Enhancing the tropism of bacteria via genetically programmed biosensors

Application Evaluation and Performance-Directed Improvement of the Native and Engineered Biosensors

Transcription factor (TF)-based biosensors (TFBs) have received considerable attention in various fields due to their capability of converting biosignals, such as molecule concentrations, into analyzable signals, thereby bypassing the dependence on time-consuming and laborious detection techniques. Natural TFs are evolutionarily optimized to maintain microbial survival and metabolic balance rather than for laboratory scenarios. As a result, native TFBs often exhibit poor performance, such as low specificity, narrow dynamic range, and limited sensitivity, hindering their application in laboratory and industrial settings. This work analyzes four types of regulatory mechanisms underlying TFBs and outlines strategies for constructing efficient sensing systems. Recent advances in TFBs across various usage scenarios are reviewed with a particular focus on the challenges of commercialization. The systematic improvement of TFB performance by modifying the constituent elements is thoroughly discussed. Additionally, we propose future directions of TFBs for developing rapid-responsive biosensors and addressing the challenge of application isolation. Furthermore, we look to the potential of artificial intelligence (AI) technologies and various models for programming TFB genetic circuits. This review sheds light on technical suggestions and fundamental instructions for constructing and engineering TFBs to promote their broader applications in Industry 4.0, including smart biomanufacturing, environmental and food contaminants detection, and medical science.

Programmable bacteria synergize with PD-1 blockade to overcome cancer cell-intrinsic immune resistance mechanisms

Interferon-γ (IFN-γ) is a potent cytokine critical for response to immunotherapy, yet conventional methods to systemically deliver this cytokine have been hindered by severe dose-limiting toxicities. Here, we engineered a strain of probiotic bacteria that home to tumors and locally release IFN-γ. A single intratumoral injection of these IFN-γ-producing bacteria was sufficient to drive systemic tumor antigen-specific antitumor immunity, without observable toxicity. Although cancer cells use various resistance mechanisms to evade immune responses, bacteria-derived IFN-γ overcame primary resistance to programmed cell death 1 (PD-1) blockade via activation of cytotoxic Foxp3-CD4+ and CD8+ T cells. Moreover, by activating natural killer (NK) cells, bacteria-derived IFN-γ also overcame acquired resistance mechanisms to PD-1 blockade, specifically loss-of-function mutations in IFN-γ signaling and antigen presentation pathways. Collectively, these results demonstrate the promise of combining IFN-γ-producing bacteria with PD-1 blockade as a therapeutic strategy for overcoming immunotherapy-resistant, locally advanced, and metastatic disease.

Engineering bacterial theranostics: from logic gates to in vivo applications

Over the past 2 decades, rapid advances in synthetic biology have enabled the design of increasingly intricate and biologically relevant systems with broad applications in healthcare. A growing area of interest is in designing bacteria that sense and respond to endogenous disease-associated signals, creating engineered theranostics that function as disease surveyors for human health. In particular, engineered cells hold potential in facilitating greatly enhanced temporal and spatial control over the release of a range of therapeutics. Such systems are particularly useful for targeting challenging, under-drugged disease targets in a more nuanced manner than is currently possible. This review provides an overview of the recent advances in the design, delivery, and dynamics of bacterial theranostics to enable safe, robust, and genetically tractable therapies to treat disease. It outlines the primary challenges in theranostic clinical translation, proposes strategies to overcome these issues, and explores promising future avenues for the field.

Recent Advances in Hydrogel-Based Biosensors for Cancer Detection

Early cancer detection is crucial for effective treatment, but current methods have limitations. Novel biomaterials, such as hydrogels, offer promising alternatives for developing biosensors for cancer detection. Hydrogels are three-dimensional and cross-linked networks of hydrophilic polymers that have properties similar to biological tissues. They can be combined with various biosensors to achieve high sensitivity, specificity, and stability. This review summarizes the recent advances in hydrogel-based biosensors for cancer detection, their synthesis, their applications, and their challenges. It also discusses the implications and future directions of this emerging field.

Programmable Bacteria with Dynamic Virulence Modulation System for Precision Antitumor Immunity

Engineered bacteria-mediated antitumor approaches have been proposed as promising immunotherapies for cancer. However, the off-target bacterial toxicity narrows the therapeutic window. Living microbes will benefit from their controllable immunogenicity within tumors for safer antitumor applications. In this study, a genetically encoded microbial activation strategy is reported that uses tunable and dynamic expression of surface extracellular polysaccharides to improve bacterial biocompatibility while retaining therapeutic efficacy. Based on screening of genes associated with Salmonella survival in macrophages, a novel attenuated Salmonella chassis strain AIS (htrA gene-deficient) highly enriched in tumors after administration and rapidly cleared from normal organs are reported. Subsequently, an engineered bacterial strain, AISI-H, is constructed based on the AIS strain and an optimized quorum-sensing regulatory system. The AISI-H strain can achieve recovery of dynamic tumor-specific bacterial virulence through a novel HTRA-RCSA axis-based and quorum-sensing synthetic gene circuit-mediated increase in extracellular polysaccharide content. These strains act "off" in normal organs to avoid unwanted immune activation and "on" in tumors for precise tumor suppression in mice. The AISI-H strain shows significant tumor inhibition and potent activation of anticancer immunity in a melanoma mouse model. The AISI-H strain exhibits excellent biocompatibility. This bacterial regulation strategy expands the applications of microbe-based antitumor therapeutics.

Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives

The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.

