Gut solutions to a gut problem: bacteriocins, probiotics and bacteriophage for control of Clostridium difficile infection

Fecal microbiota transplantation and next-generation therapies: A review on targeting dysbiosis in metabolic disorders and beyond

The human microbiome, particularly the gut microbiome, has emerged as a central determinant of health and disease. Dysbiosis, an imbalance in the microbial composition of the gut, is associated with a variety of metabolic and other diseases, highlighting the potential for microbiota-targeted treatments. Fecal microbiota transplantation has received considerable attention as a promising therapy to modulate the gut microbiome and restore microbial homeostasis. However, challenges remain, including standardization, safety, and long-term efficacy. This review summarizes current knowledge on fecal microbiota transplantation and describes the next generation therapies targeting microbiome. This review looked at the mechanistic understanding of fecal microbiota transplantation and alternative strategies, elucidating their potential role in improving dysbiosis-associated metabolic disorders, such as obesity, and type 2 diabetes and others. Additionally, this review discussed the growing application of therapies targeting the gut microbiome. Insights from clinical trials, preclinical studies, and emerging technologies provide a comprehensive overview of the evolving landscape of microbiome-based interventions. Through a critical assessment of current advances and prospects, this review aims to highlight the therapeutic potential of targeting gut microbiome and pave the way for innovative approaches in precision medicine and personalized treatments.

Sequence-activity mapping via depletion reveals striking mutational tolerance and elucidates functional motifs in Tur1a antimicrobial peptide

Proline-rich antimicrobial peptides (PrAMPs) are attractive antibiotic candidates that target gram-negative bacteria ribosomes. We elucidated the sequence-function landscape of 43 000 variants of a recently discovered family member, Tur1a, using the validated SAMP-Dep platform that measures intracellular AMP potency in a high-throughput manner via self-depletion of the cellular host. The platform exhibited high replicate reproducibility (ρ = 0.81) and correlation between synonymous genetic variants (R2 = 0.93). Only two segments within Tur1a exhibited stringent mutational requirements to sustain potency: residues 9YLP11 and 19FP20. This includes the aromatic residue in the hypothesized binding domain but not the PRP domain. Along with unexpected mutational tolerance of PRP, the data contrast hypothesized importance of the 1RRIR4 motif and arginines in general. In addition to mutational tolerance of residue segments with presumed significance, 77% of mutations are functionally neutral. Multimutant performance mainly shows compounding effects from removed combinations of prolines and arginines in addition to the two segments of residues showing individual importance. Several variants identified as active from SAMP-Dep were externally produced and maintained activity when applied to susceptible species exogenously.

Effects of microbial-derived biotics (meta/pharma/post-biotics) on the modulation of gut microbiome and metabolome; general aspects and emerging trends

Potential effects of metabiotics (probiotics effector molecules or signaling factors), pharmabiotics (pro-functional metabolites produced by gut microbiota (GMB)) and postbiotics (multifunctional metabolites and structural compounds of food-grade microorganisms) on GMB have been rarely reviewed. These multifunctional components have several promising capabilities for prevention, alleviation and treatment of some diseases or disorders. Correlations between these essential biotics and GMB are also very interesting and important in human health and nutrition. Furthermore, these natural bioactives are involved in modulation of the immune function, control of metabolic dysbiosis and regulation of the signaling pathways. This review discusses the potential of meta/pharma/post-biotics as new classes of pharmaceutical agents and their effective mechanisms associated with GMB-host cell to cell communications with therapeutic benefits which are important in balance and the integrity of the host microbiome. In addition, cutting-edge findings about bioinformatics /metabolomics analyses related to GMB and these essential biotics are reviewed.

Variations on gut health and energy metabolism in pigs and humans by intake of different dietary fibers

Many studies have reported that dietary fibers play a crucial role in promoting intestinal health of the host, since it strengthens functions of epithelial barrier and meanwhile maintains intestinal homeostasis of the host by modulating gut microbiota and short-chain fatty acid (SCFA) production. Pig is a good animal model to study effects of dietary fiber on gut health and microbial community. This review has summarized the relevant knowledge available based on roles of various dietary fibers in gut health and energy metabolism of pigs and humans. Evidences summarized in our review indicated that modulating intestinal microbial composition and SCFA production by consuming specific dietary fibers properly could be conducive to health improvement and disease prevention of the host. However, types of dietary fiber from edible foods exert divergent impacts on gut health, energy metabolism, microbial composition, and SCFA production. Therefore, more attention should be focused on different responses of various dietary fibers intake on host metabolism and health.

Proteus mirabilis Employs a Contact-Dependent Killing System against Competing Enterobacteriaceae

Many bacterial species employ systems for interference competition with other microorganisms. Some systems are effective without contact (e.g., through secretion of toxins), while other systems (e.g., type VI secretion system [T6SS]) require direct contact between cells. Here, we provide the initial characterization of a novel contact-dependent competition system for Proteus mirabilis. In neonatal mice, a commensal P. mirabilis strain apparently eliminated commensal Escherichia coli. We replicated the phenotype in vitro and showed that P. mirabilis efficiently reduced the viability of several Enterobacteriaceae species but not Gram-positive species or yeast cells. Importantly, P. mirabilis strains isolated from humans also killed E. coli. A reduction of viability occurred from early stationary phase to 24 h of culture and was observed in shaking liquid media as well as on solid media. Killing required contact but was independent of T6SS, which is the only contact-dependent killing system described for P. mirabilis. Expression of the killing system was regulated by osmolarity and components secreted into the supernatant. Stationary-phase P. mirabilis culture supernatant itself did not kill but was sufficient to induce killing in an exponentially growing coculture. In contrast, killing was largely prevented in media with low osmolarity. In summary, we provide the initial characterization of a potentially novel interbacterial competition system used by P. mirabilis.

