Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models

Controlling biofilms using synthetic biology approaches

Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.

Reducing residual antibiotic levels in animal feces using intestinal Escherichia coli with surface-displayed erythromycin esterase

Antibiotics are widely used in livestock and poultry industries, which results in large quantities of antibiotic residues in manure that influences subsequent treatments. In this study, an Escherichia coli strain was engineered to display erythromycin esterase on its cell surface. The engineered strain (E. coli ereA) efficiently degraded erythromycin by opening the macrocyclic 14-membered lactone ring in solution. Erythromycin (50 mg/L) was completely degraded in a solution by E. coli ereA (1 × 10⁹ CFU/mL) within 24 h. E. coli ereA retained over 86.7 % of the initial enzyme activity after 40 days of storage at 25 °C, and 78.5 % of the initial activity after seven repeated batch reactions in solution at 25 °C. Mice were fed with E. coli ereA and real-time quantitative PCR data showed that E. coli ereA colonized in the mice large intestine. The mice group fed E. coli ereA exhibited 83.13 % decrease in erythromycin levels in their feces compared with the mice group not fed E. coli ereA. E. coli ereA eliminated antibiotics from the source preventing its release into the environment. The surface-engineered strain therefore is an effective alternative agent for treating recalcitrant antibiotics, and has the potential to be applied in livestock and poultry industries.

Developing a new class of engineered live bacterial therapeutics to treat human diseases

A complex interplay of metabolic and immunological mechanisms underlies many diseases that represent a substantial unmet medical need. There is an increasing appreciation of the role microbes play in human health and disease, and evidence is accumulating that a new class of live biotherapeutics comprised of engineered microbes could address specific mechanisms of disease. Using the tools of synthetic biology, nonpathogenic bacteria can be designed to sense and respond to environmental signals in order to consume harmful compounds and deliver therapeutic effectors. In this perspective, we describe considerations for the design and development of engineered live biotherapeutics to achieve regulatory and patient acceptance.

The role microbes play in human health and the ability of synthetic biology to engineer microbial properties opens up new ways of treating disease. In this perspective, the authors describe the design and development of these living therapeutics.

The Prospects for the Therapeutic Implications of Genetically Engineered Probiotics

The interest in the therapeutic use of probiotic microorganisms has been increased during the last decade although the doubts have ascended about the probiotics mainly because their beneficial effects are not fully understood, and, in many cases, their usefulness has not been validated in clinical trials. Consequently, the notion got a considerable interest in those strains having proven probiotic potential to be engineered for improvement in their beneficial features. The process of genetic engineering can also be used for probiotic strains for the reversion of antimicrobial resistance and other modifications for their safer and effective human applications. The lactic acid bacilli are predominantly opposite as they already have gained attention owing to their health-promoting benefits and their safety for human consumption; therefore, their use, especially as a delivery agent of vaccines and drugs, is gaining attention. The tailoring of probiotic strains will not only improve the data regarding the probiotic potential of these strains but also clinch the doubts concerning these probiotics. This article focuses on the approaches of bioengineered probiotics and discusses the potential prospects for their therapeutic applications including immunomodulation, cognitive health, and anticancer therapeutics.

Quorum sensing for population-level control of bacteria and potential therapeutic applications

Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.

Engineered Living Materials Based on Adhesin-Mediated Trapping of Programmable Cells

Engineered living materials have the potential for wide-ranging applications such as biosensing and treatment of diseases. Programmable cells provide the functional basis for living materials; however, their release into the environment raises numerous biosafety concerns. Current designs that limit the release of genetically engineered cells typically involve the fabrication of multilayer hybrid materials with submicrometer porous matrices. Nevertheless the stringent physical barriers limit the diffusion of macromolecules and therefore the repertoire of molecules available for actuation in response to communication signals between cells and their environment. Here, we engineer a novel living material entitled "Platform for Adhesin-mediated Trapping of Cells in Hydrogels" (PATCH). This technology is based on engineered E. coli that displays an adhesion protein derived from an Antarctic bacterium with a high affinity for glucose. The adhesin stably anchors E. coli in dextran-based hydrogels with large pore diameters (10-100 μm) and reduces the leakage of bacteria into the environment by up to 100-fold. As an application of PATCH, we engineered E. coli to secrete the bacteriocin lysostaphin which specifically kills Staphyloccocus aureus with low probability of raising antibiotic resistance. We demonstrated that living materials containing this lysostaphin-secreting E. coli inhibit the growth of S. aureus, including the strain resistant to methicillin (MRSA). Our tunable platform allows stable integration of programmable cells in dextran-based hydrogels without compromising free diffusion of macromolecules and could have potential applications in biotechnology and biomedicine.