Towards Understanding Tumour Colonisation by Probiotic Bacterium E. coli Nissle 1917

The last decade has seen a rapid increase in studies utilising a genetically modified probiotic, Escherichia coli Nissle 1917 (EcN), as a chassis for cancer treatment and detection. This approach relies on the ability of EcN to home to and selectively colonise tumours over normal tissue, a characteristic common to some bacteria that is thought to result from the low-oxygen, nutrient-rich and immune-privileged niche the tumour provides. Pre-clinical studies have used genetically modified EcN to deliver therapeutic payloads that show efficacy in reducing tumour burden as a result of high-tumour and low off-target colonisation. Most recently, the EcN chassis has been expanded into an effective tumour-detection tool. These advances provide strong justification for the movement of genetically modified EcN into clinical oncology trials. What is currently unknown in the field is a deep mechanistic understanding of how EcN distributes to and localises within tumours. This review summarises the existing EcN literature, with the inclusion of research undertaken with other tumour-homing and pathogenic bacteria, to provide insights into possible mechanisms of EcN tumour homing for future validation. Understanding exactly how and why EcN colonises neoplastic tissue will inform the design and testing of the next generation of EcN chassis strains to address biosafety and containment concerns and optimise the detection and treatment of cancer.

Sialidase-Chimeric Bioengineered Bacteria for Tumor-Sialoglycan-Triggered Solid Tumor Therapy

Adoptive cell therapies for solid tumors are usually limited by off-target antigens, incapable tissue infiltration, and cell function exhaustion. In contrast, bacterial cells possess the inherent competencies of preferential tumor targeting, deep tissue penetration, and high intratumoral bioactivity and represent promising alternatives to overcome these challenges. Here, a sialic-acid-responsive regulatory gene circuit is engineered into Escherichia coli MG1655 to express cytolysin of hemolysin E (HlyE). Furthermore, sialidases are bioorthogonally decorated onto the surface of azido-functionalized bioengineered bacteria for recognizing tumor sialoglycans and cleaving their sialosides into free sialic acids. As chemical inducers, sialic acids feedbackingly activate the bacterial gene circuit to produce HlyE and lyse tumor cells. This study mimics the tumor antigen-induced cytotoxin production and cell lysis that occurs in chimeric antigen receptor T (CAR-T) cells yet surmounts the intrinsic limitations of adoptive cell therapies. Moreover, sialidase-mediated tumor cell desialylation also reverses the immunosuppressive effect of glycoimmune checkpoints and further improves the therapeutic effect of solid tumors.

Engineered Bacteria as Living Biosensors in Dermal Tattoos

Dermal tattoo biosensors are promising platforms for real-time monitoring of biomarkers, with skin used as a diagnostic interface. Traditional tattoo sensors have utilized small molecules as biosensing elements. However, the rise of synthetic biology has enabled the potential employment of engineered bacteria as living analytical tools. Exploiting engineered bacterial sensors will allow for potentially more sensitive detection across a broad biomarker range, with advanced processing and sense/response functionalities using genetic circuits. Here, the interfacing of bacterial biosensors as living analytics in tattoos is shown. Engineered bacteria are encapsulated into micron-scale hydrogel beads prepared through scalable microfluidics. These biosensors can sense both biochemical cues (model biomarkers) and biophysical cues (temperature changes, using RNA thermometers), with fluorescent readouts. By tattooing beads into skin models and confirming sensor activity post-tattooing, our study establishes a foundation for integrating bacteria as living biosensing entities in tattoos.

Physiochemically and Genetically Engineered Bacteria: Instructive Design Principles and Diverse Applications

With the comprehensive understanding of microorganisms and the rapid advances of physiochemical engineering and bioengineering technologies, scientists are advancing rationally-engineered bacteria as emerging drugs for treating various diseases in clinical disease management. Engineered bacteria specifically refer to advanced physiochemical or genetic technologies in combination with cutting edge nanotechnology or physical technologies, which have been validated to play significant roles in lysing tumors, regulating immunity, influencing the metabolic pathways, etc. However, there has no specific reviews that concurrently cover physiochemically- and genetically-engineered bacteria and their derivatives yet, let alone their distinctive design principles and various functions and applications. Herein, the applications of physiochemically and genetically-engineered bacteria, and classify and discuss significant breakthroughs with an emphasis on their specific design principles and engineering methods objective to different specific uses and diseases beyond cancer is described. The combined strategies for developing in vivo biotherapeutic agents based on these physiochemically- and genetically-engineered bacteria or bacterial derivatives, and elucidated how they repress cancer and other diseases is also underlined. Additionally, the challenges faced by clinical translation and the future development directions are discussed. This review is expected to provide an overall impression on physiochemically- and genetically-engineered bacteria and enlighten more researchers.

Biomimetic Nucleic Acid Drug Delivery Systems for Relieving Tumor Immunosuppressive Microenvironment

Immunotherapy combats tumors by enhancing the body's immune surveillance and clearance of tumor cells. Various nucleic acid drugs can be used in immunotherapy, such as DNA expressing cytokines, mRNA tumor vaccines, small interfering RNAs (siRNA) knocking down immunosuppressive molecules, and oligonucleotides that can be used as immune adjuvants. Nucleic acid drugs, which are prone to nuclease degradation in the circulation and find it difficult to enter the target cells, typically necessitate developing appropriate vectors for effective in vivo delivery. Biomimetic drug delivery systems, derived from viruses, bacteria, and cells, can protect the cargos from degradation and clearance, and deliver them to the target cells to ensure safety. Moreover, they can activate the immune system through their endogenous activities and active components, thereby improving the efficacy of antitumor immunotherapeutic nucleic acid drugs. In this review, biomimetic nucleic acid delivery systems for relieving a tumor immunosuppressive microenvironment are introduced. Their immune activation mechanisms, including upregulating the proinflammatory cytokines, serving as tumor vaccines, inhibiting immune checkpoints, and modulating intratumoral immune cells, are elaborated. The advantages and disadvantages, as well as possible directions for their clinical translation, are summarized at last.