IMPORTANCE The study of bacterial competition systems has received significant attention in recent years. These systems are important in a multitude of polymicrobial environments and collectively shape the composition of complex ecosystems like the mammalian gut. They are also being explored as narrow-spectrum alternatives to specifically eliminate problematic pathogenic species. However, only a small fraction of the estimated number of interbacterial competition systems has been identified. We discovered a competition system that is novel for Proteus mirabilis. Inspired by an observation in infant mice, we confirmed in vitro that P. mirabilis was able to efficiently kill several Enterobacteriaceae species. This killing system might represent a new function of a known competition system or even a novel system, as the observed characteristics do not fit with described contact-dependent competition systems. Further characterization of this system might help understand how P. mirabilis competes with other Enterobacteriaceae in various niches.

Effects of Dietary Alteration on the Gut Microbiome and Metabolome of the Rescued Bengal Slow Loris

Bengal slow lorises (Nycticebus bengalensis) are threatened by illegal trade. Subsequently, numerous wild-born individuals are rescued and transferred to rescue centers. Metabonomic analysis of intestinal microbiomes has increasingly played a vital role in evaluating the effects of dietary alteration on the captive status of endangered non-human primates. A synthetic analysis was done to test the differences in gut microbes and fecal metabolites between two dietary groups of Bengal slow lorises across 8 weeks. Dietary interventions led to intra-group convergence and inter-group variation in the composition of intestinal flora, metabolites, and short-chain fatty acids (SCFAs). The control diet, consisting of gums and honey, significantly increased the abundance of some potential probiotics, such as Bifidobacterium and Roseburia, and the concentration of some anti-disease related metabolites. The decrease in some amino acid metabolites in the original group fed without gums was attributed to poor body condition. Some distinct SCFAs found in the control group indicated the dietary alteration herein was fat-restricted but fiber deficient. Cognizant of this, plant exudates and fiber-enriched food supplies should be considered an optimal approach for dietary improvement of the confiscated and captive Bengal slow lorises.

Bacteriophage endolysins as a potential weapon to combat Clostridioides difficile infection

Clostridioides difficile is the leading cause of health-care-associated infection throughout the developed world and contributes significantly to patient morbidity and mortality. Typically, antibiotics are used for the primary treatment of C. difficile infections (CDIs), but they are not universally effective for all ribotypes and can result in antibiotic resistance and recurrent infection, while also disrupting the microbiota. Novel targeted therapeutics are urgently needed to combat CDI. Bacteriophage-derived endolysins are required to disrupt the bacterial cell wall of their target bacteria and are possible alternatives to antibiotics. These lytic proteins could potentially replace or augment antibiotics in CDI treatment. We discuss candidate therapeutic lysins derived from phages/prophages of C. difficile and their potential as antimicrobials against CDI. Additionally, we review the antibacterial potential of some recently identified homologues of C. difficile endolysins. Finally, the challenges of endolysins are considered with respect to the development of novel lysin-based therapies.

Growing consumption of antibiotics and epidemiology of Clostridioides difficile infections in Poland: A need to develop new solutions

Clostridioides (formerly Clostridium) difficile infections (CDIs) are becoming more common and more serious. C. difficile is the etiologic agent of antibiotic-associated diarrhea, pseudomembranous enterocolitis, and toxic megacolon while CDIs recur in 7.9% of patients. About 42.9 CDI cases/10,000 patient-days are diagnosed each day in Europe, whereas in Poland 5.6 CDI cases/10,000 patient-days are reported; however, the median for European countries is 2.9 CDI cases/10,000 patient-days. Epidemiology of CDIs has changed in recent years and risk of developing the disease has doubled in the past decade that is largely determined by use of antibiotics. Studies show that rate of antibiotic consumption in the non-hospital sector in Poland is much higher than the European average (27 vs. 21.8 DDD/1,000 patient-days), and this value has increased in recent years. Antibiotic consumption has also increased in the hospital sector, especially in the intensive care units - 1,520 DDD/1,000 patient-days (ranging from 620 to 3,960 DDD/1,000 patient-days) - and was significantly higher than in Germany 1,305 (ranging from 463 to 2,216 DDD/1,000 patient-days) or in Sweden 1,147 (ranging from 605 to 2,134 DDD/1,000 patient-days). The recent rise in CDI incidence has prompted a search for alternative treatments. Great hope is placed in probiotics, bacteriocins, monoclonal antibodies, bacteriophages, and developing new vaccines.

