Patho-biotechnology: using bad bugs to do good things

Lacticaseibacillus rhamnosus: A Suitable Candidate for the Construction of Novel Bioengineered Probiotic Strains for Targeted Pathogen Control

Probiotics, with their associated beneficial effects, have gained popularity for the control of foodborne pathogens. Various sources are explored with the intent to isolate novel robust probiotic strains with a broad range of health benefits due to, among other mechanisms, the production of an array of antimicrobial compounds. One of the shortcomings of these wild-type probiotics is their non-specificity. A pursuit to circumvent this limitation led to the advent of the field of pathobiotechnology. In this discipline, specific pathogen gene(s) are cloned and expressed into a given probiotic to yield a novel pathogen-specific strain. The resultant recombinant probiotic strain will exhibit enhanced species-specific inhibition of the pathogen and its associated infection. Such probiotics are also used as vehicles to deliver therapeutic agents. As fascinating as this approach is, coupled with the availability of numerous probiotics, it brings a challenge with regard to deciding which of the probiotics to use. Nonetheless, it is indisputable that an ideal candidate must fulfil the probiotic selection criteria. This review aims to show how Lacticaseibacillus rhamnosus, a clinically best-studied probiotic, presents as such a candidate. The objective is to spark researchers’ interest to conduct further probiotic-engineering studies using L. rhamnosus, with prospects for the successful development of novel probiotic strains with enhanced beneficial attributes.

Connecting the Dots Between Inflammatory Bowel Disease and Metabolic Syndrome: A Focus on Gut-Derived Metabolites

The role of the microbiome in health and disease has gained considerable attention and shed light on the etiology of complex diseases like inflammatory bowel disease (IBD) and metabolic syndrome (MetS). Since the microorganisms inhabiting the gut can confer either protective or harmful signals, understanding the functional network between the gut microbes and the host provides a comprehensive picture of health and disease status. In IBD, disruption of the gut barrier enhances microbe infiltration into the submucosae, which enhances the probability that gut-derived metabolites are translocated from the gut to the liver and pancreas. Considering inflammation and the gut microbiome can trigger intestinal barrier dysfunction, risk factors of metabolic diseases such as insulin resistance may have common roots with IBD. In this review, we focus on the overlap between IBD and MetS, and we explore the role of common metabolites in each disease in an attempt to connect a common origin, the gut microbiome and derived metabolites that affect the gut, liver and pancreas.

Engineered Probiotics: Applications and Biological Containment

Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.

Advances in the Microbiome: Applications to Clostridium difficile Infection

Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.

Recombinant lactic acid bacteria as delivery vectors of heterologous antigens: the future of vaccination?

Lactic acid bacteria (LABs) are good candidates for the development of new oral vaccines and are attractive alternatives to attenuated pathogens. This review focuses on the use of wild-type and recombinant lactococci and lactobacilli with emphasis on their molecular design, immunomodulation and treatment of bacterial infections. The majority of studies related to recombinant LABs have focused on Lactococcus lactis, however, molecular tools have been successfully used for Lactobacillus spp.

RESEARCH

Recombinant lactobacilli and lactococci have several health benefits, such as immunomodulation, restoration of the microbiota, synthesis of antimicrobial substances and inhibition of virulence factors. In addition, protective immune responses that are well tolerated are induced by the expression of heterologous antigens from recombinant probiotics.

Under the microscope: From pathogens to probiotics and back

The review centers on the human gastrointestinal tract; focusing first on the bacterial stress responses needed to overcome the physiochemical defenses of the host, specifically how these stress survival strategies can be used as targets for alternative infection control strategies. The concluding section focuses on recent developments in molecular diagnostics; centring on the shifting paradigm from culture to molecular based diagnostics.

Designer probiotics: Development and applications in gastrointestinal health

Given the increasing commercial and clinical relevance of probiotics, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Herein, I review the current state of the art in the design of engineered probiotic cultures, with a specific focus on their utility as therapeutics for the developing world; from the treatment of chronic and acute enteric infections, and their associated diarrhoeal complexes, to targeting HIV and application as novel mucosal vaccine delivery vehicles.

Metagenomics and novel gene discovery: promise and potential for novel therapeutics

Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.