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.

Inducible cell-to-cell signaling for tunable dynamics in microbial communities

The last decade has seen bacteria at the forefront of biotechnological innovation, with applications including biomolecular computing, living therapeutics, microbiome engineering and microbial factories. These emerging applications are all united by the need to precisely control complex microbial dynamics in spatially extended environments, requiring tools that can bridge the gap between intracellular and population-level coordination. To address this need, we engineer an inducible quorum sensing system which enables precise tunability of bacterial dynamics both at the population and community level. As a proof-of-principle, we demonstrate the advantages of this system when genetically equipped for cargo delivery. In addition, we exploit the absence of cross-talk with respect to the majority of well-characterized quorum sensing systems to demonstrate inducibility of multi-strain communities. More broadly, this work highlights the unexplored potential of remotely inducible quorum sensing systems which, coupled to any gene of interest, may facilitate the translation of circuit designs into applications.

Quantifying and Engineering Mucus Adhesion of Probiotics

Mucus in the gastrointestinal (GI) tract is the primary point-of-interaction between humans and their gut microbiota. This intimates that mucus not only ensures protection against endogenous and exogenous opportunists but also provisions for the human microbiota to reside and flourish. With the emergence of living therapeutics, engineered microbes can deliver and produce increasingly complex medicine, and controlling the mucoadhesive properties of different microbial chassis can dictate dose-response in a patient. Here we present a redesigned, in vitro, plate-based assay to measure the mucus adhesion of various probiotics. Cell-mucus interactions were isolated by immobilizing mucus to the plate surface. Binding parameters were derived for each probiotic strain by measuring cell adhesion over a wide range of cell concentrations, providing dose-dependent adhesion metrics. Surface proteins and cell components known to influence mucoadhesion were then heterologously expressed or altered in Lactococcus lactis MG1363 and Escherichia coli Nissle 1917 to control mucus-binding capacity, avidity, and cooperativity.

Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging

Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.

Biosensing in Smart Engineered Probiotics

Engineered microbes are exciting alternatives to current diagnostics and therapeutics. Researchers have developed a wide range of genetic tools and parts to engineer probiotic and commensal microbes. Among these tools and parts, biosensors allow the microbes to sense and record or to sense and respond to chemical and environmental signals in the body, enabling them to report on health conditions of the animal host and/or deliver therapeutics in a controlled manner. This review focuses on how biosensing is applied to engineer "smart" microbes for in vivo diagnostic, therapeutic, and biocontainment goals. Hurdles that need to be overcome when transitioning from high-throughput in vitro systems to low-throughput in vivo animal models, new technologies that can be implemented to alleviate this experimental gap, and areas where future advancements can be made to maximize the utility of biosensing for medical applications are also discussed. As technologies for engineering microbes continue to be developed, these engineered organisms will be used to address many medical challenges.

The Strategies of Pathogen-Oriented Therapy on Circumventing Antimicrobial Resistance

The emerging antimicrobial resistance (AMR) poses serious threats to the global public health. Conventional antibiotics have been eclipsed in combating with drug-resistant bacteria. Moreover, the developing and deploying of novel antimicrobial drugs have trudged, as few new antibiotics are being developed over time and even fewer of them can hit the market. Alternative therapeutic strategies to resolve the AMR crisis are urgently required. Pathogen-oriented therapy (POT) springs up as a promising approach in circumventing antibiotic resistance. The tactic underling POT is applying antibacterial compounds or materials directly to infected regions to treat specific bacteria species or strains with goals of improving the drug efficacy and reducing nontargeting and the development of drug resistance. This review exemplifies recent trends in the development of POTs for circumventing AMR, including the adoption of antibiotic-antibiotic conjugates, antimicrobial peptides, therapeutic monoclonal antibodies, nanotechnologies, CRISPR-Cas systems, and microbiota modulations. Employing these alternative approaches alone or in combination shows promising advantages for addressing the growing clinical embarrassment of antibiotics in fighting drug-resistant bacteria.

Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor

Caenorhabditis elegans has become a key model organism within biology. In particular, the transparent gut, rapid growing time, and ability to create a defined gut microbiota make it an ideal candidate organism for understanding and engineering the host microbiota. Here we present the development of an experimental model that can be used to characterize whole-cell bacterial biosensors in vivo. A dual-plasmid sensor system responding to isopropyl β-d-1-thiogalactopyranoside was developed and fully characterized in vitro. Subsequently, we show that the sensor was capable of detecting and reporting on changes in the intestinal environment of C. elegans after introducing an exogenous inducer into the environment. The protocols presented here may be used to aid the rational design of engineered bacterial circuits, primarily for diagnostic applications. In addition, the model system may serve to reduce the use of current animal models and aid in the exploration of complex questions within general nematode and host-microbe biology.

Biointerfacial self-assembly generates lipid membrane coated bacteria for enhanced oral delivery and treatment

The gut microbiota represents a huge community of microorganisms that play essential roles in immune modulation and homeostasis maintenance. Microbiota transplantation is an important approach to prevent and treat disease as it can inhibit pathogen colonization and positively modulate bacterial composition. However, the development of oral bacterial therapeutics has been restricted by low bioavailability and limited retention in the gastrointestinal tract. Here, we report a simple yet highly efficient method to coat gut microbes via biointerfacial supramolecular self-assembly. Coating can be performed within 15 min by simply vortexing with biocompatible lipids. Bacteria coated with an extra self-assembled lipid membrane exhibit significantly improved survival against environmental assaults and almost unchanged viability and bioactivity. We demonstrate their enhanced efficacies in oral delivery and treatment using two murine models of colitis. We suggest that biointerfacial supramolecular self-assembly may provide a unique platform to generate advanced bacterial therapeutics for the treatment of various diseases.

Oral microbiota delivery is an approach to treat and prevent disease but suffers from low retention and bioavailability. Here the authors report on a lipid coating to protect against environmental assault maintaining viability and bioactivity of the bacteria and demonstrate effective application in a colitis model.

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut

Mucosal healing plays a critical role in combatting the effects of inflammatory bowel disease, fistulae and ulcers. While most treatments for such diseases focus on systemically delivered anti-inflammatory drugs, often leading to detrimental side effects, mucosal healing agents that target the gut epithelium are underexplored. We genetically engineer Escherichia coli Nissle 1917 (EcN) to create fibrous matrices that promote gut epithelial integrity in situ. These matrices consist of curli nanofibers displaying trefoil factors (TFFs), known to promote intestinal barrier function and epithelial restitution. We confirm that engineered EcN can secrete the curli-fused TFFs in vitro and in vivo, and is non-pathogenic. We observe enhanced protective effects of engineered EcN against dextran sodium sulfate-induced colitis in mice, associated with mucosal healing and immunomodulation. This work lays a foundation for the development of a platform in which the in situ production of therapeutic protein matrices from beneficial bacteria can be exploited.

Advancing functional and translational microbiome research using meta-omics approaches

The gut microbiome has emerged as an important factor affecting human health and disease. The recent development of -omics approaches, including phylogenetic marker-based microbiome profiling, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics, has enabled efficient characterization of microbial communities. These techniques can provide strain-level taxonomic resolution of the taxa present in microbiomes, assess the potential functions encoded by the microbial community and quantify the metabolic activities occurring within a complex microbiome. The application of these meta-omics approaches to clinical samples has identified microbial species, metabolic pathways, and metabolites that are associated with the development and treatment of human diseases. These findings have further facilitated microbiome-targeted drug discovery and efforts to improve human health management. Recent in vitro and in vivo investigations have uncovered the presence of extensive drug-microbiome interactions. These interactions have also been shown to be important contributors to the disparate patient responses to treatment that are often observed during disease therapy. Therefore, developing techniques or frameworks that enable rapid screening, detailed evaluation, and accurate prediction of drug/host-microbiome interactions is critically important in the modern era of microbiome research and precision medicine. Here we review the current status of meta-omics techniques, including integrative multi-omics approaches, for characterizing the microbiome's functionality in the context of health and disease. We also summarize and discuss new frameworks for applying meta-omics approaches and microbiome assays to study drug-microbiome interactions. Lastly, we discuss and exemplify strategies for implementing microbiome-based precision medicines using these meta-omics approaches and high throughput microbiome assays.

