addition, the anti-cancer mechanisms of probiotics differ widely among bacterial strains, and both bacterial strains and their derivatives and metabolites have been found to have anti-cancer effects. Gut microbiota plays a significant role in early drug prevention of CRC and treatment of CRC in its middle and late stages, targeting gut microbiota may be a new strategy for colorectal cancer treatment.

Gut Distribution, Impact Factor, and Action Mechanism of Bacteriocin-Producing Beneficial Microbes as Promising Antimicrobial Agents in Gastrointestinal Infection

Gastrointestinal (GI) infection by intestinal pathogens poses great threats to human health, and the therapeutic use of antibiotics has reached a bottleneck due to drug resistance. The developments of antimicrobial peptides produced by beneficial bacteria have drawn attention by virtue of effective, safe, and not prone to developing resistance. Though bacteriocin as antimicrobial agent in gut infection has been intensively investigated and reviewed, reviews on that of bacteriocin-producing beneficial microbes are very rare. It is important to explicitly state the prospect of bacteriocin-producing microbes in prevention of gastrointestinal infection towards their application in host. This review discusses the potential of gut as an appropriate resource for mining targeted bacteriocin-producing microbes. Then, host-related factors affecting the bacteriocin production and activity of bacteriocin-producing microbes in the gut are summarized. Accordingly, the multiple mechanisms (direct inhibition and indirect inhibition) behind the preventive effects of bacteriocin-producing microbes on gut infection are discussed. Finally, we propose several targeted strategies for the manipulation of bacteriocin-producing beneficial microbes to improve their performance in antimicrobial outcomes. We anticipate an upcoming emergence of developments and applications of bacteriocin-producing beneficial microbes as antimicrobial agent in gut infection induced by pathogenic bacteria.

Production and SERS characterization of bacteriocin-like inhibitory substances by latilactobacillus sakei in whey permeate powder: exploring natural antibacterial potential

Bacteriocins are antimicrobial compounds that have awakened interest across several industries due to their effectiveness. However, their large-scale production often becomes unfeasible on an industrial scale, primarily because of high process costs. Addressing this challenge, this work analyzes the potential of using low-cost whey permeate powder, without any supplementation, to produce bacteriocin-like inhibitory substances (BLIS) through the fermentation of Latilactobacillus sakei. For this purpose, different concentrations of whey permeate powder (55.15 gL-1, 41.3 gL-1 and 27.5 gL-1) were used. The ability of L. sakei to produce BLIS was evaluated, as well as the potential of crude cell-free supernatant to act as a preservative. Raman spectroscopy and surface-enhanced Raman scattering (SERS) provided detailed insights into the composition and changes occurring during fermentation. SERS, in particular, enhanced peak definition significantly, allowing for the identification of key components, such as lactose, proteins, and phenylalanine, which are crucial in understanding the fermentation process and BLIS characteristics. The results revealed that the concentration of 55.15 gL-1 of whey permeate powder, in flasks without agitation and a culture temperature of 32.5 °C, presented the highest biological activity of BLIS, reaching 99% of inhibition of Escherichia coli and Staphylococcus aureus with minimum inhibitory concentration of 36-45%, respectively. BLIS production began within 60 h of cultivation and was associated with class II bacteriocins. The results demonstrate a promising approach for producing BLIS in an economical and environmentally sustainable manner, with potential implications for various industries.

Progress in the study of the correlation between sepsis and intestinal microecology

Sepsis, a disease with high incidence, mortality, and treatment costs, has a complex interaction with the gut microbiota. With advances in high-throughput sequencing technology, the relationship between sepsis and intestinal dysbiosis has become a new research focus. However, owing to the intricate interplay between critical illness and clinical interventions, it is challenging to establish a causal relationship between sepsis and intestinal microbiota imbalance. In this review, the correlation between intestinal microecology and sepsis was summarized, and new therapies for sepsis intervention based on microecological target therapy were proposed, and the shortcomings of bacterial selection and application timing in clinical practice were addressed. In conclusion, current studies on metabolomics, genomics and other aspects aimed at continuously discovering potential probiotics are all providing theoretical basis for restoring intestinal flora homeostasis for subsequent treatment of sepsis.