Harnessing and Mimicking Bacterial Features to Combat Cancer: From Living Entities to Artificial Mimicking Systems

Bacterial-derived micro-/nanomedicine has garnered considerable attention in anticancer therapy, owing to the unique natural features of bacteria, including specific targeting ability, immunogenic benefits, physicochemical modifiability, and biotechnological editability. Besides, bacterial components have also been explored as promising drug delivery vehicles. Harnessing these bacterial features, cutting-edge physicochemical and biotechnologies have been applied to attenuated tumor-targeting bacteria with unique properties or functions for potent and effective cancer treatment, including strategies of gene-editing and genetic circuits. Further, the advent of bacteria-inspired micro-/nanorobots and mimicking artificial systems has furnished fresh perspectives for formulating strategies for developing highly efficient drug delivery systems. Focusing on the unique natural features and advantages of bacteria, this review delves into advances in bacteria-derived drug delivery systems for anticancer treatment in recent years, which has experienced a process from living entities to artificial mimicking systems. Meanwhile, a summary of relative clinical trials is provided and primary challenges impeding their clinical application are discussed. Furthermore, future directions are suggested for bacteria-derived systems to combat cancer.

Exploiting bacteria for cancer immunotherapy

Immunotherapy has revolutionized the treatment of cancer but continues to be constrained by limited response rates, acquired resistance, toxicities and high costs, which necessitates the development of new, innovative strategies. The discovery of a connection between the human microbiota and cancer dates back 4,000 years, when local infection was observed to result in tumour eradication in some individuals. However, the true oncological relevance of the intratumoural microbiota was not recognized until the turn of the twentieth century. The intratumoural microbiota can have pivotal roles in both the pathogenesis and treatment of cancer. In particular, intratumoural bacteria can either promote or inhibit cancer growth via remodelling of the tumour microenvironment. Over the past two decades, remarkable progress has been made preclinically in engineering bacteria as agents for cancer immunotherapy; some of these bacterial products have successfully reached the clinical stages of development. In this Review, we discuss the characteristics of intratumoural bacteria and their intricate interactions with the tumour microenvironment. We also describe the many strategies used to engineer bacteria for use in the treatment of cancer, summarizing contemporary data from completed and ongoing clinical trials. The work described herein highlights the potential of bacteria to transform the landscape of cancer therapy, bridging ancient wisdom with modern scientific innovation.

Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology

Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.

Mutation of the peptide-regulated transcription factor ComR for amidated peptide specificity and heterologous function in Lactiplantibacillus plantarum WCFS1

There is a growing interest in the use of probiotic bacteria as biosensors for the detection of disease. However, there is a lack of bacterial receptors developed for specific disease biomarkers. Here, we have investigated the use of the peptide-regulated transcription factor ComR from Streptococcus spp. for specific peptide biomarker detection. ComR exhibits a number of attractive features that are potentially exploitable to create a biomolecular switch for engineered biosensor circuitry within the probiotic organism Lactiplantibacillus plantarum WCFS1. Through iterative design-build-test cycles, we developed a genomically integrated, ComR-based biosensor circuit that allowed WCFS1 to detect low nanomolar concentrations of ComR's cognate peptide XIP. By screening a library of ComR proteins with mutant residues substituted at the K100 position, we identified mutations that increased the specificity of ComR toward an amidated version of its cognate peptide, demonstrating the potential for ComR to detect this important class of biomarker.IMPORTANCEUsing bacteria to detect disease is an exciting possibility under active study. Detecting extracellular peptides with specific amino acid sequences would be particularly useful as these are important markers of health and disease (biomarkers). In this work, we show that a probiotic bacteria (Lactiplantibacillus plantarum) can be genetically engineered to detect specific extracellular peptides using the protein ComR from Streptococcus bacteria. In its natural form, ComR allowed the probiotic bacteria to detect a specific peptide, XIP. We then modified XIP to be more like the peptide biomarkers found in humans and engineered ComR so that it activated with this modified XIP and not the original XIP. This newly engineered ComR also worked in the probiotic bacteria, as expected. This suggests that with additional engineering, ComR might be able to activate with human peptide biomarkers and be used by genetically engineered probiotic bacteria to better detect disease.

Promising dawn in tumor microenvironment therapy: engineering oral bacteria

Despite decades of research, cancer continues to be a major global health concern. The human mouth appears to be a multiplicity of local environments communicating with other organs and causing diseases via microbes. Nowadays, the role of oral microbes in the development and progression of cancer has received increasing scrutiny. At the same time, bioengineering technology and nanotechnology is growing rapidly, in which the physiological activities of natural bacteria are modified to improve the therapeutic efficiency of cancers. These engineered bacteria were transformed to achieve directed genetic reprogramming, selective functional reorganization and precise control. In contrast to endotoxins produced by typical genetically modified bacteria, oral flora exhibits favorable biosafety characteristics. To outline the current cognitions upon oral microbes, engineered microbes and human cancers, related literatures were searched and reviewed based on the PubMed database. We focused on a number of oral microbes and related mechanisms associated with the tumor microenvironment, which involve in cancer occurrence and development. Whether engineering oral bacteria can be a possible application of cancer therapy is worth consideration. A deeper understanding of the relationship between engineered oral bacteria and cancer therapy may enhance our knowledge of tumor pathogenesis thus providing new insights and strategies for cancer prevention and treatment.

Rationally designed approaches to augment CAR-T therapy for solid tumor treatment

Chimeric antigen receptor T cell denoted as CAR-T therapy has realized incredible therapeutic advancements for B cell malignancy treatment. However, its therapeutic validity has yet to be successfully achieved in solid tumors. Different from hematological cancers, solid tumors are characterized by dysregulated blood vessels, dense extracellular matrix, and filled with immunosuppressive signals, which together result in CAR-T cells' insufficient infiltration and rapid dysfunction. The insufficient recognition of tumor cells and tumor heterogeneity eventually causes cancer reoccurrences. In addition, CAR-T therapy also raises safety concerns, including potential cytokine release storm, on-target/off-tumor toxicities, and neuro-system side effects. Here we comprehensively review various targeting aspects, including CAR-T cell design, tumor modulation, and delivery strategy. We believe it is essential to rationally design a combinatory CAR-T therapy via constructing optimized CAR-T cells, directly manipulating tumor tissue microenvironments, and selecting the most suitable delivery strategy to achieve the optimal outcome in both safety and efficacy.