Resilient living materials built by printing bacterial spores

Materials can be made multifunctional by embedding them with living cells that perform sensing, synthesis, energy production, and physical movement. A challenge is that the conditions needed for living cells are not conducive to materials processing and require continuous water and nutrients. Here, we present a three dimensional (3D) printer that can mix material and cell streams to build 3D objects. Bacillus subtilis spores were printed within the material and germinated on its exterior surface, including spontaneously in new cracks. The material was resilient to extreme stresses, including desiccation, solvents, osmolarity, pH, ultraviolet light, and γ-radiation. Genetic engineering enabled the bacteria to respond to stimuli or produce chemicals on demand. As a demonstration, we printed custom-shaped hydrogels containing bacteria that can sense or kill Staphylococcus aureus, a causative agent of infections. This work demonstrates materials endued with living functions that can be used in applications that require storage or exposure to environmental stresses.

The role of the gut microbiota in the treatment of inflammatory bowel diseases

The human intestinal microbiota coevolves with its host through a symbiotic relationship and exerts great influence on substantial functions including aspects of physiology, metabolism, nutrition and regulation of immune responses leading to physiological homeostasis. Over the last years, several studies have been conducted toward the assessment of the host-gut microbiota interaction, aiming to elucidate the mechanisms underlying the pathogenesis of several diseases. A defect on the microbiota-host crosstalk and the concomitant dysregulation of immune responses combined with genetic and environmental factors have been implicated in the pathogenesis of inflammatory bowel diseases (IBD). To this end, novel therapeutic options based on the gut microbiota modulation have been an area of extensive research interest. In this review we present the recent findings on the association of dysbiosis with IBD pathogenesis, we focus on the role of gut microbiota on the treatment of IBD and discuss the novel and currently available therapeutic strategies in manipulating the composition and function of gut microbiota in IBD patients. Applicable and emerging microbiota treatment modalities, such as the use of antibiotics, prebiotics, probiotics, postbiotics, synbiotics and fecal microbiota transplantation (FMT) constitute promising therapeutic options. However, the therapeutic potential of the aforementioned approaches is a topic of investigation and further studies are needed to elucidate their position in the present treatment algorithms of IBD.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides

Antimicrobial peptides (AMPs) are regarded as attractive alternatives to conventional antibiotics, but their production in microbes remains challenging due to their inherent bactericidal nature. To address these limitations, we have developed a novel AMP fusion protein system based on an encapsulin nanocompartment protein and have demonstrated its utility in enhancing expression of HBCM2, an AMP with activity against Gram-negative bacteria. Here, HBCM2 was fused to the N-terminus of several Encapsulin monomer (Enc) variants engineered with multiple TEV protease recognition site insertions to facilitate proteolytic release of the fused HBCM2. Fusion of HBCM2 to the Enc variants, but not other common carrier proteins, enabled robust overexpression in Escherichia coli C43(DE3) cells. Interestingly, variants with a TEV site insertion following residue K71 in Enc exhibited the highest overexpression and HBCM2 release efficiencies compared to other variants but were deficient in cage formation. HBCM2 was purified from the highest expressing variant following TEV protease digestion and was found to be highly active in inhibiting E. coli growth (MIC = 5 μg/ml). Our study demonstrates the potential use of the Enc system to enhance expression of AMPs for biomanufacturing and therapeutic applications.

Engineering bacteria for cancer therapy

The engineering of living cells and microbes is ushering in a new era of cancer therapy. Due to recent microbiome studies indicating the prevalence of bacteria within the human body and specifically in tumor tissue, bacteria have generated significant interest as potential targets for cancer therapy. Notably, a multitude of empirical studies over the past decades have demonstrated that administered bacteria home and grow in tumors due to reduced immune surveillance of tumor necrotic cores. Given their specificity for tumors, bacteria present a unique opportunity to be engineered as intelligent delivery vehicles for cancer therapy with synthetic biology techniques. In this review, we discuss the history, current state, and future challenges associated with using bacteria as a cancer therapy.

Recent progress in experimental and human disease-associated multi-species biofilms

Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown about the spatial organizations and interspecies interactions of individual species within the human microbiota. Bacterial cells tend to form surface-attached biofilms in many natural environments, which enable intercellular communications and interactions in a microbial ecosystem. In this review, we summarize the recent progresses on the experimental and human disease-associated multi-species biofilm studies. We hypothesize that engineering biofilm structures and interspecies interactions might provide a tool for manipulating the composition and function of human microbiota.

