Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts

Leveraging strain competition to address antimicrobial resistance with microbiota therapies

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation

Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (1012 cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.

Design and regulation of engineered bacteria for environmental release

Emerging products of biotechnology involve the release of living genetically modified microbes (GMMs) into the environment. However, regulatory challenges limit their use. So far, GMMs have mainly been tested in agriculture and environmental cleanup, with few approved for commercial purposes. Current government regulations do not sufficiently address modern genetic engineering and limit the potential of new applications, including living therapeutics, engineered living materials, self-healing infrastructure, anticorrosion coatings and consumer products. Here, based on 47 global studies on soil-released GMMs and laboratory microcosm experiments, we discuss the environmental behaviour of released bacteria and offer engineering strategies to help improve performance, control persistence and reduce risk. Furthermore, advanced technologies that improve GMM function and control, but lead to increases in regulatory scrutiny, are reviewed. Finally, we propose a new regulatory framework informed by recent data to maximize the benefits of GMMs and address risks.

Harnessing the Power of Probiotics: Boosting Immunity and Safeguarding against Various Diseases and Infections

The human microbiome, a diverse microorganism community, crucially defends against pathogens. Probiotics, postbiotics, and paraprobiotics alone and in combination are potent in countering fungal and waterborne infections, particularly against viral threats. This review focuses on the mechanisms of the microbiome against viral infections, emphasizing probiotic interventions. Certain Lactic Acid Bacteria (LAB) strains effectively eliminate toxic aflatoxin B1 (AFB1) from microfungi-produced mycotoxins. LAB binding to AFB1 persists post-gastric digestion, and pre-incubation with mycotoxins reduces probiotic adhesion to mucus. Oral probiotic administration in animals increases mycotoxin excretion, reducing associated health risks. Bifidobacterium longum and Lactobacillus rhamnosus show exceptional efficacy in removing cyanobacterial toxin microcystin-LR from drinking water. Engineered probiotics promise advanced therapeutic applications for metabolic disorders, Alzheimer's, and type 1 diabetes, serving as diagnostic tools for detecting pathogens and inflammation markers. In antimicrobial peptide production, genetically modified probiotics producing human β-defensin 2 (HBD2) treat Crohn's disease with implemented biocontainment strategies preventing unintended environmental impacts.

Antibacterial action, proteolytic immunity, and in vivo activity of a Vibrio cholerae microcin

Microcins are small antibacterial proteins that mediate interbacterial competition. Their narrow-spectrum activity provides opportunities to discover microbiome-sparing treatments. However, microcins have been found almost exclusively in Enterobacteriaceae. Their broader existence and potential implications in other pathogens remain unclear. Here, we identify and characterize a microcin active against pathogenic Vibrio cholerae: MvcC. We show that MvcC is reliant on the outer membrane porin OmpT to cross the outer membrane. MvcC then binds the periplasmic protein OppA to reach and disrupt the cytoplasmic membrane. We demonstrate that MvcC's cognate immunity protein is a protease, which precisely cleaves MvcC to neutralize its activity. Importantly, we show that MvcC is active against diverse cholera isolates and in a mouse model of V. cholerae colonization. Our results provide a detailed analysis of a microcin outside of Enterobacteriaceae and its potential to influence V. cholerae infection.

Recent Advancements in Harnessing Lactic Acid Bacterial Metabolites for Fruits and Vegetables Preservation

Postharvest losses in fruits and vegetables exert substantial economic and environmental repercussions. Chemical interventions are being widely utilized for the past six decades which may lead to significant health complications. Bioprotection of fruits and vegetables is the need of the hour in which use of lactic acid bacteria (LAB) with GRAS status predominantly stands out. Incorporation of LAB in postharvest fruits and vegetables suppresses the growth of spoilage organisms by synthesizing various antimicrobial compounds such as bacteriocins, organic acids, hydrogen peroxide (H2O2), exopolysaccharides (EPS), and BLIS. For example, Pediococcus acidilactici, Lactobacillus plantarum, and Limosilactobacillus fermentum convert natural sugars in fruits and vegetables to lactic acid and create an acidic environment that do not favour spoilage organisms. LAB can improve the bioavailability of vitamins and minerals and enrich the phenolic profile and bioactivity components. LAB has remarkable physiological characteristics like resistance towards bacteriophage, proteolytic activity, and polysaccharide production which adds to the safety of foods. They modify the sensory properties and preserve the nutritional quality of fruits and vegetables. They can also perform therapeutic role in the intestinal tract as they tolerate low pH, high salt concentration. Thus application of LAB, whether independently or in conjunction with stabilizing agents as edible coatings, is regarded as an exceptionally promising methodology for ensuring safer consumption of fruits and vegetables. This review addresses the most recent research findings that harness the antagonistic property of lactic acid bacterial metabolites, formulations and coatings containing their bioactive compounds for extended shelf life of fruits and vegetables.

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.

Synthetic Biology-Driven Microbial Therapeutics for Disease Treatment

The human microbiome, consisting of microorganisms that coexist symbiotically with the body, impacts health from birth. Alterations in gut microbiota driven by factors such as diet and medication can contribute to diseases beyond the gut. Synthetic biology has paved the way for engineered microbial therapeutics, presenting promising treatments for a variety of conditions. Using genetically encoded biosensors and dynamic regulatory tools, engineered microbes can produce and deliver therapeutic agents, detect biomarkers, and manage diseases. This review organizes engineered microbial therapeutics by disease type, emphasizing innovative strategies and recent advancements. The scope of diseases includes gastrointestinal disorders, cancers, metabolic diseases, infections, and other ailments. Synthetic biology facilitates precise targeting and regulation, improving the efficacy and safety of these therapies. With promising results in animal models, engineered microbial therapeutics provide a novel alternative to traditional treatments, heralding a transformative era in diagnostics and treatment for numerous diseases.