Reprogramming a Doxycycline-Inducible Gene Switch System for Bacteria-Mediated Cancer Therapy

PURPOSE

Attenuated Salmonella typhimurium is a potential biotherapeutic antitumor agent because it can colonize tumors and inhibit their growth. The present study aimed to develop a doxycycline (Doxy)-inducible gene switch system in attenuated S. typhimurium and assess its therapeutic efficacy in various tumor-bearing mice models.

PROCEDURES

A Doxy-inducible gene switch system comprising two plasmids was engineered to trigger the expression of cargo genes (Rluc8 and clyA). Attenuated S. typhimurium carrying Rluc8 were injected intravenously into BALB/c mice bearing CT26 tumors, and bioluminescence images were captured at specified intervals post-administration of doxycycline. The tumor-suppressive effects of bacteria carrying clyA were evaluated in BALB/c mice bearing CT26 tumors and in C57BL/6 mice bearing MC38 tumors.

RESULTS

Expression of the fimE gene, induced only in the presence of Doxy, triggered a unidirectional switch of the POXB20 promoter to induce expression of the cargo genes. The switch event was maintained over a long period of bacterial culture. After intravenous injection of transformed Salmonella into mice bearing CT26 tumors, the bacteria transformed with the Doxy-inducible gene switch system for Rluc8 targeted only tumor tissues and expressed the payloads 2 days after Doxy treatment. Notably, bacteria carrying the Doxy-inducible gene switch system for clyA effectively suppressed tumor growth and prolonged survival, even after just one Doxy induction.

CONCLUSIONS

These results suggest that attenuated S. typhimurium carrying this novel gene switch system elicited significant therapeutic effects through a single induction triggering and were a potential biotherapeutic agent for tumor therapy.

Bacterial therapies at the interface of synthetic biology and nanomedicine

Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.

Engineering bacteria for cancer immunotherapy

Bacterial therapeutics have emerged as promising delivery systems to target tumors. These engineered live therapeutics can be harnessed to modulate the tumor microenvironment or to deliver and selectively release therapeutic payloads to tumors. A major challenge is to deliver bacteria systemically without causing widespread inflammation, which is critical for the many tumors that are not accessible to direct intratumoral injection. We describe potential strategies to address this challenge, along with approaches for specific payload delivery and biocontainment to ensure safety. These strategies will pave the way for the development of cost-effective, widely applicable next-generation cancer therapeutics.

Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer

Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.

Engineering Probiotic E. coli Nissle 1917 for Release of Therapeutic Nanobodies

Bioengineered probiotics enable new opportunities to improve cancer treatment strategies due to their tumor-colonizing capabilities. Here, we will describe the development of a probiotic E. coli Nissle 1917 platform encoding a synchronized lysis mechanism for the localized and sustained release of blocking nanobodies against immune checkpoint molecules like programmed cell death protein-ligand 1 and cytotoxic T lymphocyte-associated protein-4. Specifically, we will detail the experimental protocols needed to (1) encode and validate binding of recombinantly produced checkpoint blockade nanobodies, (2) evaluate the therapeutic efficacy and safety of the probiotic platform in syngeneic tumor-bearing mice, and (3) analyze the immunophenotype of the tumor microenvironment.

Design of synthetic bacterial biosensors

Novel whole-cell bacterial biosensor designs require an emphasis on moving toward field deployment. Many current sensors are characterized under specified laboratory conditions, which frequently do not represent actual deployment conditions. To this end, recent developments such as toolkits for probing new host chassis that are more robust to environments of interest, have paved the way for improved designs. Strategies for rational tuning of genetic components or tools such as genetic amplifiers or designs that allow post hoc tuning are essential in optimizing existing biosensors for practical application. Furthermore, recent work has seen a rise in directed evolution techniques, which can be immensely valuable in both tuning existing sensors and developing sensors for new analytes that lack characterized sensors. Combined with advancements in bioinformatics and capabilities in rewiring two-component systems, many new sensors can be established, broadening biosensor use cases. Last, recent work in CRISPR-based dynamic regulation and memory mechanisms, as well as kill-switches for biosafety and innovative output integration concepts, represents promising steps toward designing bacterial biosensors for deployment in dynamic and heterogeneous conditions.

A synthetic biology approach to engineering circuits in immune cells

A synthetic circuit in a biological system involves the designed assembly of genetic elements, biomolecules, or cells to create a defined function. These circuits are central in synthetic biology, enabling the reprogramming of cellular behavior and the engineering of cells with customized responses. In cancer therapeutics, engineering T cells with circuits have the potential to overcome the challenges of current approaches, for example, by allowing specific recognition and killing of cancer cells. Recent advances also facilitate engineering integrated circuits for the controlled release of therapeutic molecules at specified locations, for example, in a solid tumor. In this review, we discuss recent strategies and applications of synthetic receptor circuits aimed at enhancing immune cell functions for cancer immunotherapy. We begin by introducing the concept of circuits in networks at the molecular and cellular scales and provide an analysis of the development and implementation of several synthetic circuits in T cells that have the goal to overcome current challenges in cancer immunotherapy. These include specific targeting of cancer cells, increased T-cell proliferation, and persistence in the tumor microenvironment. By harnessing the power of synthetic biology, and the characteristics of certain circuit architectures, it is now possible to engineer a new generation of immune cells that recognize cancer cells, while minimizing off-target toxicities. We specifically discuss T-cell circuits for antigen density sensing. These circuits allow targeting of solid tumors that share antigens with normal tissues. Additionally, we explore designs for synthetic circuits that could control T-cell differentiation or T-cell fate as well as the concept of synthetic multicellular circuits that leverage cellular communication and division of labor to achieve improved therapeutic efficacy. As our understanding of cell biology expands and novel tools for genome, protein, and cell engineering are developed, we anticipate further innovative approaches to emerge in the design and engineering of circuits in immune cells.