Caenorhabditis Elegans and Probiotics Interactions from a Prolongevity Perspective

Probiotics exert beneficial effects on host health through different mechanisms of action, such as production of antimicrobial substances, competition with pathogens, enhancement of host mucosal barrier integrity and immunomodulation. In the context of ageing, which is characterized by several physiological alterations leading to a low grade inflammatory status called inflammageing, evidences suggest a potential prolongevity role of probiotics. Unraveling the mechanisms underlying anti-ageing effects requires the use of simple model systems. To this respect, the nematode Caenorhabditis elegans represents a suitable model organism for the study of both host-microbe interactions and for ageing studies, because of conserved signaling pathways and host defense mechanisms involved in the regulation of its lifespan. Therefore, this review analyses the impact of probiotics on C. elegans age-related parameters, with particular emphasis on oxidative stress, immunity, inflammation and protection from pathogen infections. The picture emerging from our analysis highlights that several probiotic strains are able to exert anti-ageing effects in nematodes by acting on common molecular pathways, such as insulin/insulin-like growth factor-1 (IIS) and p38 mitogen-activated protein kinase (p38 MAPK). In this perspective, C. elegans appears to be advantageous for shedding light on key mechanisms involved in host prolongevity in response to probiotics supplementation.

Emerging Frontiers in Microbiome Engineering

The gut microbiome has a significant impact on health and disease and can actively contribute to obesity, diabetes, inflammatory bowel disease, cardiovascular disease, and neurological disorders. We do not yet have the necessary tools to fine-tune the microbial communities that constitute the microbiome, though such tools could unlock extensive benefits to human health. Here, we provide an overview of the current state of technological tools that may be used for microbiome engineering. These tools can enable investigators to define the parameters of a healthy microbiome and to determine how gut bacteria may contribute to the etiology of a variety of diseases. These tools may also allow us to explore the exciting prospect of developing targeted therapies and personalized treatments for microbiome-linked diseases.

Detection of virulence and multidrug resistance operons in Pseudomonas aeruginosa isolated from Egyptian Baladi sheep and goat

Background:

Pseudomonas aeruginosa is a pit of an enormous group of free-living bacteria that are able to live everywhere and suggested to be the causative agent of great scope of acute and chronic animal infections.

Aim:

The current study was carried out to illustrate the prevalence of P. aeruginosa in small ruminants and existence of some virulence operons as well as its antimicrobial resistance.

Materials and Methods:

A total of 155 samples from sheep and 105 samples from goats (mouth abscesses, fecal swabs, nasal, tracheal swabs, and lung tissue) were collected for bacteriological study, existence of some virulence expression operons with the study of their sensitivity to the antimicrobials using disc diffusion and presence of mexR operon which is responsible for multidrug resistance (MDR).

Results:

The bacteriological examination revealed that P. aeruginosa was isolated from nine out of 155 samples from sheep (5.8%) and four isolates out of 105 samples from goat (3.8%). It is found that 12 (92.3%), 10 (76.9 %), and 8 (61.5%) of P. aeruginosa isolates harbored hemolysin phospholipase gene (pcl H), gene (exo S), and enterotoxin gene (tox A), respectively. The results of antibiotic sensitivity test showed that all tested isolates were resistant to ampicillin, bacitracin, erythromycin, streptomycin, tetracycline, trimethoprim-sulfamethoxazole, and tobramycin but sensitive to ciprofloxacin and norfloxacin. The MDR (mex R) operon was existed in all isolates.

Conclusion:

There is a growing risk for isolation of virulent MDR P. aeruginosa from sheep and goat illness cases, and this should be regarded in the efficient control programs.

Efficient engineered probiotics using synthetic biology approaches: A review

The uses of probiotics-based food supplements are getting emphasis due to their power to ensure better health conditions. Probiotics have diverse and significant applications in the health sector, so probiotic strains require an understanding of the genome level organizations. Probiotics elucidate various functional parameters that control their metabolic functions. In this review, we have compiled aspects of synthetic biology, which are used for the optimization of metabolic processes in probiotics for their use as a supplement in allopathic medicines. Synthetic biology approaches provide information about diverse biosynthetic pathways and also facilitate the novel metabolic engineering approaches for probiotics strain improvement. We have discussed the synthetic biology approaches for producing engineered probiotics via genetic circuits, expression systems, and genome editing tools like CRISPR-Cas and PEVLAB. This review also enlightens future challenges in the development of engineered probiotics.