Bile salt metabolism is not the only factor contributing to Clostridioides (Clostridium) difficile disease severity in the murine model of disease

Susceptibility of patients to antibiotic-associated C. difficile disease is intimately associated with specific changes to gut microbiome composition. In particular, loss of microbes that modify bile salt acids (BSA) play a central role; primary bile acids stimulate spore germination whilst secondary bile acids limit C. difficile vegetative growth. To determine the relative contribution of bile salt (BS) metabolism on C. difficile disease severity, we treated mice with three combinations of antibiotics prior to infection. Mice given clindamycin alone became colonized but displayed no tissue pathology while severe disease, exemplified by weight loss and inflammatory tissue damage occurred in animals given a combination of five antibiotics and clindamycin. Animals given only the five antibiotic cocktails showed only transient colonization and no disease. C. difficile colonization was associated with a reduction in bacterial diversity, an inability to amplify bile salt hydrolase (BSH) sequences from fecal DNA and a relative increase in primary bile acids (pBA) in cecal lavages from infected mice. Further, the link between BSA modification and the microbiome was confirmed by the isolation of strains of Lactobacillus murinus that modified primary bile acids in vitro, thus preventing C. difficile germination. Interestingly, BSH activity did not correlate with disease severity which appeared linked to alternations in mucin, which may indirectly lead to increased exposure of the epithelial surface to inflammatory signals. These data confirm the role of microbial metabolic activity in protection of the gut and highlights the need for greater understanding the function of bacterial communities in disease prevention.

Nutraceuticals as modulators of gut microbiota: Role in therapy

As our knowledge of the various roles of the gut microbiota in the maintenance of homeostasis grows and as we learn how a disrupted microbiota may contribute to disease, therapeutic strategies that target our microbial fellow-travellers become ever more attractive. Most appealing are those interventions that seek to modify or supplement our diet through the addition of nutraceuticals. We now know that our diet, whether in the short or long term, is a major modifier of microbiota composition and function. Of the various nutraceuticals, two categories, prebiotics and probiotics, have received the greatest attention in basic research and product development. While our understanding of the impacts of prebiotics and probiotics on the indigenous microbiota and host biology have been described in great detail in vitro and in animal models, the clinical literature leaves much to be desired. While many claims have been made, few are supported by high quality clinical trials. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.

Bacteriocins From LAB and Other Alternative Approaches for the Control of Clostridium and Clostridiodes Related Gastrointestinal Colitis

The gut microbiome is considered as a promising target for future non-conventional therapeutic treatment of inflammatory and infectious diseases. The search for appropriate safe and beneficial (lactic acid bacterial and other) putative probiotic strains and/or their antimicrobial metabolites represents a challenging approach for combating several problematic and emerging infections. The process of selecting suitable strains, especially of lactic acid bacteria (LAB) with superior properties, has been accelerated and intensified during the past two decades, also thanks to recent developments in lab techniques. Currently, special focus is on the potential of antimicrobial metabolites produced by some LAB strains and their application as active therapeutic agents. The vision is to develop a scientific basis for 'biotherapeutics' as alternative to conventional approaches in both human and veterinary medicine. Consequently, innovative and promising applications of LAB to the therapeutic practice are presently emerging. An overview of the existing literature indicates that some antimicrobial metabolites such as bacteriocins, widely produced by different bacterial species including LAB, are promising biotherapeutic agents for controlling infections caused by potential pathogens, such as Clostridium and Clostridiodes. Non-conventional, safe and well designed therapeutic treatments may contribute to the improvement of gut dysbiotic conditions. Thereby gut homeostasis can be restored and inflammatory conditions such as gastrointestinal colitis ameliorated. Combining the knowledge on the production, characterization and application of bacteriocins from probiotic LAB, together with their antibacterial properties, appears to be a promising and novel approach in biotherapy. In this overview, different scenarios for the control of Clostridium spp. by application of bacteriocins as therapeutic agents, also in synergistic combination with antibiotics, will be discussed.

Lactobacillus gasseri APC 678 Reduces Shedding of the Pathogen Clostridium difficile in a Murine Model

Clostridium difficile is a common cause of health-care acquired diarrhea, resulting in a spectrum of disease from mild diarrhea to life-threatening illness. Sixty Lactobacillus strains were screened for anti-C. difficile activity using a co-culture method. Based on their ability to inhibit C. difficile, L. gasseri APC 678 and L. rhamnosus DPC 6111 were selected for study in a murine model of C. difficile infection. L. gasseri ATCC 33323, was included as a control. It was established that, relative to control mice not fed Lactobacillus, feeding with L. gasseri APC 678 resulted in a significant reduction by day 7 (8-fold, p = 0.017) of viable C. difficile VPI 10463 in the feces of mice. In contrast, neither L. rhamnosus DPC 6111 nor L. gasseri ATCC 33323 significantly reduced fecal C. difficile shedding. Sequencing of the cecal microbiota showed that in mice fed L. gasseri APC 678 there was a significant increase in bacterial diversity across a number of indices when compared to the control or other Lactobacillus-fed groups. There was no significant change in the relative abundance of Firmicutes or Bacteroidetes in the group fed L. gasseri APC 678 relative to the control, while the groups fed L. rhamnosus DPC 6111 or L. gasseri ATCC 33323 showed a significant decrease in the relative abundance of Firmicutes (p = 0.002 and p = 0.019, respectively) and a significant increase in Bacteroidetes (p = 0.002 and p = 0.023, respectively). These results highlight the potential of L. gasseri APC 678 as a live therapeutic agent to target C. difficile infection.

Bacteriocins and Bacteriophages: Therapeutic Weapons for Gastrointestinal Diseases?