Programming therapeutic probiotics by self-tunable sense-and-respond genetic circuits

Probiotics can be programmed to sense and respond to intracellular disease signals to deliver the desired therapeutic effectors. The sense-and-respond genetic circuits, especially self-tunable ones, hold promise in improving the precision, effectiveness, and intelligence of therapeutic activities. Here, we present notable advances in the creation of engineered probiotics that harbour sense-and-respond genetic circuits.

The triple interactions between gut microbiota, mycobiota and host immunity

The gut microbiome is mainly composed of microbiota and mycobiota, both of which play important roles in the development of the host immune system, metabolic regulation, and maintenance of intestinal homeostasis. With the increasing awareness of the pathogenic essence of infectious, immunodeficiency, and tumor-related diseases, the interactions between gut bacteria, fungi, and host immunity have been shown to directly influence the disease process or final therapeutic outcome, and collaborative and antagonistic relationships are commonly found between bacteria and fungi. Interventions represented by probiotics, prebiotics, engineered probiotics, fecal microbiota transplantation (FMT), and drugs can effectively modulate the triple interactions. In particular, traditional probiotics represented by Bifidobacterium and Lactobacillus and next-generation probiotics represented by Akkermansia muciniphila and Faecalibacterium prausnitzii showed a high enrichment trend in the gut of patients with a high response to inflammation remission and tumor immunotherapy, which predicts the potential medicinal value of these beneficial microbial formulations. However, there are bottlenecks in all these interventions that need to be broken. Meanwhile, further unraveling the underlying mechanisms of the "triple interactions" model can guide precise interventions and ultimately improve the efficiency of interventions on the host gut microbiome and immune modulation, thus directly or indirectly improving anti-inflammatory and tumor immunotherapy effects.

Decoding the microbiome: advances in genetic manipulation for gut bacteria

Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene-host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to 'taming' the gut microbiome, GM tools allow molecular understanding of host-microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.

Engineered live bacteria as disease detection and diagnosis tools

Sensitive and minimally invasive medical diagnostics are essential to the early detection of diseases, monitoring their progression and response to treatment. Engineered bacteria as live sensors are being developed as a new class of biosensors for sensitive, robust, noninvasive, and in situ detection of disease onset at low cost. Akin to microrobotic systems, a combination of simple genetic rules, basic logic gates, and complex synthetic bioengineering principles are used to program bacterial vectors as living machines for detecting biomarkers of diseases, some of which cannot be detected with other sensing technologies. Bacterial whole-cell biosensors (BWCBs) can have wide-ranging functions from detection only, to detection and recording, to closed-loop detection-regulated treatment. In this review article, we first summarize the unique benefits of bacteria as living sensors. We then describe the different bacteria-based diagnosis approaches and provide examples of diagnosing various diseases and disorders. We also discuss the use of bacteria as imaging vectors for disease detection and image-guided surgery. We conclude by highlighting current challenges and opportunities for further exploration toward clinical translation of these bacteria-based systems.

Systems and synthetic biology-driven engineering of live bacterial therapeutics

The past decade has seen growing interest in bacterial engineering for therapeutically relevant applications. While early efforts focused on repurposing genetically tractable model strains, such as Escherichia coli, engineering gut commensals is gaining traction owing to their innate capacity to survive and stably propagate in the intestine for an extended duration. Although limited genetic tractability has been a major roadblock, recent advances in systems and synthetic biology have unlocked our ability to effectively harness native gut commensals for therapeutic and diagnostic purposes, ranging from the rational design of synthetic microbial consortia to the construction of synthetic cells that execute "sense-and-respond" logic operations that allow real-time detection and therapeutic payload delivery in response to specific signals in the intestine. In this review, we outline the current progress and latest updates on microbial therapeutics, with particular emphasis on gut commensal engineering driven by synthetic biology and systems understanding of their molecular phenotypes. Finally, the challenges and prospects of engineering gut commensals for therapeutic applications are discussed.

Probiotic-guided CAR-T cells for solid tumor targeting

A major challenge facing tumor-antigen targeting therapies such as chimeric antigen receptor (CAR)-T cells is the identification of suitable targets that are specifically and uniformly expressed on heterogeneous solid tumors. By contrast, certain species of bacteria selectively colonize immune-privileged tumor cores and can be engineered as antigen-independent platforms for therapeutic delivery. To bridge these approaches, we developed a platform of probiotic-guided CAR-T cells (ProCARs), in which tumor-colonizing probiotics release synthetic targets that label tumor tissue for CAR-mediated lysis in situ. This system demonstrated CAR-T cell activation and antigen-agnostic cell lysis that was safe and effective in multiple xenograft and syngeneic models of human and mouse cancers. We further engineered multifunctional probiotics that co-release chemokines to enhance CAR-T cell recruitment and therapeutic response.

Build-a-bug workshop: Using microbial-host interactions and synthetic biology tools to create cancer therapies

Many systemically administered cancer therapies exhibit dose-limiting toxicities that reduce their effectiveness. To increase efficacy, bacterial delivery platforms have been developed that improve safety and prolong treatment. Bacteria are a unique class of therapy that selectively colonizes most solid tumors. As delivery vehicles, bacteria have been genetically modified to express a range of therapies that match multiple cancer indications. In this review, we describe a modular "build-a-bug" method that focuses on five design characteristics: bacterial strain (chassis), therapeutic compound, delivery method, immune-modulating features, and genetic control circuits. We emphasize how fundamental research into gut microbe pathogenesis has created safe bacterial therapies, some of which have entered clinical trials. The genomes of gut microbes are fertile grounds for discovery of components to improve delivery and modulate host immune responses. Future work coupling these delivery vehicles with insights from gut microbes could lead to the next generation of microbial cancer therapy.

Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium

Through the implementation of designable genetic circuits, engineered probiotic microorganisms could be used as noninvasive diagnostic tools for the gastrointestinal tract. For these living cells to report detected biomarkers or signals after exiting the gut, the genetic circuits must be able to record these signals by using genetically encoded memory. Complex memory register circuits could enable multiplex interrogation of biomarkers and signals. A theory-based approach to create genetic circuits containing memory, known as sequential logic circuits, was previously established for a model laboratory strain of Escherichia coli, yet how circuit component performance varies for nonmodel and clinically relevant bacterial strains is poorly understood. Here, we develop a scalable computational approach to design robust sequential logic circuits in probiotic strain Escherichia coli Nissle 1917 (EcN). In this work, we used TetR-family transcriptional repressors to build genetic logic gates that can be composed into sequential logic circuits, along with a set of engineered sensors relevant for use in the gut environment. Using standard methods, 16 genetic NOT gates and nine sensors were experimentally characterized in EcN. These data were used to design and predict the performance of circuit designs. We present a set of genetic circuits encoding both combinational logic and sequential logic and show that the circuit outputs are in close agreement with our quantitative predictions from the design algorithm. Furthermore, we demonstrate an analog-like concentration recording circuit that detects and reports three input concentration ranges of a biochemical signal using sequential logic.

Artificially engineered bacteria to treat gastrointestinal disease and cancer

Therapeutics based on living organisms provide a roadmap for next-generation biomedicine. Bacteria have an essential role in the development, regulation, and treatment of gastrointestinal disease and cancer through similar mechanisms. However, primitive bacteria lack the stability to overcome complex drug delivery barriers, and their multifunctionality in reinforcing both conventional and emerging therapeutics is limited. Artificially engineered bacteria (ArtBac) with modified surfaces and genetic functions show promise for tackling these problems. Herein, we discuss recent applications of ArtBac as living biomedicine for the treatment of gastrointestinal diseases and tumors. Future perspectives are given to guide the rational design of ArtBac toward safe multifunctional medicine.

Impact of the host microbiota on fungal infections: new possibilities for intervention?

Many human fungal pathogens are opportunistic. They are primarily benign residents of the human body and only become infectious when the host's immunity and microbiome are compromised. Bacteria dominate the human microbiome, playing an essential role in keeping fungi harmless and acting as the first line of defense against fungal infection. The Human Microbiome Project, launched by NIH in 2007, has stimulated extensive investigation and significantly advanced our understanding of the molecular mechanisms governing the interaction between bacteria and fungi, providing valuable insights for developing future antifungal strategies by exploiting the interaction. This review summarizes recent progress in this field and discusses new possibilities and challenges. We must seize the opportunities presented by researching bacterial-fungal interplay in the human microbiome to address the global spread of drug-resistant fungal pathogens and the drying pipelines of effective antifungal drugs.

Coordinated microbial lysis bursts into the drug delivery scene

To address limitations in dosing and releasing cargo from engineered microbes, Din et al. harnessed a previously designed oscillatory genetic circuit to achieve the synchronized release of cancer-killing protein payloads. Here, we briefly recap this study published in 2016 and its transformative impact on the field.

Synthetic bacterial therapies for intestinal diseases based on quorum- sensing circuits

Bacterial therapy has become a key strategy against intestinal infectious diseases in recent years. Moreover, regulating the gut microbiota through traditional fecal microbiota transplantation and supplementation of probiotics faces controllability, efficacy, and safety challenges. The infiltration and emergence of synthetic biology and microbiome provide an operational and safe treatment platform for live bacterial biotherapies. Synthetic bacterial therapy can artificially manipulate bacteria to produce and deliver therapeutic drug molecules. This method has the advantages of solid controllability, low toxicity, strong therapeutic effects, and easy operation. As an essential tool for dynamic regulation in synthetic biology, quorum sensing (QS) has been widely used for designing complex genetic circuits to control the behavior of bacterial populations and achieve predefined goals. Therefore, QS-based synthetic bacterial therapy might become a new direction for the treatment of diseases. The pre-programmed QS genetic circuit can achieve a controllable production of therapeutic drugs on particular ecological niches by sensing specific signals released from the digestive system in pathological conditions, thereby realizing the integration of diagnosis and treatment. Based on this as well as the modular idea of synthetic biology, QS-based synthetic bacterial therapies are divided into an environmental signal sensing module (senses gut disease physiological signals), a therapeutic molecule producing module (plays a therapeutic role against diseases), and a population behavior regulating module (QS system). This review article summarized the structure and function of these three modules and discussed the rational design of QS gene circuits as a novel intervention strategy for intestinal diseases. Moreover, the application prospects of QS-based synthetic bacterial therapy were summarized. Finally, the challenges faced by these methods were analyzed to make the targeted recommendations for developing a successful therapeutic strategy for intestinal diseases.

Engineered bacteria for augmented in situ tumor vaccination

In situ tumor vaccination has aroused tremendous interest with its capability for eliciting strong and systemic antitumor immune responses. Unlike traditional cancer vaccines, in situ tumor vaccination avoids the laborious process of tumor antigen identification and can modulate tumor immunosuppressive microenvironment at the same time. In recent years, bacteria have been used as both efficient tumor-targeted delivery vehicles and potent adjuvants. Regarding the rapid development in this area, in this review, we summarize recent advances in the application of bacteria for in situ cancer vaccination. We illustrate the mechanisms of bacteria as both efficient tumor immunogenic cell death inducers and tumor-targeted delivery platforms. Then we comprehensively review the engineering strategies for designing bacteria-based in situ vaccination, including chemical modification, nanotechnology, and genetic engineering. The current dilemma and future directions are discussed at the end of this review.

Stability, robustness, and containment: preparing synthetic biology for real-world deployment

As engineered microbes are used in increasingly diverse applications across human health and bioproduction, the field of synthetic biology will need to focus on strategies that stabilize and contain the function of these populations within target environments. To this end, recent advancements have created layered sensing circuits that can compute cell survival, genetic contexts that are less susceptible to mutation, burden, and resource control circuits, and methods for population variability reduction. These tools expand the potential for real-world deployment of complex microbial systems by enhancing their environmental robustness and functional stability in the face of unpredictable host response and evolutionary pressure.