Probiotic strains detect and suppress cholera in mice

Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen Vibrio cholerae. Oral administration of Lactococcus lactis, a common dietary fermentative bacterium, reduced intestinal V. cholerae burden and improved survival in infected infant mice through the production of lactic acid. Furthermore, we engineered an L. lactis strain that specifically detects quorum-sensing signals of V. cholerae in the gut and triggers expression of an enzymatic reporter that is readily detected in fecal samples. We postulate that preventive dietary interventions with fermented foods containing natural and engineered L. lactis strains may hinder cholera progression and improve disease surveillance in populations at risk of cholera outbreaks.

Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech

This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.

Genetic Circuit-Assisted Smart Microbial Engineering

Rapid advances in DNA synthesis, genetic manipulation, and biosensors have greatly improved the ability to engineer microorganisms with complex functions. By accurately integrating quality biosensors and complex genetic circuits, recently emerged smart microorganisms have enabled exciting opportunities for dissecting complex signaling networks and making responses without artificial intervention. However, because of the lack of design principles, developing such smart microorganisms remains challenging. In this review, we propose the concept of smart microbial engineering (SME) and describe the general features of basic SME, including the circuit architecture, components, and design process. We also summarize the latest SME achievements, remaining challenges, and potential solutions in this growing field.

Non-antibiotic therapy for Clostridioides difficile infection: a review

Clostridioides difficile infection (CDI) is a common infectious disease that is mainly caused by antibiotics. Antibiotic therapy is still the dominant treatment for CDI, although it is accompanied by side effects. Probiotics, fecal microbiota transplantation (FMT), engineered microorganisms, bacteriophages, diet, natural active substances, nanoparticles and compounds are examples of emerging non-antibiotic therapies that have received a great amount of attention. In this review, we collected data about different non-antibiotic therapies for CDI and provided a comprehensive analysis and detailed comparison of these therapies. The mechanism of action, therapeutic efficacy, and the strengths and weaknesses of these non-antibiotic therapies have been investigated to provide a basis for the reasonable alternative of non-antibiotic therapies for CDI. In summary, probiotics and FMT are currently the best choice for non-antibiotic therapy for CDI.

Recent advances in gut Microbiota mediated therapeutic targets in inflammatory bowel diseases: Emerging modalities for future pharmacological implications

The inflammatory bowel diseases (IBDs) are chronic inflammatory conditions, which are increasing in prevalence worldwide. The IBDs are thought to result from an aberrant immune response to gut microbes in genetically susceptible individuals. Dysbiosis of the gut microbiome, both functional and compositional, promotes patient susceptibility to colonization by pathobionts. Manipulating gut microbial communities and gut microbiota-immune system interactions to restore gut homeostasis or reduce inflammation are appealing therapeutic models. We discuss the therapeutic potential of precision microbiota editing, natural and engineered probiotics, the use of gut microbiota-derived metabolites in colitogenic phenotypes, and intestinal stem cells, in maintaining gut microbiota balance, restoring the mucosal barrier, and having positive immunomodulatory effects in experimental IBD. This review highlights that we are only just beginning to understand the complexity of the microbiota and how it can be manipulated for health benefits, including treatment and prevention of the clinical IBDs in future.

The honey bee gut microbiota: strategies for study and characterization

Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of Ap. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general and to aid design of future experiments in this growing field.

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli

Microbiota play important roles in the internal environment and health of humans, livestock and wild animals. Short-chain fatty acids (SCFAs) and lactate are primary metabolites that can impact the composition and function of human microbiota. According to the well-characterized key synthesis genes, many SCFA- and lactate-producing bacteria have been identified in the gut microbiota. However, unknown genes may also contribute to the formation of SCFAs and lactate. The identification of such genes will provide new engineering targets and new strategies for maintaining a stable structure of beneficial microbiota. In this study, we used Escherichia coli as a model to analyze possible genes related to SCFAs and lactate production besides the well-characterized ones. The functions of nineteen candidate genes were studied by targeted gene deletion and overexpression. Results indicated thioesterase genes such as yciA, tesA, tesB, and menI can contribute to acetate and/or butyrate formation. As for lactate, mgsA and lldD can function in addition to ldh gene. At the same time, the distribution of these functional genes in gut microbiota was investigated. Most bacteria contain the well-studied genes whereas some bacteria contain some of the described unusual ones. The results provide insights and genetic targets for the discovery of new SCFA- and lactate-producing bacteria in gut microbiota.