Bacteriocins are bactericidal peptides, ribosomally synthesized, with an inhibitory activity against diverse groups of undesirable microorganisms. Bacteriocins are produced by both gram-positive and gram-negative bacteria, and to a lesser extent by some archaea. Bacteriophages are viruses that are able to infect bacterial cells and force them to produce viral components, using a lytic or lysogenic cycle. They constitute a large community in the human gut called the phageome, the most abundant part of the gut virome. Bacteriocins and bacteriophages may have an influence on both human health and diseases, thanks to their ability to modulate the gut microbiota and regulate the competitive relationship among the different microorganisms, strains and cells living in the human intestine. In this review, we explore the role of bacteriocins and bacteriophages in the most frequent gastrointestinal diseases by dissecting their interaction with the complex environment of the human gut, analyzing a possible link with extra-intestinal diseases, and speculating on their possible therapeutic application with the end goal of promoting gut health.

Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections

The history of phage therapy started with its first clinical application in 1919 and continues its development to this day. Phages continue to lack any market approval in Western medicine as a recognized drug, but are increasingly used as an experimental therapy for the compassionate treatment of patients experiencing antibiotic failure. The few formal experimental phage clinical trials that have been completed to date have produced inconclusive results on the efficacy of phage therapy, which contradicts the many successful treatment outcomes observed in historical accounts and recent individual case reports. It would therefore be wise to identify why such a discordance exists between trials and compassionate use in order to better develop future phage treatment and clinical applications. The multitude of observations reported over the years in the literature constitutes an invaluable experience, and we add to this by presenting a number of cases of patients treated compassionately with phages throughout the past decade with a focus on osteoarticular infections. Additionally, an abundance of scientific literature into phage-related areas is transforming our knowledge base, creating a greater understanding that should be applied for future clinical applications. Due to the increasing number of treatment failures anticipatedfrom the perspective of a possible post-antibiotic era, we believe that the introduction of bacteriophages into the therapeutic arsenal seems a scientifically sound and eminently practicable consideration today as a substitute or adjuvant to antibiotic therapy.

Clostridium difficile, the Difficult "Kloster" Fuelled by Antibiotics

Clostridium difficile is normally present in low numbers in a healthy adult gastro-intestinal tract (GIT). Drastic changes in the microbial population, e.g., dysbiosis caused by extensive treatment with antibiotics, stimulates the growth of resistant strains and the onset of C. difficile infection (CDI). Symptoms of infection varies from mild diarrhea to colitis (associated with dehydration and bleeding), pseudomembranous colitis with yellow ulcerations in the mucosa of the colon, to fulminant colitis (perforation of the gut membrane), and multiple organ failure. Inflamed epithelial cells and damaged mucosal tissue predisposes the colon to other opportunistic pathogens such as Clostridium perfringens, Staphylococcus aureus, Klebsiella oxytoca, Candida spp., and Salmonella spp. This may lead to small intestinal bacterial overgrowth (SIBO), sepsis, toxic megacolon, and even colorectal cancer. Many stains of C. difficile are resistant to metronidazole and vancomycin. Vaccination may be an answer to CDI, but requires more research. Success in treatment with probiotics depends on the strains used. Oral or rectal fecal transplants are partly effective, as spores in the small intestine may germinate and colonize the colon. The effect of antibiotics on C. difficile and commensal gut microbiota is summarized and changes in gut physiology are discussed. The need to search for non-antibiotic methods in the treatment of CDI and C. difficile-associated disease (CDAD) is emphasized.

Characterization of Bacteriophages Infecting Clinical Isolates of Clostridium difficile

Clostridium difficile is recognized as a problematic pathogen, causing severe enteric diseases including antibiotic-associated diarrhea and pseudomembranous colitis. The emergence of antibiotic resistant C. difficile has driven a search for alternative anti-infection modalities. A promising strategy for controlling bacterial infection includes the use of bacteriophages and their gene products. Currently, knowledge of phages active against C. difficile is still relatively limited by the fact that the isolation of phages for this organism is a technically demanding method since bacterial host themselves are difficult to culture. To isolate and characterize phages specific to C. difficile, a genotoxic agent, mitomycin C, was used to induce temperate phages from 12 clinical isolates of C. difficile. Five temperate phages consisting of ΦHR24, ΦHN10, ΦHN16-1, ΦHN16-2, and ΦHN50 were successfully induced and isolated. Spotting assays were performed against a panel of 92 C. difficile isolates to screen for susceptible bacterial hosts. The results revealed that all the C. difficile phages obtained in this work displayed a relatively narrow host range of 0-6.5% of the tested isolates. Electron microscopic characterization revealed that all isolated phages contained an icosahedral head connected to a long contractile tail, suggesting that they belonged to the Myoviridae family. Restriction enzyme analysis indicated that these phages possess unique double-stranded DNA genome. Further electron microscopic characterization revealed that the ΦHN10 absorbed to the bacterial surface via attachment to cell wall, potentially interacting with S-layer protein. Bacteriophages isolated from this study could lead to development of novel therapeutic agents and detection strategies for C. difficile.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung

Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome.