Understanding of probiotic origin antimicrobial peptides: a sustainable approach ensuring food safety

The practice of preserving and adding value to food dates back to over 10,000 BCE, when unintentional microbial-driven chemical reactions imparted flavor and extended the shelf life of fermented foods. The process evolved, and with the urbanization of society, significant shifts in dietary habits emerged, accompanied by sporadic food poisoning incidents. The repercussions of the COVID-19 pandemic have intensified the search for antibiotic alternatives owing to the rise in antibiotic-resistant pathogens, emphasizing the exploration of probiotic-origin antimicrobial peptides to alleviate human microbiome collateral damage. Often termed 'molecular knives', these peptides outstand as potent antimicrobials due to their compatibility with innate microflora, amenability to bioengineering, target specificity, versatility and rapidity in molecular level mode of action. This review centres on bacteriocins sourced from lactic acid bacteria found in ethnic fermented foods, accentuating their desirable attributes, technological applications as nanobiotics and potential future applications in the modern context of ensuring food safety.

Comparative genomics-based insights into Xanthomonas indica, a non-pathogenic species of healthy rice microbiome with bioprotection function

Xanthomonas species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic Xanthomonas (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly Xanthomonas indica, a newly discovered NPX species from rice. The study establishes the relationship of X. indica strains within clade I of Xanthomonads with another NPX species, X. sontii, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic Xanthomonas indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of X. indica and X. sontii were found to protect rice from bacterial leaf blight pathogen, X. oryzae pv. oryzae (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocin-encoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies.IMPORTANCEThe Xanthomonas group of bacteria is known for its characteristic lifestyle as a phytopathogen. However, the discovery of non-pathogenic Xanthomonas (NPX) species is a major shift in understanding this group of bacteria. Multi-strain, in-depth genomic, evolutionary and functional studies on each of these NPX species are still lacking. This study on diverse non-pathogenic strains provides novel insights into genome diversity, dynamics, and evolutionary trends of NPX species from rice microbiome apart from its relationship with other relatives that form a sub-clade. Interestingly, we also uncovered that NPX species protect rice from pathogenic Xanthomonas species. The plant protection property shows their importance as a part of a healthy plant microbiome. Furthermore, finding an open pan-genome and large-scale variation at lipopolysaccharide biosynthetic locus indicates a significant role of the NPX community in host adaptation. The findings and high-quality genomic resources of NPX species and the strains will allow further systematic molecular and host-associated microbial community studies for plant health.

The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides

Lugdunin is a microbiome-derived antibacterial agent with good activity against Gram-positive pathogens in vitro and in animal models of nose colonization and skin infection. We have previously shown that lugdunin depletes bacterial energy resources by dissipating the membrane potential of Staphylococcus aureus. Here, we explored the mechanism of action of lugdunin in more detail and show that lugdunin quickly depolarizes cytoplasmic membranes of different bacterial species and acidifies the cytoplasm of S. aureus within minutes due to protonophore activity. Varying the salt species and concentrations in buffers revealed that not only protons are transported, and we demonstrate the binding of the monovalent cations K+, Na+, and Li+ to lugdunin. By comparing known ionophores with various ion transport mechanisms, we conclude that the ion selectivity of lugdunin largely resembles that of 15-mer linear peptide gramicidin A. Direct interference with the main bacterial metabolic pathways including DNA, RNA, protein, and cell wall biosyntheses can be excluded. The previously observed synergism of lugdunin with dermcidin-derived peptides such as DCD-1 in killing S. aureus is mechanistically based on potentiated membrane depolarization. We also found that lugdunin was active against certain eukaryotic cells, however strongly depending on the cell line and growth conditions. While adherent lung epithelial cell lines were almost unaffected, more sensitive cells showed dissipation of the mitochondrial membrane potential. Lugdunin seems specifically adapted to its natural environment in the respiratory tract. The ionophore mechanism is refractory to resistance development and benefits from synergy with host-derived antimicrobial peptides.