On-chip dielectrophoretic recovery and detection of a lactate sensing probiotic from model human saliva

Early detection has led to increased survival for multiple cancers; however, the 5-year survival rate of oral carcinoma (OC) has remained at 40% for the last several decades. Screening for OC is routinely done via visual examinations, followed by tissue biopsy and laboratory testing. Point-of-care testing would be a more convenient and widely available alternative for at-risk individuals. Increased lactate production is a hallmark of many head-and-neck tumors, due to the Warburg Effect, where tumor cells favor glycolysis in the place of oxidative phosphorylation. To detect excess lactate, we have modified the commensal bacterium Escherichia coli Nissle 1917 to express fluorescent reporter genes in response to extracellular lactate. Administering this commensal as a mouth wash and subsequently collecting saliva for the detection of the reporter may allow for noninvasive, early detection of cancerous lesions in at-risk individuals. Furthermore, we demonstrate a new on-chip electrokinetic technique to recover these probiotic probes from model saliva fluid to improve the detection of reporter gene activation.

Near-Infrared Nano-Optogenetic Activation of Cancer Immunotherapy via Engineered Bacteria

Certain anaerobic microbes with the capability to colonize the tumor microenvironment tend to express the heterologous gene in a sustainable manner, which will inevitably compromise the therapeutic efficacy and induce off-tumor toxicity in vivo. To improve the therapeutic precision and controllability of bacteria-based therapeutics, Escherichia coli Nissle 1917 (EcN), engineered to sense blue light and release the encoded flagellin B (flaB), is conjugated with lanthanide upconversion nanoparticles (UCNPs) for near-infrared (NIR) nano-optogenetic cancer immunotherapy. Upon 808 nm photoirradiation, UCNPs emit at the blue region to photoactivate the EcN for secretion of flaB, which subsequently binds to Toll-like receptor 5 expressed on the membrane of macrophages for activating immune response via MyD88-dependent signal pathway. Such synergism leads to significant tumor regression in different tumor models and metastatic tumors with negligible side effects. These studies based on the NIR nano-optogenetic platform highlight the rational of leveraging the optogenetic tools combined with natural propensity of certain bacteria for cancer immunotherapy.

Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia

Microbes naturally coexist in complex, multistrain communities. However, extracting individual microbes from and specifically manipulating the composition of these consortia remain challenging. The sequence-specific nature of CRISPR guide RNAs can be leveraged to accurately differentiate microorganisms and facilitate the creation of tools that can achieve these tasks. We developed a computational program, ssCRISPR, which designs strain-specific CRISPR guide RNA sequences with user-specified target strains, protected strains, and guide RNA properties. We experimentally verify the accuracy of the strain specificity predictions in both Escherichia coli and Pseudomonas spp. and show that up to three nucleotide mismatches are often required to ensure perfect specificity. To demonstrate the functionality of ssCRISPR, we apply computationally designed CRISPR-Cas9 guide RNAs to two applications: the purification of specific microbes through one- and two-plasmid transformation workflows and the targeted removal of specific microbes using DNA-loaded liposomes. For strain purification, we utilize gRNAs designed to target and kill all microbes in a consortium except the specific microbe to be isolated. For strain elimination, we utilize gRNAs designed to target only the unwanted microbe while protecting all other strains in the community. ssCRISPR will be of use in diverse microbiota engineering applications.

Characterization of Eight Bacterial Biosensors for Microbial Diagnostic and Therapeutic Applications

The engineering of microbial cells to produce and secrete therapeutics directly in the human body, known as advanced microbial therapeutics, is an exciting alternative to current drug delivery routes. These living therapeutics can be engineered to sense disease biomarkers and, in response, deliver a therapeutic activity. This strategy allows for precise and self-regulating delivery of a therapeutic that adapts to the disease state of the individual patient. Numerous sensing systems have been characterized for use in prokaryotes, but a very limited number of advanced microbial therapeutics have incorporated such sensors. We characterized eight different sensors that respond to physiologically relevant conditions and molecules found in the human body in the probiotic strain Escherichia coli Nissle 1917. The resulting sensors were characterized under aerobic and anaerobic conditions and were demonstrated to be functional under gut-like conditions using the nematode Caenorhabditis elegans as an in vivo model. We show for the first time how a biosensor is able to detect in vivo the bile acid-like molecule Δ4-dafachronic acid, a small molecule in C. elegans that regulates lifespan. Furthermore, we exemplify how bacterial sensors can be used to dynamically report on changes in the intestinal environment of C. elegans, by demonstrating the use of a biosensor able to detect changes in lactate concentrations in the gut lumen of individual C. elegans. The biosensors presented in this study allow for dynamic control of expression in vivo and represent a valuable tool in further developing advanced microbiome therapeutics.

Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer

Synthetic biology enables the engineering of bacteria to safely deliver potent payloads to tumors for effective anti-cancer therapies. However, a central challenge for translation is determining ideal bacterial therapy candidates for specific cancers and integrating them with other drug treatment strategies to maximize efficacy. To address this, we designed a screening and evaluation pipeline for characterization of bacterial therapies in lung cancer models. We screened 10 engineered bacterial toxins across 6 non-small cell lung cancer patient-derived cell lines and identified theta toxin as a promising therapeutic candidate. Using a bacteria-spheroid co-culture system (BSCC), analysis of differentially expressed transcripts and gene set enrichment revealed significant changes in at least 10 signaling pathways with bacteria-producing theta toxin. We assessed combinatorial treatment of small molecule pharmaceutical inhibitors targeting 5 signaling molecules and of 2 chemotherapy drugs along with bacterially-produced theta toxin and showed improved dose-dependent response. This combination strategy was further tested and confirmed, with AKT signaling as an example, in a mouse model of lung cancer. In summary, we developed a pipeline to rapidly characterize bacterial therapies and integrate them with current targeted therapies for lung cancer.