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review

Fecal microbiota transplant (FMT) has emerged as a highly efficacious treatment for difficult cases of refractory and/or recurrent Clostridium difficile infection (CDI). There have been many well-conducted randomized controlled trials and thousands of patients reported in case series that describe success rates of approximately 90% following one or more FMT. Although the exact mechanisms of FMT have yet to be fully elucidated, replacement or restoration of a 'normal' microbiota (or at least a microbiota resembling those who have never had CDI) appears to have a positive effect on the gut dysbiosis that is thought to exist in these patients. Furthermore, despite being aesthetically unappealing, this 'ultimate probiotic' is a particularly attractive solution to a difficult problem that avoids repeated courses of antibiotics. The lack of clarity about the exact mechanism of action and the 'active ingredient' of FMT (e.g., individual or communities of bacteria, bacteriophage, or bioactive molecules such as bile acids) has hindered the ability to produce a standardized and well-characterized FMT product. There is no standard method to produce material for FMT, and there are a multitude of factors that can vary between institutions that offer this therapy. Only a few studies have directly compared clinical efficacy in groups of patients who have been treated with FMT prepared differently (e.g., fresh vs. frozen) or administered by different route (e.g., by nasojejunal tube, colonoscopy or by oral administration of encapsulated product). More of these studies should be undertaken to clarify the superiority or otherwise of these variables. This review describes the methods and protocols that two English NHS hospitals independently adopted over the same time period to provide FMT for patients with recurrent CDI. There are several fundamental differences in the methods used, including selection and testing of donors, procedures for preparation and storage of material, and route of administration. These methods are described in detail in this review highlighting differing practice. Despite these significant methodological variations, clinical outcomes in terms of cure rate appear to be remarkably similar for both FMT providers. Although both hospitals have treated only modest numbers of patients, these findings suggest that many of the described differences may not be critical factors in influencing the success of the procedure. As FMT is increasingly being proposed for a number of conditions other than CDI, harmonization of methods and techniques may be more critical to the success of FMT, and thus it will be important to standardize these as far as practically possible.

In vitro antifungal, probiotic, and antioxidant functional properties of a novel Lactobacillus paraplantarum isolated from fermented dates in Saudi Arabia

BACKGROUND

Fermented foods produced using dates are used in Gulf countries as beneficial and healthful foods. The beneficial microbial flora in fermented dates contributes to maintaining the nutritional properties of dates by preventing the growth of spoilage fungi. Here, we examined the antifungal, probiotic, and antioxidant properties of the novel Lactobacillus strain D-3 isolated from fermented dates.

RESULTS

Analyzing the morphological, physiological, and biochemical characteristics of this strain demonstrated that it was similar to Lactobacillus species, and molecular-level amplification of the 16S rRNA gene showed that it belonged to Lactobacillus paraplantarum. Under shake flask cultivation using date juice, the strain produced significant amounts of ethanol and lactic, succinic, and acetic acids. Purification of benzoic acid extracted from the extracellular fermentation medium was confirmed by nuclear magnetic resonance, and infrared and mass spectral data revealed minimum inhibitory concentration values of 10, 20, 10, 5, and 10 mg mL^-1 for Aspergillus fumigates, Curvularia lunata, Fusarium oxysporum, Gibberella moniliformis, and Penicillium chrysogenum, respectively. The strain showed several advantages, including the ability to survive under conditions similar to the gastrointestinal tract (low pH, bile salts, and antimicrobial susceptibility) and high levels of extracellular enzyme activities. The strain's growth patterns under various concentrations of H₂ O₂ and its scavenging properties towards hydroxyl radical (64.85%) and DPPH (84.97%) were also interesting properties.

CONCLUSION

The antifungal, probiotic, and antioxidant properties of L. paraplantarum D3 may provide health benefits to consumers. © 2017 Society of Chemical Industry.

Narrow-Spectrum Antibacterial Agents

While broad spectrum antibiotics play an invaluable role in the treatment of bacterial infections, there are some drawbacks to their use, namely selection for and spread of resistance across multiple bacterial species, and the detrimental effect they can have upon the host microbiome. If the causitive agent of the infection is known, the use of narrow-spectrum antibacterial agents has the potential to mitigate some of these issues. This review outlines the advantages and challenges of narrow-spectrum antibacterial agents, discusses the progress that has been made toward developing diagnostics to enable their use, and describes some of the narrow-spectrum antibacterial agents currently being investigated against some of the most clinically important bacteria including Clostridium difficile, Mycobacterium tuberculosis and several ESKAPE pathogens.

Bacteriocins: antibiotics in the age of the microbiome

Antibiotics have revolutionised the treatment of infectious disease and improved the lives of billions of people worldwide over many decades. With the rise in antimicrobial resistance (AMR) and corresponding lack of antibiotic development, we find ourselves in dire need of alternative treatments. Bacteriocins are a class of bacterially produced, ribosomally synthesised, antimicrobial peptides that may be narrow or broad in their spectra of activity. Animal models have demonstrated the safety and efficacy of bacteriocins in treating a broad range of infections; however, one of the principal drawbacks has been their relatively narrow spectra when compared with small-molecule antibiotics. In an era where we are beginning to appreciate the role of the microbiota in human and animal health, the fact that bacteriocins cause much less collateral damage to the host microbiome makes them a highly desirable therapeutic. This review makes a case for the implementation of bacteriocins as therapeutic antimicrobials, either alone or in combination with existing antibiotics to alleviate the AMR crisis and to lessen the impact of antibiotics on the host microbiome.

Proteome mining for the identification and in-silico characterization of putative drug targets of multi-drug resistant Clostridium difficile strain 630

Clostridium difficile is an enteric pathogen that causes approximately 20% to 30% of antibiotic-associated diarrhea. In recent years, there has been a substantial rise in the rate of C. difficile infections as well as the emergence of virulent and antibiotic resistant C. difficile strains. So, there is an urgent need for the identification of therapeutic potential targets and development of new drugs for the treatment and prevention of C. difficile infections. In the current study, we used a hybrid approach by combining sequence similarity-based approach and protein-protein interaction network topology-based approach to identify and characterize the potential drug targets of C. difficile. A total of 155 putative drug targets of C. difficile were identified and the metabolic pathway analysis of these putative drug targets using DAVID revealed that 46 of them are involved in 9 metabolic pathways. In-silico characterization of these proteins identified seven proteins involved in pathogen-specific peptidoglycan biosynthesis pathway. Three promising targets viz. homoserine dehydrogenase, aspartate-semialdehyde dehydrogenase and aspartokinase etc. were found to be involved in multiple enzymatic pathways of the pathogen. These 3 drug targets are of particular interest as they can be used for developing effective drugs against multi-drug resistant C. difficile strain 630 in the near future.