Synthetic Gene Circuits Enable Systems-Level Biosensor Trigger Discovery at the Host-Microbe Interface

Engineering synthetic circuits into intestinal bacteria to sense, record, and respond to in vivo signals is a promising new approach for the diagnosis, treatment, and prevention of disease. However, because the design of disease-responsive circuits is limited by a relatively small pool of known biosensors, there is a need for expanding the capacity of engineered bacteria to sense and respond to the host environment. Here, we apply a robust genetic memory circuit in Escherichia coli to identify new bacterial biosensor triggers responding in the healthy and diseased mammalian gut, which may be used to construct diagnostic or therapeutic circuits. We developed a pipeline for rapid systems-level library construction and screening, using next-generation sequencing and computational analysis, which demonstrates remarkably reliable identification of responsive biosensor triggers from pooled libraries. By testing libraries of potential triggers-each consisting of a promoter and ribosome binding site (RBS)-and using RBS variation to augment the range of trigger sensitivity, we identify and validate triggers that selectively activate our synthetic memory circuit during transit through the gut. We further identify biosensor triggers with increased response in the inflamed gut through comparative screening of one of our libraries in healthy mice and those with intestinal inflammation. Our results demonstrate the power of systems-level screening for the identification of novel biosensor triggers in the gut and provide a platform for disease-specific screening that is capable of contributing to both the understanding and clinical management of intestinal illness.IMPORTANCE The gut is a largely obscure and inaccessible environment. The use of live, engineered probiotics to detect and respond to disease signals in vivo represents a new frontier in the management of gut diseases. Engineered probiotics have also shown promise as a novel mechanism for drug delivery. However, the design and construction of effective strains that respond to the in vivo environment is hindered by our limited understanding of bacterial behavior in the gut. Our work expands the pool of environmentally responsive synthetic circuits for the healthy and diseased gut, providing insight into host-microbe interactions and enabling future development of increasingly complex biosensors. This method also provides a framework for rapid prototyping of engineered systems and for application across bacterial strains and disease models, representing a practical step toward the construction of clinically useful synthetic tools.

CRISPR-based curing and analysis of metabolic burden of cryptic plasmids in Escherichia coli Nissle 1917

E. coli Nissle 1917 (EcN) has long been used as an over-the-counter probiotic and has shown potential to be used as a live biotherapeutic. It contains two stably replicating cryptic plasmids, pMUT1, and pMUT2, the function of which is unclear but the presence of which may increase the metabolic burden on the cell, particularly in the context of added recombinant plasmids. In this work, we present a clustered regularly interspaced short palindromic repeats-Cas9-based method of curing cryptic plasmids, producing strains cured of one or both plasmids. We then assayed heterologous protein production from three different recombinant plasmids in wild-type and cured EcN derivatives and found that production of reporter proteins was not significantly different across strains. In addition, we replaced pMUT2 with an engineered version containing an inserted antibiotic resistance reporter gene and demonstrated that the engineered plasmid was stable over 90 generations without selection. These findings have broad implications for the curing of cryptic plasmids and for stable heterologous expression of proteins in this host. Specifically, curing of cryptic plasmids may not be necessary for optimal heterologous expression in this host.

Editing the microbiome the CRISPR way

Our bodies are colonized by a complex ecosystem of bacteria, unicellular eukaryotes and their viruses that together play a major role in our health. Over the past few years tools derived from the prokaryotic immune system known as CRISPR-Cas have empowered researchers to modify and study organisms with unprecedented ease and efficiency. Here we discuss how various types of CRISPR-Cas systems can be used to modify the genome of gut microorganisms and bacteriophages. CRISPR-Cas systems can also be delivered to bacterial population and programmed to specifically eliminate members of the microbiome. Finally, engineered CRISPR-Cas systems can be used to control gene expression and modulate the production of metabolites and proteins. Together these tools provide exciting opportunities to investigate the complex interplay between members of the microbiome and our bodies, and present new avenues for the development of drugs that target the microbiome. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Rapid screening of engineered microbial therapies in a 3D multicellular model

Synthetic biology is transforming therapeutic paradigms by engineering living cells and microbes to intelligently sense and respond to diseases including inflammation, infections, metabolic disorders, and cancer. However, the ability to rapidly engineer new therapies far outpaces the throughput of animal-based testing regimes, creating a major bottleneck for clinical translation. In vitro approaches to address this challenge have been limited in scalability and broad applicability. Here, we present a bacteria-in-spheroid coculture (BSCC) platform that simultaneously tests host species, therapeutic payloads, and synthetic gene circuits of engineered bacteria within multicellular spheroids over a timescale of weeks. Long-term monitoring of bacterial dynamics and disease progression enables quantitative comparison of critical therapeutic parameters such as efficacy and biocontainment. Specifically, we screen Salmonella typhimurium strains expressing and delivering a library of antitumor therapeutic molecules via several synthetic gene circuits. We identify candidates exhibiting significant tumor reduction and demonstrate high similarity in their efficacies, using a syngeneic mouse model. Last, we show that our platform can be expanded to dynamically profile diverse microbial species including Listeria monocytogenes, Proteus mirabilis, and Escherichia coli in various host cell types. This high-throughput framework may serve to accelerate synthetic biology for clinical applications and for understanding the host-microbe interactions in disease sites.