Probiotics in Action: Enhancing Immunity and Combatting Diseases for Optimal Health

This review offers an in-depth examination of the mechanisms underlying the microbiome's defense against viral infections, with a specific focus on probiotic interventions. Mycotoxins, secondary compounds produced by microfungi, pose significant health risks. Yet, certain strains of Lactic Acid Bacteria (LAB) have exhibited remarkable efficacy in eliminating aflatoxin B1 (AFB1), the most toxic member of the aflatoxin family. Experimental setups demonstrated AFB1 binding to specific LAB strains, persisting even after gastric digestion. Laboratory studies revealed a potential protective mechanism wherein pre-incubation of probiotics with mycotoxins reduced their adhesion to mucus. Animal trials further underscored the benefits of oral probiotic administration, showcasing increased fecal excretion of mycotoxins and mitigation of associated health risks. Cyanobacteria-generated microcystins in drinking water pose a significant threat to human health. Probiotic bacteria, particularly strains like Bifidobacterium longum and Lactobacillus rhamnosus, have demonstrated exceptional efficacy in removing the cyanobacterial peptide toxin microcystin-LR. Optimized conditions resulted in rapid toxin elimination, highlighting the potential of probiotics in water purification. Engineered probiotics represent a cutting-edge approach to tailor microorganisms for specific therapeutic applications, exhibiting promise in treating metabolic disorders, Alzheimer's disease, and type 1 diabetes. Additionally, they serve as innovative diagnostic tools, capable of detecting pathogens and inflammation markers within the body. In the realm of antimicrobial peptide production, probiotics offer a promising platform, with genetically modified strains engineered to produce human β-defensin 2 (HBD2) for treating Crohn's disease, showcasing their potential in targeted theurapetic delivery. Biocontainment strategies have been implemented to prevent unintended environmental impacts.

The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide

Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.

Postbiotics: the new horizons of microbial functional bioactive compounds in food preservation and security

In recent decades, consumers, manufacturers, and researchers have been more interested in functional foods, which include probiotics, prebiotics, and postbiotics. Probiotics are live microbes that, when regulated in enough quantities, provide health benefits on the host, while the prebiotics are substrates that host microorganisms selectively use. Postbiotics are metabolites and cell-wall components that are beneficial to the host and are released by living bacteria or after lysis. Postbiotic dietary supplements are more stable than probiotics and prebiotics. Many bioactivities of postbiotics are unknown or poorly understood. Hence, this study aims to present a synopsis of the regular elements and new developments of the postbiotics including health-promoting effects, production, conceptualization of terms, bioactivities, and applications in the field of food safety and preservation. Postbiotics aid in bio preservation and the reduction of biofilm development in food due to their organic acids, bacteriocins, and other antibacterial activities. The present study examines the production of postbiotic metabolites in situ in food and the effects of external and internal food components. The antimicrobial roles, removal of biofilms, and its applications in preservation and food safety have also been discussed. This paper also explored the various aspects like manipulation of postbiotic composition in the food system and its safety measures.

Graphical Abstract

Improving quality of poultry and its meat products with probiotics, prebiotics, and phytoextracts

Remarkable changes have occurred in poultry farming and meat processing in recent years, driven by advancements in breeding technology, feed processing technology, farming conditions, and management practices. The incorporation of probiotics, prebiotics, and phytoextracts has made significant contributions to the development of poultry meat products that promote both health and functionality throughout the growth phase and during meat processing. Poultry fed with these substances improve meat quality, while incorporating probiotics, prebiotics, and phytoextracts in poultry processing, as additives or supplements, inhibits pathogens and offers health benefits to consumers. However, it is vital to assess the safety of functional fermented meat products containing these compounds and their potential effects on consumer health. Currently, there's still uncertainty in these aspects. Additionally, research on utilizing next-generation probiotic strains and synergistic combinations of probiotics and prebiotics in poultry meat products is in its early stages. Therefore, further investigation is required to gain a comprehensive understanding of the beneficial effects and safety considerations of these substances in poultry meat products in the future. This review offered a comprehensive overview of the applications of probiotics and prebiotics in poultry farming, focusing on their effects on nutrient utilization, growth efficiency, and gut health. Furthermore, potential of probiotics, prebiotics, and phytoextracts in enhancing poultry meat production was explored for improved health benefits and functionality, and possible issues associated with the use of these substances were discussed. Moreover, the conclusions drawn from this review and potential future perspectives in this field are presented.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

Genetic Circuits for Feedback Control of Gamma-Aminobutyric Acid Biosynthesis in Probiotic Escherichia coli Nissle 1917

Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate the production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.

Expectations for employing Escherichia coli Nissle 1917 in food science and nutrition

As a promising probiotic strain, Escherichia coli Nissle 1917 (EcN) has been demonstrated to confer beneficial effects on intestinal health, immune function, and pathogen prevention. Additionally, EcN has also been widely studied due to its clear genomic information, tractable gene regulation, and simple growth conditions. This review summarizes the various applications potential of EcN in food science and nutrition, including inflammation prevention, tumor-targeting therapy, antibacterial agents for food, and nutrient production with a focus on specific case studies. Moreover, we highlight the major challenges of employing EcN in food science and nutrition, including regulatory approval, stability during food processing, and consumer acceptance. Finally, we conclude with a discussion on perspectives related to employing EcN in food science and nutrition.

Antibiotic perturbations to the gut microbiome

Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.

Enhancing the antibacterial function of probiotic Escherichia coli Nissle: when less is more

Probiotic bacteria confer multiple health benefits, including preventing the growth, colonization, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria, and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probiotic Escherichia coli strain Nissle (EcN) the ability to produce microcin C (McC) from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon while ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in a Galleria mellonella infection model of enterohemorrhagic E. coli, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little-to-none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic, or diagnostic applications. Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial "probiotic" bacteria to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side effects on the performance of such bacteria, thereby compromising their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic, or diagnostic applications.

Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides

Helicobacter pylori is the primary cause of 78% of gastric cancer cases, providing an opportunity to prevent cancer by controlling a single bacterial pathogen within the complex gastric microbiota. We developed highly selective antimicrobial agents against H. pylori by fusing an H. pylori-binding guide peptide (MM1) to broad-spectrum antimicrobial peptides. The common dairy probiotic Lactococcus lactis was then engineered to secrete these guided antimicrobial peptides (gAMPs). When co-cultured in vitro with H. pylori, the gAMP probiotics lost no toxicity compared to unguided AMP probiotics against the target, H. pylori, while losing >90% of their toxicity against two tested off-target bacteria. To test binding to H. pylori, the MM1 guide was fused to green fluorescent protein (GFP), resulting in enhanced binding compared to unguided GFP as measured by flow cytometry. In contrast, MM1-GFP showed no increased binding over GFP against five different off-target bacteria. These highly selective gAMP probiotics were then tested by oral gavage in mice infected with H. pylori. As a therapy, the probiotics outperformed antibiotic treatment, effectively eliminating H. pylori in just 5 days, and also protected mice from challenge infection as a prophylactic. As expected, the gAMP probiotics were as toxic against H. pylori as the unguided AMP probiotics. However, a strong rebound in gastric species diversity was found with both the selective gAMP probiotics and the non-selective AMP probiotics. Eliminating the extreme microbial dysbiosis caused by H. pylori appeared to be the major factor in diversity recovery. IMPORTANCE Alternatives to antibiotics in the control of Helicobacter pylori and the prevention of gastric cancer are needed. The high prevalence of H. pylori in the human population, the induction of microbial dysbiosis by antibiotics, and increasing antibiotic resistance call for a more sustainable approach. By selectively eliminating the pathogen and retaining the commensal community, H. pylori control may be achieved without adverse health outcomes. Antibiotics are typically used as a therapeutic post-infection, but a more targeted, less disruptive approach could be used as a long-term prophylactic against H. pylori or, by extension, against other gastrointestinal pathogens. Furthermore, the modular nature of the guided antimicrobial peptide (gAMP) technology allows for the substitution of different guides for different pathogens and the use of a cocktail of gAMPs to avoid the development of pathogen resistance.

Bacillus subtilis PM5 from Camel Milk Boosts Chicken Immunity and Abrogates Salmonella entertitidis Infections

With the practice of a successful livestock industry using antibiotics, which has continued for more than five decades, researchers have long been interested in finding alternatives to antibiotics for poultry production. Probiotics can potentially reduce enteric diseases in livestock and enhance their productivity. The aim of this study was to isolate putative probiotics from camel milk and test them against Salmonella infection as well as host immune development. Thirteen different isolates were obtained from six different camel milk samples from dairy farms in Saudi Arabia. Three of the six isolates (PM1, PM2, PM3, PM4, PM5, and PM6) that showed Gram-positive characters reacted negatively to catalase and hemolytic assays. PM1, PM5, and PM6 showed significant nonpolar surface properties (>51% hydrophobic) and potent antimicrobial activities against avian pathogens, namely S. enterica, S. typhi, S. aureus, and E. coli. PM5 exhibited substantial probiotic traits; therefore, further focus was given to it. PM5 was identified as Bacillus subtilis OQ913924 by the 16S rRNA sequencing method and showed similarity matrix > 99%. An in vivo chicken model was used to access the health benefits of probiotics. After salmonella infection, the mucosal immune response was significantly increased (p < 0.01), and none of the challenge protocols caused mortality or clinical symptoms after infection in intestinal contents. S. enterica organ infiltration in the spleen, thymus, and small intestine was significantly reduced in the B. subtilis PM5-fed chickens. The S. enterica load in chicken feces was reduced from CFU 7.2 to 5.2 in oral-fed B. subtilis PM5-fed chickens. Probiotic-fed chickens showed buffered intestinal content and positively regulated the level of butyric acid (p < 0.05), and intestinal interleukin 1 beta (IL1-β), C-reactive protein (CRP), and interferon gamma (IFN-γ) levels were reduced (p < 0.05). In addition, B. subtilis PM5 showed significant binding to peritoneal macrophages cells and inhibited S. enterica surface adhesion, indicating co-aggregation of B. subtilis PM5 in macrophage cells. It could be concluded that supplementation with probiotics can improve the growth performance of broilers and the quality of broiler chickens against enteric pathogens. The introduction of this probiotic into the commercial poultry feed market in the near future may assist in narrowing the gap that now exists between chicken breeding and consumer demand.

Genetic circuits for feedback control of gamma-aminobutyric acid biosynthesis in probiotic Escherichia coli Nissle 1917

Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase (GadB) from E. coli and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically-encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.

Salmonella antimicrobials inherited and the non-inherited resistance: mechanisms and alternative therapeutic strategies

Salmonella spp. is one of the most important foodborne pathogens. Typhoid fever and enteritis caused by Salmonella enterica are associated with 16-33 million infections and 500,000 to 600,000 deaths annually worldwide. The eradication of Salmonella is becoming increasingly difficult because of its remarkable capacity to counter antimicrobial agents. In addition to the intrinsic and acquired resistance of Salmonella, increasing studies indicated that its non-inherited resistance, which commonly mentioned as biofilms and persister cells, plays a critical role in refractory infections and resistance evolution. These remind the urgent demand for new therapeutic strategies against Salmonella. This review starts with escape mechanisms of Salmonella against antimicrobial agents, with particular emphasis on the roles of the non-inherited resistance in antibiotic failure and resistance evolution. Then, drug design or therapeutic strategies that show impressive effects in overcoming Salmonella resistance and tolerance are summarized completely, such as overcoming the barrier of outer membrane by targeting MlaABC system, reducing persister cells by limiting hydrogen sulfide, and applying probiotics or predatory bacteria. Meanwhile, according to the clinical practice, the advantages and disadvantages of above strategies are discussed. Finally, we further analyze how to deal with this tricky problems, thus can promote above novel strategies to be applied in the clinic as soon as possible. We believed that this review will be helpful in understanding the relationships between tolerance phenotype and resistance of Salmonella as well as the efficient control of antibiotic resistance.