IMPORTANCE

The vast majority of antimicrobial peptides produced by members of the microbiome target the bacterial cell envelope by many different mechanisms. These compounds and their producers have evolved side-by-side with their host and were constantly challenged by the host's immune system. These molecules are optimized to be well tolerated at their physiological site of production, and their modes of action have proven efficient in vivo. Imbalancing the cellular ion homeostasis is a prominent mechanism among antibacterial natural products. For instance, over 120 naturally occurring polyether ionophores are known to date, and antimicrobial peptides with ionophore activity have also been detected in microbiomes. In this study, we elucidated the mechanism underlying the membrane potential-dissipating activity of the thiazolidine-containing cycloheptapeptide lugdunin, the first member of the fibupeptides discovered in a commensal bacterium from the human nose, which is a promising future probiotic candidate that is not prone to resistance development.

Deciphering the gastrointestinal carriage of Klebsiella pneumoniae

Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.

Comparative genome analysis of microbial strains marketed for probiotic interventions: an extension of the Integrated Probiotic Database

Background: Members of the Bifidobacterium genus and lactobacilli are the most commonly used probiotics to promote human health. In this context, genome-based in silico analyses have been demonstrated as a fast and reliable tool for identifying and characterizing health-promoting activities imputed to probiotics. Methods: This study is an extension of the Integrated Probiotic Database (IPDB) previously created on probiotics of the genus Bifidobacterium, facilitating a comprehensive understanding of the genetic characteristics that contribute to the diverse spectrum of beneficial effects of probiotics. The strains integrated into this new version of the IPDB, such as various lactobacilli and strains belonging to the species Streptococcus thermophilus (S. thermophilus) and Heyndrickxia coagulans (H. coagulans) (formerly Bacillus coagulans), were selected based on the labels of probiotic formulations currently on the market and using the bacterial strains whose genome had already been sequenced. On these bacterial strains, comparative genome analyses were performed, mainly focusing on genetic factors that confer structural, functional, and chemical characteristics predicted to be involved in microbe-host and microbe-microbe interactions. Results: Our investigations revealed marked inter- and intra-species variations in the genetic makeup associated with the biosynthesis of external structures and bioactive metabolites putatively associated with microbe- and host-microbe interactions. Conclusion: Although genetic differences need to be confirmed as functional or phenotypic differences before any probiotic intervention, we believe that considering these divergences will aid in improving effective and personalized probiotic-based interventions.

Bacteriocin diversity, function, discovery and application as antimicrobials

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

Oral microbiota and metabolites: key players in oral health and disorder, and microbiota-based therapies

The review aimed to investigate the diversity of oral microbiota and its influencing factors, as well as the association of oral microbiota with oral health and the possible effects of dysbiosis and oral disorder. The oral cavity harbors a substantial microbial burden, which is particularly notable compared to other organs within the human body. In usual situations, the microbiota exists in a state of equilibrium; however, when this balance is disturbed, a multitude of complications arise. Dental caries, a prevalent issue in the oral cavity, is primarily caused by the colonization and activity of bacteria, particularly streptococci. Furthermore, this environment also houses other pathogenic bacteria that are associated with the onset of gingival, periapical, and periodontal diseases, as well as oral cancer. Various strategies have been employed to prevent, control, and treat these disorders. Recently, techniques utilizing microbiota, like probiotics, microbiota transplantation, and the replacement of oral pathogens, have caught the eye. This extensive examination seeks to offer a general view of the oral microbiota and their metabolites concerning oral health and disease, and also the resilience of the microbiota, and the techniques used for the prevention, control, and treatment of disorders in this specific area.