Emerging importance of holobionts in evolution and in probiotics

The existence of microbe free animals or plants in nature is virtually impossible as they and plants have a certain degree of symbiotic association with microbes. This symbiotic association leads to the formation of holobiont (host and its symbionts). This mutual coexistence is not merely at the physical or chemical level but also at the genetic level leading to the emergence of the concept of hologenome (gene pool of host and its associated symbionts). The abundance of symbionts with the associated gene diversity contributes to the fitness of the holobiont under varying environmental conditions. The hologenome theory of evolution considers the dynamic holobiont as a single unit for natural selection and provides a more accommodating view of evolution blending Darwinism and Lamarkism. Additionally, holobionts are providing scientific basis to our understanding of the growing importance of probiotics in human health and in disease management.

Codon optimisation to improve expression of a Mycobacterium avium ssp. paratuberculosis-specific membrane-associated antigen by Lactobacillus salivarius

Subunit and DNA-based vaccines against Mycobacterium avium ssp. paratuberculosis (MAP) attempt to overcome inherent issues associated with whole-cell formulations. However, these vaccines can be hampered by poor expression of recombinant antigens from a number of disparate hosts. The high G+C content of MAP invariably leads to a codon bias throughout gene expression. To investigate if the codon bias affects recombinant MAP antigen expression, the open reading frame of a MAP-specific antigen MptD (MAP3733c) was codon optimised for expression against a Lactobacillus salivarius host. Of the total 209 codons which constitute MAP3733c, 172 were modified resulting in a reduced G+C content from 61% for the native gene to 32.7% for the modified form. Both genes were placed under the transcriptional control of the PnisA promoter; allowing controlled heterologous expression in L. salivarius. Expression was monitored using fluorescence microscopy and microplate fluorometry via GFP tags translationally fused to the C-termini of the two MptD genes. A > 37-fold increase in expression was observed for the codon-optimised MAP3733synth variant over the native gene. Due to the low cost and improved expression achieved, codon optimisation significantly improves the potential of L. salivarius as an oral vaccine stratagem against Johne's disease.

A single point mutation in the listerial betL σ(A)-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

Betaine uptake in Listeria monocytogenes is mediated by three independent transport systems, the simplest of which in genetic terms is the secondary transporter BetL. Using a random mutagenesis approach, based on the E. coli XL1 Red mutator strain, we identified a single point mutation in a putative promoter region upstream of the BetL coding region which leads to a significant increase in betL transcript levels under osmo- and chill-stress conditions and a concomitant increase in stress tolerance. Furthermore, the mutation appears to counter the heretofore unreported “twisted” cell morphology observed for L. monocytogenes grown at elevated osmolarities in tryptone soy broth.

Mining the human gut microbiome for novel stress resistance genes

With the rapid advances in sequencing technologies in recent years, the human genome is now considered incomplete without the complementing microbiome, which outnumbers human genes by a factor of one hundred. The human microbiome, and more specifically the gut microbiome, has received considerable attention and research efforts over the past decade. Many studies have identified and quantified "who is there?," while others have determined some of their functional capacity, or "what are they doing?" In a recent study, we identified novel salt-tolerance loci from the human gut microbiome using combined functional metagenomic and bioinformatics based approaches. Herein, we discuss the identified loci, their role in salt-tolerance and their importance in the context of the gut environment. We also consider the utility and power of functional metagenomics for mining such environments for novel genes and proteins, as well as the implications and possible applications for future research.

Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome

Metagenomics is a powerful tool that allows for the culture-independent analysis of complex microbial communities. One of the most complex and dense microbial ecosystems known is that of the human distal colon, with cell densities reaching up to 10(12) per gram of faeces. With the majority of species as yet uncultured, there are an enormous number of novel genes awaiting discovery. In the current study, we conducted a functional screen of a metagenomic library of the human gut microbiota for potential salt-tolerant clones. Using transposon mutagenesis, three genes were identified from a single clone exhibiting high levels of identity to a species from the genus Collinsella (closest relative being Collinsella aerofaciens) (COLAER_01955, COLAER_01957 and COLAER_01981), a high G+C, Gram-positive member of the Actinobacteria commonly found in the human gut. The encoded proteins exhibit a strong similarity to GalE, MurB and MazG. Furthermore, pyrosequencing and bioinformatic analysis of two additional fosmid clones revealed the presence of an additional galE and mazG gene, with the highest level of genetic identity to Akkermansia muciniphila and Eggerthella sp. YY7918, respectively. Cloning and heterologous expression of the genes in the osmosensitive strain, Escherichia coli MKH13, resulted in increased salt tolerance of the transformed cells. It is hoped that the identification of atypical salt tolerance genes will help to further elucidate novel salt tolerance mechanisms, and will assist our increased understanding how resident bacteria cope with the osmolarity of the gastrointestinal tract.