Modulation of the gut microbiota by prebiotic fibres and bacteriocins

The gut microbiota is considered an organ that co-develops with the host throughout its life. The composition and metabolic activities of the gut microbiota are subject to a complex interplay between the host genetics and environmental factors, such as lifestyle, diet, stress and antimicrobials. It is evident that certain prebiotics, and antimicrobials produced by lactic acid bacteria (LAB), can shape the composition of the gut microbiota and its metabolic activities to promote host health and/or prevent diseases. In this review, we aim to give an overview of the impact of prebiotic fibres, and bacteriocins from LAB, on the gut microbiota and its activities, which affect the physiology and health of the host. These represent two different mechanisms in modulating the gut microbiota, the first involving exploitative competition by which the growth of beneficial bacteria is promoted and the latter involving interference competition by which the growth of pathogens and other unwanted bacteria is prevented. For interference competition in the gut, bacteriocins offer special advantages over traditional antibiotics, in that they can be designed to act towards specific unwanted bacteria and other pathogens, without any remarkable collateral effects on beneficial microbes sharing the same niche.

The Potential of Class II Bacteriocins to Modify Gut Microbiota to Improve Host Health

Production of bacteriocins is a potential probiotic feature of many lactic acid bacteria (LAB) as it can help prevent the growth of pathogens in gut environments. However, knowledge on bacteriocin producers in situ and their function in the gut of healthy animals is still limited. In this study, we investigated five bacteriocin-producing strains of LAB and their isogenic non-producing mutants for probiotic values. The LAB bacteriocins, sakacin A (SakA), pediocin PA-1 (PedPA-1), enterocins P, Q and L50 (enterocins), plantaricins EF and JK (plantaricins) and garvicin ML (GarML), are all class II bacteriocins, but they differ greatly from each other in terms of inhibition spectrum and physicochemical properties. The strains were supplemented to mice through drinking water and changes on the gut microbiota composition were interpreted using 16S rRNA gene analysis. In general, we observed that overall structure of the gut microbiota remained largely unaffected by the treatments. However, at lower taxonomic levels, some transient but advantageous changes were observed. Some potentially problematic bacteria were inhibited (e.g., Staphylococcus by enterocins, Enterococcaceae by GarML, and Clostridium by plantaricins) and the proportion of LAB was increased in the presence of SakA-, plantaricins- and GarML-producing bacteria. Moreover, the treatment with GarML-producing bacteria co-occurred with decreased triglyceride levels in the host mice. Taken together, our results indicate that several of these bacteriocin producers have potential probiotic properties at diverse levels as they promote favorable changes in the host without major disturbance in gut microbiota, which is important for normal gut functioning.

Efficacy of probiotics as an adjuvant agent in eradication of Helicobacter pylori infection and associated side effects

The intestinal tract is a host to various types of bacteria that are essential to health. Interactions between intestinal bacteria, i.e. the normal microbiota of the host’s intestine, have been a subject of intensive research, as they may influence disease cycles. Recent studies of selected probiotic species and their therapeutic benefits have suggested a potential efficacy in treatment of several gastrointestinal illnesses, including Helicobacter pylori infection. The increasing evidence from these clinical studies supports the promising role of probiotics in improving the treatment of H. pylori by increasing eradication rates as well as decreasing the adverse effects of current medication therapy. However, many unsolved questions remain which require high quality trials on specific probiotic strains in the future. The main part of this review will focus on the effects of supplementary probiotic products during standard triple H. pylori therapy.

Bacteriocins synthesized by Bacillus thuringiensis: generalities and potential applications

The members of the Bacillus thuringiensis group, commonly known as Bt, produce a huge number of metabolites, which show biocidal and antagonistic activity. B. thuringiensis is widely known for synthesizing Cry, Vip and Cyt proteins, active against insects and other parasporins with biocidal activity against certain types of cancerous cells. Nevertheless, B. thuringiensis also synthesizes compounds with antimicrobial activity, especially bacteriocins. Some B. thuringiensis bacteriocins resemble lantibiotics and other small linear peptides (class IIa) from the lactic acid bacteria bacteriocins classification system. Although many bacteriocins produced by Bt have been reported, there is no proper classification for them. In this work, we have grouped these based on molecular weight and functionality. Bacteriocins are small peptides synthesized by bacteria, presenting inhibitory activity against Gram-positive and Gram-negative bacteria and to a lesser extent against fungi. These molecules represent a good study model in the search for microbial control alternatives. Lactic acid bacteria produces a huge number of these types of molecules with great potential. Nonetheless, members of the Bacillus, cereus group, especially B. thuringiensis, emerge as an attractive alternative for obtaining bacteriocins showing novel activities. This review describes the potential applications of B. thuringiensis bacteriocins in the control of foodborne pathogens, environment and medical area.