Fermented Fish Products: Balancing Tradition and Innovation for Improved Quality

The flavor profile of fermented fish products is influenced by the complex interplay of microbial and enzymatic actions on the raw materials. This review summarizes the various factors contributing to the unique taste and aroma of these traditional foods. Key ingredients include locally sourced fish species and a variety of spices and seasonings that enhance flavor while serving as cultural markers. Starter cultures also play a critical role in standardizing quality and accelerating fermentation. Flavor compounds in fermented fish are primarily derived from the metabolism of carbohydrates, lipids, and proteins, producing a diverse array of free amino acids, peptides, and volatile compounds such as aldehydes, ketones, alcohols, and esters. The fermentation process can be shortened by certain methods to reduce production time and costs, allowing for faster product turnover and increased profitability in the fermented fish market. Fermented fish products also show potent beneficial effects. This review highlights the importance of integrating traditional practices with modern scientific approaches. Future research directions to enhance the quality of fermented fish products are suggested.

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.

Optimization of culture conditions for endophytic bacteria in mangrove plants and isolation and identification of bacteriocin

Introduction: The antibacterial protein PAG14 was extracted from a metabolite of Bacillus G14 isolated from mangrove plants. Methods: In this study, Pseudomonas aeruginosa, Pasteurell multocide, Enterobacter aerogenes, and Enterococcus faecalis were used as indicator bacteria to screen endophytes that exhibited antibacterial activity. The endophyte culture conditions were optimized to enhance productivity. Subsequently, the culture supernatant was salted using ammonium sulfate, followed by purification using dextran gel chromatography and ion exchange column techniques. Finally, the structures of antibacterial proteins were identified using mass spectrometry. Results and Discussion: The optimal culture conditions for Bacillus G14 were 2% mannitol, 0.5% fish peptone, 0.05% KH2PO4 + 0.05% K2HPO4 + 0.025% MnSO4·H2O. The antibacterial substances exhibited stability within the temperature range of 30-40°C and pH range of 5.0-7.0, while displaying sensitivity toward enzymes. The antibacterial activity decreased as the duration of UV irradiation increased. The antibacterial protein PAG14, isolated from the culture broth of Bacillus G14 through purification using dextran gel and ion-exchange columns, was identified as a class III bacteriocin using LC-MS/MS, similar to Lysozyme C. These findings serve as a theoretical foundation for the investigation and application of bacteriocins in food products.

Bacteriocins sourced from traditional fermented foods for ensuring food safety: the microbial guards

Concerns about food safety have consistently driven the exploration of potent antimicrobials with probiotic origins. Identification of probiotic-derived bacteriocins as robust alternatives to antibiotics has gained traction following the COVID-19 pandemic. Additionally, the global market is witnessing an increasing preference for minimally processed food products free from chemical additives. Another contributing factor to the search for potent antimicrobials is the escalating number of infections caused by antibiotic-resistant bacteria and the need to mitigate the significant damage inflicted on the commensal human microbiota by broad-spectrum antibiotics. As an alternative bio-preservation strategy, there is substantial enthusiasm for the use of bacteriocins or starter cultures producing bacteriocins in preserving a variety of food items. This review specifically focuses on bacteriocins originating from lactic acid bacteria associated with fermented foods and explores their technological applications as nanobiotics. The food-grade antibiotic alternatives, whether utilized independently or in combination with other antimicrobials and administered directly or encapsulated, are anticipated to possess qualities of safety, stability and non-toxicity suitable for application in the food sector. © 2024 Society of Chemical Industry.

Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective

The incidence of antibiotic-resistant bacterial infections is increasing, and development of new antibiotics has been deprioritised by the pharmaceutical industry. Interdisciplinary research approaches, based on the ecological principles of bacterial fitness, competition, and transmission, could open new avenues to combat antibiotic-resistant infections. Many facultative bacterial pathogens use human mucosal surfaces as their major reservoirs and induce infectious diseases to aid their lateral transmission to new host organisms under some pathological states of the microbiome and host. Beneficial bacterial commensals can outcompete specific pathogens, thereby lowering the capacity of the pathogens to spread and cause serious infections. Despite the clinical relevance, however, the understanding of commensal-pathogen interactions in their natural habitats remains poor. In this Personal View, we highlight directions to intensify research on the interactions between bacterial pathogens and commensals in the context of human microbiomes and host biology that can lead to the development of innovative and sustainable ways of preventing and treating infectious diseases.