Enhancing the stress responses of probiotics for a lifestyle from gut to product and back again

Before a probiotic bacterium can even begin to fulfill its biological role, it must survive a battery of environmental stresses imposed during food processing and passage through the gastrointestinal tract (GIT). Food processing stresses include extremes in temperature, as well as osmotic, oxidative and food matrix stresses. Passage through the GIT is a hazardous journey for any bacteria with deleterious lows in pH encountered in the stomach to the detergent-like properties of bile in the duodenum. However, bacteria are equipped with an array of defense mechanisms to counteract intracellular damage or to enhance the robustness of the cell to withstand lethal external environments. Understanding these mechanisms in probiotic bacteria and indeed other bacterial groups has resulted in the development of a molecular toolbox to augment the technological and gastrointestinal performance of probiotics. This has been greatly aided by studies which examine the global cellular responses to stress highlighting distinct regulatory networks and which also identify novel mechanisms used by cells to cope with hazardous environments. This review highlights the latest studies which have exploited the bacterial stress response with a view to producing next-generation probiotic cultures and highlights the significance of studies which view the global bacterial stress response from an integrative systems biology perspective.

Compatible solutes: the key to Listeria's success as a versatile gastrointestinal pathogen?

Recently we reported a role for compatible solute uptake in mediating bile tolerance and increased gastrointestinal persistence in the foodborne pathogen Listeria monocytogenes[1]. Herein, we review the evolution in our understanding of how these low molecular weight molecules contribute to growth and survival of the pathogen both inside and outside the body, and how this stress survival mechanism may ultimately be used to target and kill the pathogen.

Probiotic therapy - recruiting old friends to fight new foes

Against a backdrop of increasing antibiotic resistance, and the emergence of new and evolving pathogens, clinicians are increasingly forced to consider alternative therapies - probiotics are one such alternative.

Compatible solutes: A listerial passe-partout?

Recently we reported a role for compatible solute uptake in mediating bile tolerance and increased gastrointestinal persistence in the foodborne pathogen Listeria monocytogenes.1 Herein, we review the evolution in our understanding of how these low molecular weight molecules contribute to growth and survival of the pathogen both inside and outside the body, and how this stress survival mechanism may ultimately be used to target and kill the pathogen.

Probiotics and gastrointestinal disease: successes, problems and future prospects

Gastrointestinal disease is a major cause of morbidity and mortality worldwide each year. Treatment of chronic inflammatory gastrointestinal conditions such as ulcerative colitis and Crohn's disease is difficult due to the ambiguity surrounding their precise aetiology. Infectious gastrointestinal diseases, such as various types of diarrheal disease are also becoming increasingly difficult to treat due to the increasing dissemination of antibiotic resistance among microorganisms and the emergence of the so-called 'superbugs'. Taking into consideration these problems, the need for novel therapeutics is essential. Although described for over a century probiotics have only been extensively researched in recent years. Their use in the treatment and prevention of disease, particularly gastrointestinal disease, has yielded many successful results, some of which we outline in this review. Although promising, many probiotics are hindered by inherent physiological and technological weaknesses and often the most clinically promising strains are unusable. Consequently we discuss various strategies whereby probiotics may be engineered to create designer probiotics. Such innovative approaches include; a receptor mimicry strategy to create probiotics that target specific pathogens and toxins, a patho-biotechnology approach using pathogen-derived genes to create more robust probiotic stains with increased host and processing-associated stress tolerance profiles and meta-biotechnology, whereby, functional metagenomics may be used to identify novel genes from diverse and vastly unexplored environments, such as the human gut, for use in biotechnology and medicine.