Advanced delivery systems for peptide antibiotics

Antimicrobial peptides (AMPs) hold promise as alternatives to traditional antibiotics for preventing and treating multidrug-resistant infections. Although they have potent antimicrobial efficacy, AMPs are mainly limited by their susceptibility to proteases and potential off-site cytotoxicity. Designing the right delivery system for peptides can help to overcome such limitations, thus improving the pharmacokinetic and pharmacodynamic profiles of these drugs. The versatility of peptides and their genetically encodable structure make them suitable for both conventional and nucleoside-based formulations. In this review, we describe the main drug delivery procedures developed so far for peptide antibiotics: lipid nanoparticles, polymeric nanoparticles, hydrogels, functionalized surfaces, and DNA- and RNA-based delivery systems.

Export of diverse and bioactive peptides through a type I secretion system

Microcins are peptide antibiotics secreted by Gram-negative bacteria that inhibit the growth of neighboring microbes. They are exported from the cytosol to the environment in a one-step process through a specific type I secretion system (T1SS). While the rules governing export of natural or non-native substrates have been resolved for T1SSs that secrete large proteins, relatively little is known about substrate requirements for peptides exported through T1SSs that secrete microcins. Here, we investigate the prototypic microcin V T1SS from Escherichia coli and show it can export a remarkably wide range of natural and synthetic peptides. We demonstrate that secretion through this system is not affected by peptide charge or hydrophobicity and appears only constrained by peptide length. A varied range of bioactive peptides, including an antibacterial peptide, a microbial signaling factor, a protease inhibitor, and a human hormone, can all be secreted and elicit their intended biological effect. Secretion through this system is not limited to E. coli , and we demonstrate its function in additional Gram-negative species that can inhabit the gastrointestinal tract. Our findings uncover the highly promiscuous nature of peptide export thorough the microcin V T1SS, which has implications for native cargo capacity and use of Gram-negative bacteria for peptide research and delivery.

Importance

Microcin type I secretion systems in Gram-negative bacteria transport antibacterial peptides from the cytoplasm to the extracellular environment in single step. In nature, each microcin secretion system is generally paired with a specific peptide. We know little about the export capacity of these transporters and how peptide sequence influences secretion. Here, we investigate the microcin V type I secretion system. Remarkably, our studies show this system can export diverse peptides and is only limited by peptide length. Furthermore, we demonstrate that various bioactive peptides can be secreted, and this system can be used in Gram-negative species that colonize the gastrointestinal tract. These finding expand our understanding of secretion through type I systems and their potential uses in peptide applications.

Enterococcus faecium from chicken feces improves chicken immune response and alleviates Salmonella infections: a pilot study

Probiotics reduce the emergence of antibiotic resistance in the livestock industry. Chicken feces are reservoirs of beneficial microbiomes. The aim of this study was to isolate putative probiotics from the intestinal contents of broiler chickens. Five fecal samples were collected from two poultry farms in Al-Ahsa, Saudi Arabia. Of the 11 morphologically distinct isolates from chicken feces (CF) samples, five isolates displayed positive reactions to Gram staining, catalase, and oxidase tests, and reacted negatively to a hemolytic assay. The isolates CF1, CF2, CF3, CF8, and CF11 were selected for further analysis of probiotic characterization, gastric survival capacity, antibiotic susceptibility, and antimicrobial activity against poultry infected with Salmonella enterica. CF2 and CF11 showed the highest hydrophobic values (> 51% hydrophobic nature). CF1, CF2, and CF11 showed potent antimicrobial activities. The active isolate CF2 was identified as Enterococcus faecium by 16s rRNA sequencing and showed a genetic similarity of 99.1%. An in vivo study was conducted using a chicken model. Enterococcus faecium-fed chickens showed an improved body weight and a lower mortality rate (17-34%). Salmonella enterica colony-forming unit (CFU) invasion in the spleen and thymus was significantly reduced in the E. faecium-fed chickens. The fecal S. enterica load was reduced from CFU 6.8 to 3.9/g in oral-administered E. faecium-fed chickens. Enterococcus faecium-fed chickens showed increased levels (P < 0.01) of butyric acid and reduced levels (P < 0.01) of intestinal interleukin 1 beta, C-reactive protein, and interferon gamma levels compared to those in the S. enterica-infected chicken group. In addition, E. faecium showed significant binding to Caco-2 epithelial cells in vitro and inhibited S. enterica colonization, indicating co-aggregation of E. faecium in epithelial cells. These results revealed that an E. faecium formulation could prevent bacterial infection and improve the quality of broiler chickens.

In Vitro and In Vivo Evaluation of Lacticaseibacillus rhamnosus GG and Bifidobacterium lactis Bb12 Against Avian Pathogenic Escherichia coli and Identification of Novel Probiotic-Derived Bioactive Peptides

Avian pathogenic E. coli (APEC), an extra-intestinal pathogenic E. coli (ExPEC), causes colibacillosis in poultry and is also a potential foodborne zoonotic pathogen. Currently, APEC infections in poultry are controlled by antibiotic medication; however, the emergence of multi-drug-resistant APEC strains and increased restrictions on the use of antibiotics in food-producing animals necessitate the development of new antibiotic alternative therapies. Here, we tested the anti-APEC activity of multiple commensal and probiotic bacteria in an agar-well diffusion assay and identified Lacticaseibacillus rhamnosus GG and Bifidobacterium lactis Bb12 producing strong zone of inhibition against APEC. In co-culture assay, L. rhamnosus GG and B. lactis Bb12 completely inhibited the APEC growth by 24 h. Further investigation revealed that antibacterial product(s) in the culture supernatants of L. rhamnosus GG and B. lactis Bb12 were responsible for the anti-APEC activity. The analysis of culture supernatants using LC-MS/MS identified multiple novel bioactive peptides (VQAAQAGDTKPIEV, AFDNTDTSLDSTFKSA, VTDTSGKAGTTKISNV, and AESSDTNLVNAKAA) in addition to the production of lactic acid. The oral administration (10⁸ CFU/chicken) of L. rhamnosus GG significantly (P < 0.001) reduced the colonization (~ 1.6 logs) of APEC in the cecum of chickens. Cecal microbiota analysis revealed that L. rhamnosus GG moderated the APEC-induced alterations of the microbial community in the cecum of chickens. Further, L. rhamnosus GG decreased (P < 0.05) the abundance of phylum Proteobacteria, particularly those belonging to Enterobacteriaceae (Escherichia-Shigella) family. These studies indicate that L. rhamnosus GG is a promising probiotic to control APEC infections in chickens. Further studies are needed to optimize the delivery of L. rhamnosus GG in feed or water and in conditions simulating the field to facilitate its development for commercial applications.