Postbiotics-peptidoglycan, lipoteichoic acid, exopolysaccharides, surface layer protein and pili proteins-Structure, activity in wounds and their delivery systems

Chronic wound healing is a pressing global public health concern. Abuse and drug resistance of antibiotics are the key problems in the treatment of chronic wounds at present. Postbiotics are a novel promising strategy. Previous studies have reported that postbiotics have a wide range of biological activities including antimicrobial, immunomodulatory, antioxidant and anti-inflammatory abilities. However, several aspects related to these postbiotic activities remain unexplored or poorly known. Therefore, this work aims to outline general aspects and emerging trends in the use of postbiotics for wound healing, such as the production, characterization, biological activities and delivery strategies of postbiotics. In this review, a comprehensive overview of the physiological activities and structures of postbiotic biomolecules that contribute to wound healing is provided, such as peptidoglycan, lipoteichoic acid, bacteriocins, exopolysaccharides, surface layer proteins, pili proteins, and secretory proteins (p40 and p75 proteins). Considering the presence of readily degradable components in postbiotics, potential natural polymer delivery materials and delivery systems are emphasized, followed by the potential applications and commercialization prospects of postbiotics. These findings suggest that the treatment of chronic wounds with postbiotic ingredients will help provide new insights into wound healing and better guidance for the development of postbiotic products.

Genome-wide transcription response of Staphylococcus epidermidis to heat shock and medically relevant glucose levels

Skin serves as both barrier and interface between body and environment. Skin microbes are intermediaries evolved to respond, transduce, or act in response to changing environmental or physiological conditions. We quantified genome-wide changes in gene expression levels for one abundant skin commensal, Staphylococcus epidermidis, in response to an internal physiological signal, glucose levels, and an external environmental signal, temperature. We found 85 of 2,354 genes change up to ~34-fold in response to medically relevant changes in glucose concentration (0-17 mM; adj p ≤0.05). We observed carbon catabolite repression in response to a range of glucose spikes, as well as upregulation of genes involved in glucose utilization in response to persistent glucose. We observed 366 differentially expressed genes in response to a physiologically relevant change in temperature (37-45°C; adj p ≤ 0.05) and an S. epidermidis heat-shock response that mostly resembles the heat-shock response of related staphylococcal species. DNA motif analysis revealed CtsR and CIRCE operator sequences arranged in tandem upstream of dnaK and groESL operons. We identified and curated 38 glucose-responsive genes as candidate ON or OFF switches for use in controlling synthetic genetic systems. Such systems might be used to instrument the in-situ skin microbiome or help control microbes bioengineered to serve as embedded diagnostics, monitoring, or treatment platforms.

Increasing prevalence of bacteriocin carriage in a six-year hospital cohort of E. faecium

Vancomycin resistant enterococci (VRE) are important pathogens in hospitalized patients, however, the factors involved in VRE colonization of hospitalized patients are not well characterized. Bacteriocins provide a competitive advantage to enterococci in experimental models of colonization, but little is known about bacteriocin content in samples derived from humans and even less is known about their dynamics in the clinical setting. To identify bacteriocins which may be relevant in the transmission of VRE, we present a systematic analysis of bacteriocin content in the genomes of 2,428 patient derived E. faecium isolates collected over a six-year period from a single hospital system. We used computational methods to broadly search for bacteriocin structural genes and a functional assay to look for phenotypes consistent with bacteriocin expression. We identified homology to 15 different bacteriocins with two having high presence in this clinical cohort. Bacteriocin 43 (bac43) was found in a total of 58% of isolates, increasing from 8% to 91% presence over the six-year collection period. There was little genetic variation in the bac43 structural or immunity genes across isolates. The enterocin A structural gene was found in 98% of isolates but only 0.3% of isolates had an intact enterocin A gene cluster and displayed a bacteriocin producing phenotype. This study presents a wide survey of bacteriocins from hospital isolates and identified bac43 as highly conserved, increasing in prevalence, and phenotypically functional. This makes bac43 an interesting target for future investigation for a potential role in E. faecium transmission.