Rational design of improved pharmabiotics

Herein we review the most recent advances in probiotic research and applications with particular emphasis on the novel concept of patho-biotechnology: the application of pathogen-derived (ex vivo and in vivo) stress survival strategies for the design of more technologically robust and effective probiotic cultures with improved biotechnological and clinical applications.

The interaction between Listeria monocytogenes and the host gastrointestinal tract

Listeria monocytogenes is a ubiquitous bacterium that causes significant foodborne disease with high mortality rates in immunocompromised adults. In pregnant women foodborne infection can give rise to infection of the fetus resulting in miscarriage. In addition, the bacterium has recently been demonstrated to cause localized gastrointestinal symptoms, predominantly in immunocompetent individuals. The murine model of systemic L. monocytogenes infection has provided numerous insights into the mechanisms of pathogenesis of this organism. However, recent application of transcriptomic and proteomic approaches as well as the development of new model systems has allowed a focus upon factors that influence adaptation to gastrointestinal environments and adhesion to and invasion of the gastrointestinal mucosa. In addition, the availability of a large number of complete L. monocytogenes genome sequences has permitted inter-strain comparisons and the identification of factors that may influence the emergence of 'epidemic' phenotypes. Here we review some of the exciting recent developments in the analysis of the interaction between L. monocytogenes and the host gastrointestinal tract.

Molecular analysis of the microbial food safety implications of food reformulations for improved health

Food reformulation is commonly used as a strategy to produce foods for improved health; for example, replacing sugar with aspartame, and salt (NaCl) with KCl may help to reduce the incidence of obesity and heart disease. However, such reformulations will also change the intrinsic physicochemical properties of the food, which may in turn support the growth of foodborne pathogens and ultimately increase the incidence of foodborne disease. Thus, we need a better understanding of the microbiological food safety issues associated with product reformulation. Herein we review the most recent advances in our understanding of how microbial pathogens adapt to changes in the food composition, and how this information may ultimately be used for the design of effective pathogen control measures.

Enhancing bile tolerance improves survival and persistence of Bifidobacterium and Lactococcus in the murine gastrointestinal tract

Background

The majority of commensal gastrointestinal bacteria used as probiotics are highly adapted to the specialised environment of the large bowel. However, unlike pathogenic bacteria; they are often inadequately equipped to endure the physicochemical stresses of gastrointestinal (GI) delivery in the host. Herein we outline a patho-biotechnology strategy to improve gastric delivery and host adaptation of a probiotic strain Bifidobacterium breve UCC2003 and the generally regarded as safe (GRAS) organism Lactococcus lactis NZ9000.

Results

In vitro bile tolerance of both strains was significantly enhanced (P < 0.001), following heterologous expression of the Listeria monocytogenes bile resistance mechanism BilE. Strains harbouring bilE were also recovered at significantly higher levels (P < 0.001), than control strains from the faeces and intestines of mice (n = 5), following oral inoculation. Furthermore, a B. breve strain expressing bilE demonstrated increased efficacy relative to the wild-type strain in reducing oral L. monocytogenes infection in mice.

Conclusion

Collectively the data indicates that bile tolerance can be enhanced in Bifidobacterium and Lactococcus species through rational genetic manipulation and that this can significantly improve delivery to and colonisation of the GI tract.

High-pressure processing--effects on microbial food safety and food quality

High-pressure processing (HPP) is a nonthermal process capable of inactivating and eliminating pathogenic and food spoilage microorganisms. This novel technology has enormous potential in the food industry, controlling food spoilage, improving food safety and extending product shelf life while retaining the characteristics of fresh, preservative-free, minimally processed foods. As with other food processing methods, such as thermal processing, HPP has somewhat limited applications as it cannot be universally applied to all food types, such as some dairy and animal products and shelf-stable low-acid foods. Herein, we discuss the effects of high-pressure processing on microbial food safety and, to a lesser degree, food quality.