Probiotics in Poultry Nutrition as a Natural Alternative for Antibiotics

Since the early 1950s, antibiotics have been used in poultry for improving feed efficiency and growth performance. Nevertheless, various side effects have appeared, such as antibiotic resistance, antibiotic residues in eggs and meat, and imbalance of beneficial intestinal bacteria. Consequently, it is essential to find other alternatives that include probiotics that improve poultry production. Probiotics are live microorganisms administered in adequate doses and improve host health. Probiotics are available to be used as feed additives, increasing the availability of the nutrients for enhanced growth by digesting the feed properly. Immunity and meat and egg quality can be improved by supplementation of probiotics in poultry feed. Furthermore, the major reason for using probiotics as feed additives is that they can compete with various infectious diseases causing pathogens in poultry's gastrointestinal tract. Hence, this chapter focuses on the types and mechanisms of action of probiotics and their benefits, by feed supplementation, for poultry health and production.

Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic

The gastrointestinal (GI) tract is the reservoir for multidrug resistant (MDR) pathogens, specifically carbapenem-resistant (CR) Klebsiella pneumoniae and other Enterobacteriaceae, which often lead to the spread of antimicrobial resistance genes, severe extraintestinal infections, and lethal outcomes. Selective GI decolonization has been proposed as a new strategy for preventing transmission to other body sites and minimizing spreading to susceptible individuals. Here, we purify the to-date uncharacterized class IIb microcin I47 (MccI47) and demonstrate potent inhibition of numerous Enterobacteriaceae, including multidrug-resistant clinical isolates, in vitro at concentrations resembling those of commonly prescribed antibiotics. We then genetically modify the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to produce MccI47 from a stable multicopy plasmid by using MccI47 toxin production in a counterselection mechanism to engineer one of the native EcN plasmids, which renders provisions for inducible expression and plasmid selection unnecessary. We then test the clinical relevance of the MccI47-producing engineered EcN in a murine CR K. pneumoniae colonization model and demonstrate significant MccI47-dependent reduction of CR K. pneumoniae abundance after seven days of daily oral live biotherapeutic administration without disruption of the resident microbiota. This study provides the first demonstration of MccI47 as a potent antimicrobial against certain Enterobacteriaceae, and its ability to significantly reduce the abundance of CR K. pneumoniae in a preclinical animal model, when delivered from an engineered live biotherapeutic product. This study serves as the foundational step toward the use of engineered live biotherapeutic products aimed at the selective removal of MDR pathogens from the GI tract.

Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics

Engineered microbes are rapidly being developed for the delivery of therapeutic modalities to sites of disease. Escherichia coli Nissle 1917 (EcN), a genetically tractable probiotic with a well-established human safety record, is emerging as a favored chassis. Here, we summarize the latest progress in rationally engineered variants of EcN for the treatment of infectious diseases, metabolic disorders, and inflammatory bowel diseases (IBDs) when administered orally, as well as cancers when injected directly into tumors or the systemic circulation. We also discuss emerging studies that raise potential safety concerns regarding these EcN-based strains as therapeutics due to their secretion of a genotoxic colibactin that can promote the formation of DNA double-stranded breaks in mammalian DNA.

Bacteriophage Cocktail and Microcin-Producing Probiotic Escherichia coli Protect Mice Against Gut Colonization With Multidrug-Resistant Escherichia coli Sequence Type 131

Non-antibiotic measures are needed to reduce the rate of infections due to multidrug-resistant organisms (MDROs), including by eliminating the commensal reservoir that underlies such strains’ dissemination and leads to recurrent infections. Here, we tested a cocktail of pre-selected bacteriophages and an engineered microcin C7-producing probiotic Escherichia coli Nissle-1917 strain for their ability to reduce gut colonization by an E. coli strain from sequence type 131 (ST131)-H30R, which is the major clonal group of MDROs among extraintestinal clinical E. coli isolates. Although the bacteriophage cocktail was highly effective against ST131-H30R strains both in vitro and in a murine model of subcutaneous sepsis, it was only weakly and transiently effective against gut colonization by the target ST131-H30R strain (0.5 log₁₀ decrease on d + 1: p < 0.001; no significant effect on d + 4 and beyond). The probiotic strain, while also highly active against ST131-H30R in vitro, was ineffective against ST131-H30R gut colonization despite its abundant presence in feces. Nonetheless, despite failing as decolonizing agents when administered separately, when co-administered the bacteriophage cocktail and probiotic strain exhibited striking synergy against ST131-H30R gut colonization. This combinatory effect was most pronounced on d + 1 (3.3 log₁₀ target strain decrease: p < 0.001), and persisted until d + 7 (0.5 log₁₀ decrease; p < 0.02.). Although by d + 10 the ST131-H30R load was fully restored, these findings provide proof of concept for combined bacteriophage-plus-probiotic administration to reduce or, possibly, to prevent gut colonization with MDROs in high-risk individuals.