Beneficial Microbes: The pharmacy in the gut

The scientific evidence supporting the gut microbiome in relation to health maintenance and links with various disease states afflicting humans, from metabolic to mental health, has grown dramatically in the last few years. Strategies addressing the positive modulation of microbiome functionality associated with these disorders offer huge potential to the food and pharmaceutical industries to innovate and provide therapeutic solutions to many of the health issues affecting modern society. Such strategies may involve the use of probiotics and prebiotics as nutritional adjunct therapies. Probiotics are generally recognized to be a good form of therapy to keep harmful, intestinal microorganisms in check, aid digestion and nutrient absorption, and contribute to immune function. Probiotics are reported to improve microbial balance in the intestinal tract and promote the return to a baseline microbial community following a perturbing event (dysbiosis) such as antibiotic therapy. Prebiotics are selectively fermented ingredients that allow specific changes, both in the composition and/or activity in the gastrointestinal microflora, which confers benefits upon host well-being and health.

Treatment of Clostridium difficile infection in pediatric patients

Clostridium difficile causes infections that can either remain asymptomatic or manifest as clinical disease. In this report, problems, possible solutions, and future perspectives on the treatment of C. difficile infections (CDIs) in pediatric patients are discussed. CDI, despite increasing as a consequence of the overuse and misuse of antibiotics, remains relatively uncommon in pediatrics mainly because younger children are poorly susceptible to the action of C. difficile toxins. In most such cases, C. difficile disease is mild to moderate and discontinuation of the administered antibiotics in patients receiving these drugs when CDI develops, or administration of metronidazole, is sufficient to solve this problem. In severe or frequently relapsing cases, vancomycin is the drug of choice. Probiotics do not seem to add significant advantages. Other treatment options must be reserved for severe cases and be considered as a salvage treatment, although potential advantages in pediatric patients remain unclear.

Bacteriophage therapy: history and future prospects

ABSTRACT 

Bacteriophages (or phages) are viruses which infect and kill bacteria. They are ubiquitous in the environment but are inert in humans and animals. For almost 100 years they have been used therapeutically but in the West the ready availability of antibiotics has meant that they have only been used sporadically and no commercial therapeutic products are currently available. The looming antibiotic crisis means that there is now a renewed interest in phages; a number of companies are producing nontherapeutic phage products (such as food treatment sprays), some clinical trial data are available and other trials are close to commencing. Here, I review the current state of phage therapy, with reference to the historical context and discuss why the time is now right for this forgotten cure to be revisited.

Antimicrobial activity of lactic acid bacteria in dairy products and gut: effect on pathogens

The food industry seeks alternatives to satisfy consumer demands of safe foods with a long shelf-life able to maintain the nutritional and organoleptic quality. The application of antimicrobial compounds-producing protective cultures may provide an additional parameter of processing in order to improve the safety and ensure food quality, keeping or enhancing its sensorial characteristics. In addition, strong evidences suggest that certain probiotic strains can confer resistance against infection with enteric pathogens. Several mechanisms have been proposed to support this phenomenon, including antimicrobial compounds secreted by the probiotics, competitive exclusion, or stimulation of the immune system. Recent research has increasingly demonstrated the role of antimicrobial compounds as protective mechanism against intestinal pathogens and therefore certain strains could have an effect on both the food and the gut. In this aspect, the effects of the combination of different strains keep unknown. The development of multistrain probiotic dairy products with good technological properties and with improved characteristics to those shown by the individual strains, able to act not only as protective cultures in foods, but also as probiotics able to exert a protective action against infections, has gained increased interest.

Examination of bacterial inhibition using a catalytic DNA

Determination of accurate dosage of existing antibiotics and discovery of new antimicrobials or probiotics entail simple but effective methods that can conveniently track bacteria growth and inhibition. Here we explore the application of a previously reported fluorogenic E. coli-specific DNAzyme (catalytic DNA), RFD-EC1, as a molecular probe for monitoring bacterial inhibition exerted by antibiotics and for studying bacterial competition as a result of cohabitation. Because the DNAzyme method provides a convenient way to monitor the growth of E. coli, it is capable of determining the minimal inhibitory concentration (MIC) of antibiotics much faster than the conventional optical density (OD) method. In addition, since the target for RFD-EC1 is an extracellular protein molecule from E. coli, RFD-EC1 is able to identify pore-forming antibiotics or compounds that can cause membrane leakage. Finally, RFD-EC1 can be used to analyse the competition of cohabitating bacteria, specifically the inhibition of growth of E. coli by Bacillus subtilis. The current work represents the first exploration of a catalytic DNA for microbiological applications and showcases the utility of bacteria-sensing fluorogenic DNAzymes as simple molecular probes to facilitate antibiotic and probiotic research.

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

BACKGROUND

Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infections present high relapse rates and new hyper-virulent and multi-resistant strains are emerging, making the study of this nosocomial pathogen necessary to find novel therapeutic targets.

RESULTS

We present iMLTC806cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC806cdf contains 806 genes, 703 metabolites and 769 metabolic, 117 exchange and 145 transport reactions. iMLTC806cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 89.2% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs (the closest organism for which such data exists). We predict the existence of 76 essential genes and 39 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 29 of these potential therapeutic targets, we find 125 inhibitors of homologous proteins including approved drugs with the potential for drug repositioning, that when validated experimentally could serve as starting points in the development of new antibiotics.

CONCLUSIONS

We created a highly curated metabolic network model of C. difficile strain 630 and used it to predict essential genes as potential new therapeutic targets in the fight against Clostridium difficile infections.