Improving gastric transit, gastrointestinal persistence and therapeutic efficacy of the probiotic strain Bifidobacterium breve UCC2003

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiological defences of the host is an important biological goal. In order to reach the gastrointestinal tract in sufficient numbers to exert a therapeutic effect, probiotic bacteria must resist the deleterious actions of low pH, elevated osmolarity and bile salts. Cloning the listerial betaine uptake system, BetL, into the probiotic strain Bifidobacterium breve UCC2003 significantly improved probiotic tolerance to gastric juice and conditions of elevated osmolarity mimicking the gut environment. Furthermore, whilst stable colonization of the murine intestine was achieved by oral administration of B. breve UCC2003, strains harbouring BetL were recovered at significantly higher levels in the faeces, intestines and caecum of inoculated animals. Finally, in addition to improved gastric transit and intestinal persistence, this approach improved the clinical efficacy of the probiotic culture: mice fed B. breve UCC2003-BetL(+) exhibited significantly lower levels of systemic infection compared to the control strain following oral inoculation with Listeria monocytogenes.

New frontiers in probiotic research

The increasing incidence of antibiotic resistance, coupled with a growing prevalence of cancer and allergic conditions in an aging population, has forced clinical research to explore alternative therapeutic and prophylactic avenues. One such approach involves the use of probiotics: beneficial bacterial cultures, which, when administered as a part of the daily dietary intake, reduce the incidence and severity of acute and chronic infection, facilitate prevention and reduced recurrence of certain cancers and lower the incidence of several atopic conditions. Herein, we review the most recent advances in the emerging area of patho-biotechnology in the context of improving probiotic production, delivery and clinical efficacy, in addition to the emerging area of 'designer probiotics'- strains specifically tailored to target certain pathogens and/or toxins in vivo.

Extending the Host Range of Listeria monocytogenes by Rational Protein Design

In causing disease, pathogens outmaneuver host defenses through a dedicated arsenal of virulence determinants that specifically bind or modify individual host molecules. This dedication limits the intruder to a defined range of hosts. Newly emerging diseases mostly involve existing pathogens whose arsenal has been altered to allow them to infect previously inaccessible hosts. We have emulated this chance occurrence by extending the host range accessible to the human pathogen Listeria monocytogenes by the intestinal route to include the mouse. Analyzing the recognition complex of the listerial invasion protein InlA and its human receptor E-cadherin, we postulated and verified amino acid substitutions in InlA to increase its affinity for E-cadherin. Two single substitutions increase binding affinity by four orders of magnitude and extend binding specificity to include formerly incompatible murine E-cadherin. By rationally adapting a single protein, we thus create a versatile murine model of human listeriosis.

'Bioengineered Bugs' - a patho-biotechnology approach to probiotic research and applications

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Pathogenic bacteria have evolved sophisticated strategies to overcome host defences, interact with the immune system and modulate essential host systems. The 'Patho-biotechnology' concept promotes the exploitation of these valuable traits for the design of more technologically robust and effective probiotic cultures with potentially improved biotechnological and clinical applications, as well as the development of novel vaccine and drug delivery platforms.

Patho-biotechnology; using bad bugs to make good bugs better

Given the increasing commercial and clinical relevance of probiotic cultures, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Pathogenic bacteria have evolved sophisticated strategies to overcome host defences, interact with the immune system and interfere with essential host systems. We coin the term 'patho-biotechnology' to describe the exploitation of these valuable traits in biotechnology and biomedicine. This approach shows promise for the design of more technologically robust and effective probiotic cultures with improved biotechnological and clinical applications as well as the development of novel vaccine and drug delivery platforms.

Heterologous expression of BetL, a betaine uptake system, enhances the stress tolerance of Lactobacillus salivarius UCC118

Given the increasing commercial and clinical relevance of probiotic cultures, improving the technological robustness of what are often process-sensitive cultures is an important biological goal. The nisin-controlled expression system was used to direct the heterologous expression of the listerial betaine uptake system BetL in the probiotic strain Lactobacillus salivarius UCC118. Following nisin induction, strains expressing betL exhibited a significant increase in resistance to several stresses, including elevated osmo-, cryo-, baro-, and chill tolerance, as well as increased resistance to spray- and freeze-drying. The ability to confer additional stress tolerance on a probiotic culture may be an important step in delivering viable cultures for maximal efficacy.