Biosynthetic Microcin J25 Exerts Strong Antibacterial, Anti-Inflammatory Activities, Low Cytotoxicity Without Increasing Drug-Resistance to Bacteria Target

Multidrug resistant (MDR) bacterial infection has emerged, raising concerns about untreatable infections, and posing the highest health risks. Antimicrobial peptides (AMPs) are thought to be the best remedy for this problem. Here, we showed biosynthetic microcin J25 (MccJ25) exhibited excellent bactericidal activity against standard and clinically relevant veterinary MDR strains with high stability, no cytotoxicity, and no increase in drug resistance. Analysis of antimicrobial mechanism possessed by sensitive enterotoxigenic Escherichia coli (ETEC) based on electron microscopy and Sytox Green methods was carried out. Results showed excellent activity against ETEC was due to permeabilizing bacterial membranes and strong affinity. MccJ25 exhibited high endotoxin-neutralizing activity in both in vivo and in vitro environments, and mice exposed to lipopolysaccharide (LPS) showed decreased plasma LPS levels and improved survival after administration of MccJ25. In an LPS-treated mouse septicemia model, MccJ25 treatment significantly alleviated inflammatory responses by inhibiting proinflammatory factor secretion and expression. In a mouse E. coli infection model, administration of MccJ25 effectively improved host defense against clinically source cocktail of multidrug-resistant E. coli strains induced intestinal inflammation and bacteria dissemination. Results of studies on anti-inflammatory mechanisms showed that MccJ25 downregulated nuclear factor kappa B kinase and mitogen-activated protein kinase, thereby reducing the production of toll-like receptor 4, myeloid differentiation factor 88 and decreasing the key proinflammatory cytokines. These findings clarify MccJ25 may be an ideal antibacterial/antiendotoxic drug candidate that has the potential to further guide the development of anti-inflammatory and/or antimicrobial agents in the war against MDR bacterial infection.

Bacteria and bacterial derivatives as delivery carriers for immunotherapy

There is growing interest in the role of microorganisms in human health and disease, with evidence showing that new types of biotherapy using engineered bacterial therapeutics, including bacterial derivatives, can address specific mechanisms of disease. The complex interactions between microorganisms and metabolic/immunologic pathways underlie many diseases with unmet medical needs, suggesting that targeting these interactions may improve patient treatment. Using tools from synthetic biology and chemical engineering, non-pathogenic bacteria or bacterial products can be programmed and designed to sense and respond to environmental signals to deliver therapeutic effectors. This review describes current progress in biotherapy using live bacteria and their derivatives to achieve therapeutic benefits against various diseases.

Precision Postbiotics and Mental Health: the Management of Post-COVID-19 Complications

The health catastrophe originated by COVID-19 pandemic construed profound impact on a global scale. However, a plethora of research studies corroborated convincing evidence conferring severity of infection of SARS-CoV-2 with the aberrant gut microbiome that strongly speculated its importance for development of novel therapeutic modalities. The intense exploration of probiotics has been envisaged to promote the healthy growth of the host, and restore intestinal microecological balance through various metabolic and physiological processes. The demystifying effect of probiotics cannot be defied, but there exists a strong skepticism related to their safety and efficacy. Therefore, molecular signature of probiotics termed as "postbiotics" are of paramount importance and there is continuous surge of utilizing postbiotics for enhancing health benefits, but little is explicit about their antiviral effects. Therefore, it is worth considering their prospective role in post-COVID regime that pave the way for exploring the pastoral vistas of postbiotics. Based on previous research investigations, the present article advocates prospective role of postbiotics in alleviating the health burden of viral infections, especially SARS-CoV-2. The article also posits current challenges and proposes a futuristic model describing the concept of "precision postbiotics" for effective therapeutic and preventive interventions that can be used for management of this deadly disease.

Engineering living therapeutics with synthetic biology

The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.

The Use of Probiotics in the Reduction of Campylobacter spp. Prevalence in Poultry

Campylobacter spp. are widely distributed microorganisms, many of which are commensals of gastrointestinal tract in multiple animal species, including poultry. Most commonly detected are C. jejuni and C. coli. Although infections are usually asymptomatic in poultry, poultry meat and products represent main sources of infection with these bacteria to humans. According to recent EFSA report, campylobacteriosis is the most commonly reported zoonotic disease. In 2018, EFSA Panel on Biological Hazards indicated that use of feed and water additives is the second most likely strategy that can be successful in minimizing Campylobacter spp. colonization rate in broiler chickens. One of those feed and water additives are probiotics. From numerous research papers it can be concluded that probiotics exhibit plenty of mechanisms of anti-Campylobacter activity, which were evaluated under in vitro conditions. These results, to some extent, can explain the efficacy of probiotics in in vivo studies, although different outcome can be observed under these two laboratory conditions. Probiotics are capable of reducing Campylobacter spp. population count in poultry gastrointestinal tract and they can reduce carcass contamination. Potential modes of anti-Campylobacter activity of probiotics, results of in vivo studies and studies performed at a farm level are widely discussed in the paper.

Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria

An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.

Mining and Statistical Modeling of Natural and Variant Class IIa Bacteriocins Elucidate Activity and Selectivity Profiles across Species

Class IIa bacteriocin antimicrobial peptides (AMPs) are a compelling alternative to current antimicrobials because of potential specific activity toward antibiotic-resistant bacteria, including vancomycin-resistant enterococci. Engineering of these molecules would be enhanced by a better understanding of AMP sequence-activity relationships to improve efficacy in vivo and limit effects of off-target activity. Toward this goal, we experimentally evaluated 210 natural and variant class IIa bacteriocins for antimicrobial activity against six strains of enterococci. Inhibitory activity was ridge regressed to AMP sequence to predict performance, achieving an area under the curve of 0.70 and demonstrating the potential of statistical models for identifying and designing AMPs. Active AMPs were individually produced and evaluated against eight enterococcus strains and four Listeria strains to elucidate trends in susceptibility. It was determined that the mannose phosphotransferase system (manPTS) sequence is informative of susceptibility to class IIa bacteriocins, yet other factors, such as membrane composition, also contribute strongly to susceptibility. A broadly potent bacteriocin variant (lactocin DT1) from a Lactobacillus ruminis genome was identified as the only variant with inhibitory activity toward all tested strains, while a novel enterocin variant (DT2) from an Enterococcus faecium genome demonstrated specificity toward Listeria strains. Eight AMPs were evaluated for proteolytic stability to trypsin, chymotrypsin, and pepsin, and three C-terminal disulfide-containing variants, including divercin V41, were identified as compelling for future in vivo studies, given their high potency and proteolytic stability.IMPORTANCE Class IIa bacteriocin antimicrobial peptides (AMPs), an alternative to traditional small-molecule antibiotics, are capable of selective activity toward various Gram-positive bacteria, limiting negative side effects associated with broad-spectrum activity. This selective activity is achieved through targeting of the mannose phosphotransferase system (manPTS) of a subset of Gram-positive bacteria, although factors affecting this mechanism are not entirely understood. Peptides identified from genomic data, as well as variants of previously characterized AMPs, can offer insight into how peptide sequence affects activity and selectivity. The experimental methods presented here identify promising potent and selective bacteriocins for further evaluation, highlight the potential of simple computational modeling for prediction of AMP performance, and demonstrate that factors beyond manPTS sequence affect bacterial susceptibility to class IIa bacteriocins.