Probiotic characteristics of Lactobacillus fermentum strains isolated from tulum cheese

The aim of this study was to characterize the probiotic characteristics of Lactobacillus fermentum strains isolated from Tulum cheese. Seven L. fermentum strains were selected among the isolated and identified lactobacillus strains due to their abundance. When the gastric condition was considered, L. fermentum LP3 and LP4 were able to tolerate pH 2.5 and 1% bile salt. All L. fermentum strains had similar enzymatic activity and antibiotic resistance pattern but the highest antagonistic effect was detected within LP3, LP4 and LP6. Cholesterol assimilation amount of L. fermentum strains ranged between 12.1 and 45.3% in MRS and 20.7-71.1% in MRS with bile. The highest cholesterol assimilation in MRS and MRS with bile was occurred by LP3 and LP4, respectively. L. fermentum LP2 adhered to caco-2 cells more than Lactobacillus rhamnosus LGG where LP3, LP4 and LP5 adhered at similar level. In conclusion, L. fermentum LP3 and LP4 fulfilled sufficient criteria to be probiotics for use as a starter culture in the production of tulum cheese or other dairy products. Also this study indicated that some food-associated Lactobacillus strains non-predominant for gut biota have significant probiotic potential.

Novel approach of using a cocktail of designed bacteriophages against gut pathogenic E. coli for bacterial load biocontrol

BACKGROUND

This study was conducted to explore new approaches of animal biocontrol via biological control feed.

METHOD

White rats were subjected to 140 highly lytic designed phages specific against E. coli. Phages were fed via drinking water, oral injection, and vegetable capsules. Phage feeding was applied by 24 h feeding with 11 d monitoring and 20 d phage feeding and monitoring. Group of rats received external pathogenic E. coli and another group did not, namely groups A and B.

RESULTS

Phage feeding for 20 d via vegetable capsules yielded the highest reduction of fecal E. coli, 3.02 and 4.62 log, in rats group A and B respectively. Second best, feeding for 20 d via drinking water with alkali yielded 2.78 and 4.08 log in rats groups A and B respectively. The peak reduction in E. coli output was 5-10 d after phage feeding. Phage control declined after 10th day of feeding.

CONCLUSIONS

The use of cocktail of designed phages succeeded in suppressing flora or external E. coli. The phage feed biocontrol is efficient in controlling E. coli at the pre-harvest period, precisely at the 6th-8th day of phage feeding when the lowest E. coli output found.

The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor

The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, and represents a promising alternative as a bactericide. To better understand the lysis mechanism, we have determined the crystal structure of an autoproteolytic fragment of the CD27L endolysin. The structure covers the C-terminal domain of the endolysin, and represents a novel fold that is identified in a number of lysins that target Clostridia bacteria. The structure indicates endolysin cleavage occurs at the stem of the linker connecting the catalytic domain with the C-terminal domain. We also solved the crystal structure of the C-terminal domain of a slow cleaving mutant of the CTP1L endolysin that targets C. tyrobutyricum. Two distinct dimerization modes are observed in the crystal structures for both endolysins, despite a sequence identity of only 22% between the domains. The dimers are validated to be present for the full length protein in solution by right angle light scattering, small angle X-ray scattering and cross-linking experiments using the cross-linking amino acid p-benzoyl-L-phenylalanine (pBpa). Mutagenesis on residues contributing to the dimer interfaces indicates that there is a link between the dimerization modes and the autocleavage mechanism. We show that for the CTP1L endolysin, there is a reduction in lysis efficiency that is proportional to the cleavage efficiency. We propose a model for endolysin triggering, where the extended dimer presents the inactive state, and a switch to the side-by-side dimer triggers the cleavage of the C-terminal domain. This leads to the release of the catalytic portion of the endolysin, enabling the efficient digestion of the bacterial cell wall.

Clostridium difficile infection is a common cause of hospital-acquired diarrhea, following broad-spectrum antibiotic treatment particularly in elderly patients. Bacteriophage therapy could provide an alternative treatment, but a better understanding of the viral components that lyse the bacterial cell is necessary. Here, we report on the activation of two endolysins from bacteriophages that lyse Clostridia. The structures of autoproteolytic fragments of two endolysins were determined by X-ray crystallography. Based on the structures, we introduced mutations that affect the autolytic cleavage of the enzymatic portion of the endolysins, and we show that two oligomeric states have an effect on the cleavage mechanism. Moreover, the lysis activity is affected when autocleavage is inhibited for one endolysin. We propose that the cleavage and oligomerization are linked, and they provide the endolysin with a trigger and release mechanism that leads to activation. The identification of a trigger and release factor may not only be relevant to Clostridia endolysins, but could be an important factor in the triggering of many bacteriophage endolysins. A fuller understanding of this activation mechanism will help in the design of recombinant endolysins or bacteriophages with a more efficient therapeutic potential.

Exploiting gut bacteriophages for human health

The human gut contains approximately 10(15) bacteriophages (the 'phageome'), probably the richest concentration of biological entities on earth. Mining and exploiting these potential 'agents of change' is an attractive prospect. For many years, phages have been used to treat bacterial infections in humans and more recently have been approved to reduce pathogens in the food chain. Phages have also been studied as drug or vaccine delivery vectors to help treat and prevent diseases such as cancer and chronic neurodegenerative conditions. Individual phageomes vary depending on age and health, thus providing a useful biomarker of human health as well as suggesting potential interventions targeted at the gut microbiota.