Engineering bacteria as interactive cancer therapies

With increasing evidence that microbes colonize tumors, synthetic biology tools are being leveraged to repurpose bacteria as tumor-specific delivery systems. These engineered systems can modulate the tumor microenvironment using a combination of their inherent immunogenicity and local payload production. Here, we review genetic circuits that enhance spatial and temporal control of therapeutic bacteria to improve their safety and efficacy. We describe the engineering of interactions among bacteria, tumor cells, and immune cells, and the progression from bacteria as single agents toward their rational combination with other modalities. Together, these efforts are building toward an emerging concept of engineering interactions between programmable medicines using synthetic biology.

Prospect of bacteria for tumor diagnosis and treatment

In recent decades, the comprehensive cancer treatments including surgery, chemotherapy, and radiotherapy have improved the overall survival rate and quality of life of many cancer patients. However, we are still facing many difficult problems in the cancer treatment, such as unpredictable side effects, high recurrence rate, and poor curative effect. Therefore, the better intervention strategies are needed in this field. In recent years, the role and importance of microbiota in a variety of diseases were focused on as a hot research topic, and the role of some intracellular bacteria of cancer cells in carcinogenesis has recently been discovered. The impact of bacteria on cancer is not limited to their contribution to tumorigenesis, but the overall susceptibility of bacteria to subsequent tumor progression, the development of concurrent infections, and the response to anti-cancer therapy have also been found to be affected. Concerns about the contribution of bacteria in the anti-cancer response have inspired researchers to develop bacteria-based anti-cancer treatments. In this paper, we reviewed the main roles of bacteria in the occurrence and development of tumors, and summarized the mechanism of bacteria in the occurrence, development, and clinical anti-tumor treatment of tumors, providing new insights for the in-depth study of the role of bacteria in tumor diagnosis and treatment. This review aims to provide a new perspective for the development of new technologies based on bacteria to enhance anti-tumor immunotherapy.

Olfactory Receptors as an Emerging Chemical Sensing Scaffold

Chemical biosensors are an increasingly ubiquitous part of our lives. Beyond enzyme-coupled assays, recent synthetic biology advances now allow us to hijack more complex biosensing systems to respond to difficult to detect analytes, such as chemical small molecules. Here, we briefly overview recent advances in the biosensing of small molecules, including nucleic acid aptamers, allosteric transcription factors, and two-component systems. We then look more closely at a recently developed chemical sensing system, G protein-coupled receptor (GPCR)-based sensors. Finally, we consider the chemical sensing capabilities of the largest GPCR subfamily, olfactory receptors (ORs). We examine ORs' role in nature, their potential as a biomedical target, and their ability to detect compounds not amenable for detection using other biological scaffolds. We conclude by evaluating the current challenges, opportunities, and future applications of GPCR- and OR-based sensors.

Upconversion Optogenetic Engineered Bacteria System for Time-Resolved Imaging Diagnosis and Light-Controlled Cancer Therapy

Engineering bacteria can achieve targeted and controllable cancer therapy using synthetic biology technology and the characteristics of tumor microenvironment. Besides, the accurate tumor diagnosis and visualization of the treatment process are also vital for bacterial therapy. In this paper, a light control engineered bacteria system based on upconversion nanoparticles (UCNP)-mediated time-resolved imaging (TRI) was constructed for colorectal cancer theranostic and therapy. UCNP with different luminous lifetimes were separately modified with the tumor targeting molecule (folic acid) or anaerobic bacteria (Nissle 1917, EcN) to realize the co-localization of tumor tissues, thus improving the diagnostic accuracy based on TRI. In addition, blue light was used to induce engineered bacteria (EcN-pDawn-φx174E/TRAIL) lysis and the release of tumor apoptosis-related inducing ligand (TRAIL), thus triggering tumor cell death. In vitro and in vivo results indicated that this system could achieve accurate tumor diagnosis and light-controlled cancer therapy. EcN-pDawn-φx174E/TRAIL with blue light irradiation could inhibit 53% of tumor growth in comparison to that without blue light irradiation (11.8%). We expect that this engineered bacteria system provides a new technology for intelligent bacterial therapy and the construction of cancer theranostics.

Microbiome engineering: engineered live biotherapeutic products for treating human disease

The human microbiota is implicated in many disease states, including neurological disorders, cancer, and inflammatory diseases. This potentially huge impact on human health has prompted the development of microbiome engineering methods, which attempt to adapt the composition and function of the human host-microbiota system for a therapeutic purpose. One promising method is the use of engineered microorganisms that have been modified to perform a therapeutic function. The majority of these products have only been demonstrated in laboratory models; however, in recent years more concepts have reached the translational stage. This has led to an increase in the number of clinical trials, which are designed to assess the safety and efficacy of these treatments in humans. Within this review, we highlight the progress of some of these microbiome engineering clinical studies, with a focus on engineered live biotherapeutic products.

Achieving spatially precise diagnosis and therapy in the mammalian gut using synthetic microbial gene circuits

The mammalian gut and its microbiome form a temporally dynamic and spatially heterogeneous environment. The inaccessibility of the gut and the spatially restricted nature of many gut diseases translate into difficulties in diagnosis and therapy for which novel tools are needed. Engineered bacterial whole-cell biosensors and therapeutics have shown early promise at addressing these challenges. Natural and engineered sensing systems can be repurposed in synthetic genetic circuits to detect spatially specific biomarkers during health and disease. Heat, light, and magnetic signals can also activate gene circuit function with externally directed spatial precision. The resulting engineered bacteria can report on conditions in situ within the complex gut environment or produce biotherapeutics that specifically target host or microbiome activity. Here, we review the current approaches to engineering spatial precision for in vivo bacterial diagnostics and therapeutics using synthetic circuits, and the challenges and opportunities this technology presents.

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.