Probiotics in poultry feed: A comprehensive review

The use of antibiotics to maintain animal well-being, promote growth and improve efficiency has been practised for more than 50 years. However, as early as the 1950s, researchers identified concern on the development of resistant bacteria for the antibiotics streptomycin and tetracycline used in turkeys and broilers respectively. These findings laid the groundwork for agricultural officials to impose stricter regulatory parameters on the use of antibiotics in poultry feeds. Probiotics are live micro-organisms included in the diet of animals as feed additives or supplements. Commonly known as a direct-fed microbial, probiotics provide beneficial properties to the host, primarily through action in the gastrointestinal tract (GIT) of the animal. Supplementation of probiotics in the diet can improve animal health and performance, through contributions to gut health and nutrient use. For instance, supplementation of probiotics has been demonstrated to benefit farm animals in immune modulation, structural modulation and increased cytokine production, which positively affect the intestinal mucosal lining against pathogens. Bacillus subtilis has been a popular bacterium used within the industry and was shown to improve intestinal villus height. Increasing the villus height and structure of the crypts in the GIT allows for the improvement of nutrient digestion and absorption. Tight junctions maintain important defences against pathogenic bacteria and cellular homeostasis. Heat stress can be a major environmental challenge in the poultry industry. Heat stress causes the bird to fluctuate its internal core temperature beyond their comfort zone. To overcome such challenges, poultry will attempt to balance its heat production and dissipation through behavioural and physiological adaptation mechanisms.

The Role of Neurotransmitters in the Protection of Caenorhabditis Elegans for Salmonella Infection by Lactobacillus

Salmonellosis is a common foodborne disease. We previously reported the protection of Caenorhabditis elegans from Salmonella Typhimurium DT104 infection by Lactobacillus zeae LB1. However, the mechanism is not fully understood. C. elegans exhibits behavior plasticity when presented with diverse pathogenic or commensal bacteria. Whether it can exert approach avoidance to S. Typhimurium through altering its neurological activity remains to be determined. In the current study, both the wild type and mutants defective in serotonin or dopamine production of C. elegans were used to investigate olfactory preference of the nematode to L. zeae LB1, DT104, and Escherichia coli OP50 by choice assays, and its resistance to DT104 infection and the protection offered by L. zeae LB1 using a life-span assay. The expression of target genes in C. elegans was also examined by real-time quantitative PCR. Results showed that pre-exposure to L. zeae LB1 did not elicit aversive olfactory behavior of the nematode toward DT104. Both mutants tph-1 and cat-2 succumbed faster than the wild type when infected with DT104. While pre-exposure to L. zeae LB1 significantly increased the survival of both the wild type and mutant tph-1, it provided no protection to mutant cat-2. Supplementation of dopamine resulted in both the resistance of mutant cat-2 to S. Typhimurium infection and the protection from L. zeae LB1 to the same mutant. Gene expression data also supported the observations in the life-span assay. These results suggest that both serotonin and dopamine play a positive role in the host defense of C. elegans to S. Typhimurium infection and that the L. zeae LB1 protection is not dependent on modifying olfactory preference of the nematode but mediated by dopamine that may have involved the regulation of p38-mitogen-activated protein kinase and insulin/insulin-like growth factor signaling pathways.

Lasso Peptide Microcin J25 Effectively Enhances Gut Barrier Function and Modulates Inflammatory Response in an Enterotoxigenic Escherichia coli-Challenged Mouse Model

Bacterial resistance leads to severe public health and safety issues worldwide. Alternatives to antibiotics are currently needed. A promising lasso peptide, microcin J25 (MccJ25), is considered to be the best potential substitute for antibiotics to treat pathogen infection, including enterotoxigenic Escherichia coli (ETEC). This study evaluated the efficacy of MccJ25 in the prevention of ETEC infection. Forty-five female BALB/c mice of clean grade (aged seven weeks, approximately 16.15 g) were randomly divided into three experimental groups as follows: (i) control group (uninfected); (ii) ETEC infection group; (iii) MccJ25 + ETEC group. Fifteen mice per group in five cages, three mice/cage. MccJ25 conferred effective protection against ETEC-induced body weight loss, decrease in rectal temperature and increase in diarrhea scores in mice. Moreover, in ETEC-challenged mice model, MccJ25 significantly improved intestinal morphology, decreased intestinal histopathological scores and attenuated intestinal inflammation by decreasing proinflammatory cytokines and intestinal permeability, including reducing serum diamine oxidase and D-lactate levels. MccJ25 enhanced epithelial barrier function by increasing occludin expression in the colon and claudin-1 expression in the jejunum, ultimately improving intestinal health of host. MccJ25 was further found to alleviate gut inflammatory responses by decreasing inflammatory cytokine production and expression via the activation of the mitogen-activated protein kinase and nuclear factor κB signaling pathways. Taken together, the results indicated that MccJ25 protects against ETEC-induced intestinal injury and intestinal inflammatory responses, suggesting the potential application of MccJ25 as an excellent antimicrobial or anti-inflammation agent against pathogen infections.