Synthetic genetic circuits for programmable biological functionalities

Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.

Combinatorial Sensor Design in Caulobacter crescentus for Selective Environmental Uranium Detection

The ability to detect uranium (U) through environmental monitoring is of critical importance for informing water resource protection and nonproliferation efforts. While technologies exist for environmental U detection, wide-area environmental monitoring, i.e. sampling coverage over large areas not known to possess U contamination, remains a challenging prospect that necessitates the development of novel detection approaches. Herein, we describe the development of a whole-cell U sensor by integrating two functionally independent, native U-responsive two-component signaling systems (TCS), UzcRS and UrpRS, within an AND gate circuit in the bacterium Caulobacter crescentus. Through leverage of the distinct but imperfect selectivity profiles of both TCS, this combinatorial approach enabled greater selectivity relative to a prior biosensor developed with UzcRS alone; no cross-reactivity was observed with most common environmental metals (e.g, Fe, As, Cu, Ca, Mg, Cd, Cr, Al) or the U decay-chain product Th, and the selectivity against Zn and Pb was significantly improved. In addition, integration of the UzcRS signal amplifier protein UzcY within the AND gate circuit further enhanced overall sensitivity and selectivity for U. The functionality of the sensor in an environmental context was confirmed by detection of U concentrations as low as 1 μM in groundwater samples. The results highlight the value of a combinatorial approach for constructing whole-cell sensors for the selective detection of analytes for which there are no known evolved regulators.

Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut

Probiotics are living microorganisms that are increasingly used as gastrointestinal therapeutics by virtue of their innate or engineered genetic function. Unlike abiotic therapeutics, probiotics can replicate in their intended site, subjecting their genomes and therapeutic properties to natural selection. We exposed the candidate probiotic E. coli Nissle (EcN) to the mouse gastrointestinal tract over several weeks, systematically altering the diet and background microbiota complexity. In-transit EcN accumulates genetic mutations that modulate carbohydrate utilization, stress response, and adhesion to gain competitive fitness, while previous exposure to antibiotics reveals an acquisition of resistance. We then leveraged these insights to generate an EcN strain that shows therapeutic efficacy in a mouse model of phenylketonuria and found that it was genetically stable over 1 week, thereby validating EcN's utility as a chassis for engineering. Collectively, we demonstrate a generalizable pipeline that can be applied to other probiotics to better understand their safety and engineering potential.

Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition

Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.

Facile synthesis of graphene-tin oxide nanocomposite derived from agricultural waste for enhanced antibacterial activity against Pseudomonas aeruginosa

Antibacterial screening of graphene-tin oxide nanocomposites synthesized from carbonized wood and coconut shell is investigated against Pseudomonas aeruginosa for the first time. Efficient and facile one step hydrothermal process adopted in the present work for the synthesis of graphene-tin oxide nanoparticles provides an ideal method for the economic large-scale production of the same. Graphene-tin oxide nanocomposites derived from wood charcoal possess a spherical morphology whereas rod like structures are seen in the case of coconut shell derivatives. An excitation independent fluorescence response is observed in graphene-tin oxide nanohybrids while graphene oxide nanostructures exhibited an excitation dependent behavior. These hydrophilic nanostructures are highly stable and exhibited no sign of luminescence quenching or particle aggregation even after a storage of 30 months. Bactericidal effects of the nanostructures obtained from coconut shell is found to be relatively higher compared to those procured from wood. This variation in antibacterial performance of the samples is directly related to their morphological difference which in turn is heavily influenced by the precursor material used. MIC assay revealed that coconut shell derived graphene-tin oxide composite is able to inhibit the bacterial growth at a lower concentration (250 μg/mL) than the other nanostructures. Nanocomposites synthesized from agro-waste displayed significantly higher antimicrobial activity compared to the precursor and graphene oxide nanostructures thereby making them excellent candidates for various bactericidal applications such as disinfectants, sanitary agents etc.