Importance

While enterococci are a normal inhabitant of the human gut, vancomycin-resistant E. faecalis and E. faecium are urgent public health threats responsible for hospital associated infections. Bacteriocins are ribosomally synthesized antimicrobial proteins and are commonly used by bacteria to provide a competitive advantage in polymicrobial environments. Bacteriocins have the potential be used by E. faecium to invade and dominate the human gut leading to a greater propensity for transmission. In this work, we explore bacteriocin content in a defined clinically derived population of E. faecium using both genetic and phenotypic studies. We show that one highly active bacteriocin is increasing in prevalence over time and demonstrates great potential relevance to E. faecium transmission.

Classification and Multi-Functional Use of Bacteriocins in Health, Biotechnology, and Food Industry

Bacteriocins is the name given to products of the secondary metabolism of many bacterial genera that must display antimicrobial activity. Although there are several bacteriocins described today, it has not been possible to reach a consensus on the method of classification for these biomolecules. In addition, many of them are not yet authorized for therapeutic use against multi-drug-resistant microorganisms due to possible toxic effects. However, recent research has achieved considerable progress in the understanding, classification, and elucidation of their mechanisms of action against microorganisms, which are of medical and biotechnological interest. Therefore, in more current times, protocols are already being conducted for their optimal use, in the hopes of solving multiple health and food conservation problems. This review aims to synthetize the information available nowadays regarding bacteriocins, and their classification, while also providing an insight into the future possibilities of their usage for both the pharmaceutical, food, and biotechnological industry.

Synthetic microbial ecology: engineering habitats for modular consortia

Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution

Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.

Intestinal colonization resistance in the context of environmental, host, and microbial determinants

Microbial communities that colonize the human gastrointestinal (GI) tract defend against pathogens through a mechanism known as colonization resistance (CR). Advances in technologies such as next-generation sequencing, gnotobiotic mouse models, and bacterial cultivation have enhanced our understanding of the underlying mechanisms and the intricate microbial interactions involved in CR. Rather than being attributed to specific microbial clades, CR is now understood to arise from a dynamic interplay between microbes and the host and is shaped by metabolic, immune, and environmental factors. This evolving perspective underscores the significance of contextual factors, encompassing microbiome composition and host conditions, in determining CR. This review highlights recent research that has shifted its focus toward elucidating how these factors interact to either promote or impede enteric infections. It further discusses future research directions to unravel the complex relationship between host, microbiota, and environmental determinants in safeguarding against GI infections to promote human health.

Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites

BACKGROUND

Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated.

RESULTS

The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms.

CONCLUSIONS

Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Bee-Associated Beneficial Microbes-Importance for Bees and for Humans

Bees are one of the best-known and, at the same time, perhaps the most enigmatic insects on our planet, known for their organization and social structure, being essential for the pollination of agricultural crops and several other plants, playing an essential role in food production and the balance of ecosystems, being associated with the production of high-value-added inputs, and a unique universe in relation to bees' microbiota. In this review, we summarize information regarding on different varieties of bees, with emphasis on their specificity related to microbial variations. Noteworthy are fructophilic bacteria, a lesser-known bacterial group, which use fructose fermentation as their main source of energy, with some strains being closely related to bees' health status. The beneficial properties of fructophilic bacteria may be extendable to humans and other animals as probiotics. In addition, their biotechnological potential may ease the development of new-generation antimicrobials with applications in biopreservation. The concept of "One Health" brings together fundamental and applied research with the aim of clarifying that the connections between the different components of ecosystems must be considered part of a mega-structure, with bees being an iconic example in that the healthy functionality of their microbiota is directly and indirectly related to agricultural production, bee health, quality of bee products, and the functional prosperity for humans and other animals. In fact, good health of bees is clearly related to the stable functionality of ecosystems and indirectly relates to humans' wellbeing, a concept of the "One Health".

Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist

Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium's utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.