Microcin J25 Exhibits Inhibitory Activity Against Salmonella Newport in Continuous Fermentation Model Mimicking Swine Colonic Conditions

Microcin J25 (MccJ25), a 21-amino acid bacteriocin produced by Escherichia coli (E. coli), is a potent inhibitor of Enterobacteriaceae, including pathogenic E. coli, Salmonella, and Shigella. Its lasso structure makes it highly stable and therefore of interest as a possible antimicrobial agent in foods or as an alternative to antibiotics in livestock production. In the present study, we aimed to evaluate in vitro the inhibitory activity of MccJ25 against Salmonella enterica subsp. enterica serovar Newport ATCC 6962 (Salmonella Newport) used as a model pathogen under conditions simulating those of the swine proximal colon. The growth inhibition activity of MccJ25 against Salmonella Newport was examined in lysogeny broth (LB) and in modified MacFarlane medium that allows miming the swine colonic conditions. The MccJ25 activity was further determined using the Polyfermentor intestinal model (PolyFermS), an in vitro continuous fermentation model that permits deciphering the activity of any antimicrobial molecule in real colon fermentation conditions using selected microbiota. It was set up here to simulate the porcine proximal colon fermentation. In these conditions, the inhibition activity of MccJ25 was compared to those of two antimicrobial agents, reuterin and rifampicin. The minimal inhibitory concentration (MIC) of MccJ25 was determined at 0.03 μM in LB medium, compared to 1,079 and 38 μM for reuterin and rifampicin, respectively, showing a significantly higher potency of MccJ25. Total inhibition of Salmonella Newport was observed in LB medium over 24 h of incubation at concentrations starting from the MIC. In the PolyFermS model, MccJ25 induced a significantly stronger inhibition of Salmonella Newport growth than reuterin or rifampicin. A specific and sensitive LC-MS method allowed to detect and quantify MccJ25 in the PolyFermS fermentation system, showing that MccJ25 remains stable and active against Salmonella in conditions mimicking those found in swine colon. This study paves the way for further exploring the potential of this bacteriocin as an alternative to antibiotics in livestock.

Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25

In livestock production, antibiotics are used to promote animal growth, control infections and thereby increase profitability. This practice has led to the emergence of multiresistant bacteria such as Salmonella, of which some serovars are disseminated in the environment. The objective of this study is to evaluate microcin J25 as an inhibitor of Salmonella enterica serovars of various origins including human, livestock and food. Among the 116 isolates tested, 37 (31.8%) were found resistant to at least one antibiotic, and 28 were multiresistant with 19 expressing the penta-resistant phenotype ACSSuT. Microcin J25 inhibited all isolates, with minimal inhibitory concentration values ranging from 0.06 μg/ml (28.4 nM) to 400 μg/ml (189 μM). Interestingly, no cross-resistance was found between microcin J25 and antibiotics. Multiple sequence alignments of genes encoding for the different proteins involved in the recognition and transport of microcin J25 showed that only ferric-hydroxamate uptake is an essential determinant for susceptibility of S. enterica to microcin J25. Examination of Salmonella strains exposed to microcin J25 by transmission electronic microscopy showed for the first-time involvement of a pore formation mechanism. Microcin J25 was a strong inhibitor of several multiresistant isolates of Salmonella and may have a great potential as an alternative to antibiotics.

Dietary supplementation of recombinant antimicrobial peptide Epinephelus lanceolatus piscidin improves growth performance and immune response in Gallus gallus domesticus

Supplementing chicken feed with antibiotics can improve survival and prevent disease outbreaks. However, overuse of antibiotics may promote the development of antibiotic-resistant bacteria. Recently, antimicrobial peptides have been proposed as alternatives to antibiotics in animal husbandry. Here, we evaluate the effects of antimicrobial peptide, Epinephelus lanceolatus piscidin (EP), in Gallus gallus domesticus. The gene encoding EP was isolated, sequenced, codon-optimized and cloned into a Pichia pastoris recombinant protein expression system. The expressed recombinant EP (rEP) was then used as a dietary supplement for G. g. domesticus; overall health, growth performance and immunity were assessed. Supernatant from rEP-expressing yeast showed in vitro antimicrobial activity against Gram-positive and Gram-negative bacteria, according to an inhibition-zone diameter (mm) assay. Moreover, the antimicrobial peptide function of rEP was temperature independent. The fermentation broth yielded a spray-dried powder formulation containing 262.9 μg EP/g powder, and LC-MS/MS (tandem MS) analysis confirmed that rEP had a molecular weight of 4279 Da, as expected for the 34-amino acid peptide; the DNA sequence of the expression vector was also validated. We then evaluated rEP as a feed additive for G. g. domesticus. Treatment groups included control, basal diet and rEP at different doses (0.75, 1.5, 3.0, 6.0 and 12%). Compared to control, rEP supplementation increased G. g. domesticus weight gain, feed efficiency, IL-10 and IFN-γ production. Our results suggest that crude rEP could provide an alternative to traditional antibiotic feed additives for G. g. domesticus, serving to enhance growth and health of the animals.

Engineering probiotics as living diagnostics and therapeutics for improving human health

The gut microbiota that inhabit our gastrointestinal tract are well known to play an important role in maintaining human health in many aspects, including facilitating the digestion and absorption of nutrients, protecting against pathogens and regulating immune system. Gut microbiota dysbiosis is associated with a lot of diseases, such as inflammatory bowel disease, allergy, obesity, cardiovascular and neurodegenerative diseases and cancers. With the increasing knowledge of the microbiome, utilization of probiotic bacteria in modulating gut microbiota to prevent and treat a large number of disorders and diseases has gained much interest. In recent years, aided by the continuous development of tools and techniques, engineering probiotic microbes with desired characteristics and functionalities to benefit human health has made significant progress. In this paper, we summarize the recent advances in design and construction of probiotics as living diagnostics and therapeutics for probing and treating a series of diseases including metabolic disorders, inflammation and pathogenic bacteria infections. We also discuss the current challenges and future perspectives in expanding the application of probiotics for disease treatment and detection. We intend to provide insights and ideas for engineering of probiotics to better serve disease therapy and human health.