Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics

Probiotic domestication and engineering enable one-shot treatment for bladder mucosal repair

The bladder mucosa is an important blood-urine barrier in the human body, its destruction can lead to distressing cystitis. Traditional treatment approaches often require frequent catheterization and intravesical instillation of hyaluronic acid (HA), which greatly reduces patient compliance and therapeutic efficacy. Herein, we develop a probiotic-based one-shot therapy to repair bladder mucosa with improved convenience, efficacy, and biosafety. To this end, a high-biocompatible probiotic strain is engineered to secrete high-molecular-weight HA controlled by ultrasound stimulation. Meanwhile, a bacterium acclimation-inspired strategy to select bacterial cells targeting the site of bladder inflammation is also proposed. With just one-shot intravesical administration, these engineered bacteria can strongly adhere to the damaged bladder epithelium, continuously secrete HA, and stimulate the formation of protective living engineered materials on the bladder. Consequently, varying therapeutic efficacies in damaged murine model, such as reporting the site of inflammation within 28 days, accelerating mucosal repair (such as significantly increased expression of tight junction proteins occludin-1 and ZO-1), modulating innate immune reactions (such as pro-inflammatory factor levels decreased by about 50 %), and even recovering animal motion behaviors, are realized, achieving an improved therapeutic effect without detectable adverse effects.

Designing live bacterial therapeutics for cancer

Humans are home to a diverse community of bacteria, many of which form symbiotic relationships with their host. Notably, tumors can also harbor their own unique bacterial populations that can influence tumor growth and progression. These bacteria, which selectively colonize hypoxic and acidic tumor microenvironments, present a novel therapeutic strategy to combat cancer. Advancements in synthetic biology enable us to safely and efficiently program therapeutic drug production in bacteria, further enhancing their potential. This review provides a comprehensive guide to utilizing bacteria for cancer treatment. We discuss key considerations for selecting bacterial strains, emphasizing their colonization efficiency, the delicate balance between safety and anti-tumor efficacy, and the availability of tools for genetic engineering. We also delve into strategies for precise spatiotemporal control of drug delivery to minimize adverse effects and maximize therapeutic impact, exploring recent examples of engineered bacteria designed to combat tumors. Finally, we address the underlying challenges and future prospects of bacterial cancer therapy. This review underscores the versatility of bacterial therapies and outlines strategies to fully harness their potential in the fight against cancer.

Self-Adjusting Engineered Probiotic for Targeted Tumor Colonization and Local Therapeutics Delivery

Engineered bacteria have demonstrated great potential for treating a broad array of tumors. However, the precision and safety of controlling the performance of engineered bacteria in vivo remains a central challenge. Here, genetic circuit programming strategy is utilized to construct an engineered Escherichia coli Nissle 1917 with accurate targeted colonizing and on-demand payloads releasing ability. The engineered probiotic survives only in the presence of more than 5 mM L-lactate by employing an improved lactate-sensing system, which leads to preventing the growth outside the permissive environments in mice. Meanwhile an expressing α-hemolysin (SAH) circuit based on quorum-sensing system is introduced to augment anti-tumor effect. Furthermore, coagulase (Coa) induced by high-level lactate creates the closure to deprive tumor of nutrients and oxygen and may help prevent the leakage of bacteria and SAH, which enhances the therapeutic effectiveness and biosafety. This self-adjusting living biotherapeutics significantly inhibits tumor proliferation and prolongs the survival time of colorectal tumor-bearing mice. Together, this work takes a step toward safer and more effective application of living bacteria for tumor treatment in practice.

Expression of Fluorescence Reporters and Natural Products in Native Gut Escherichia coli

Escherichia coli is a widely studied model organism and an integral component of the human gut microbiome, offering significant potential for bacteria-based therapeutic applications. Despite this promise, engineering native E. coli strains remains challenging. In this study, we employed the chassis-independent recombinase-assisted genome engineering (CRAGE) technique to genetically engineer the native gut strain E. coli EcAZ-1 and the probiotic strain E. coli Nissle 1917 (EcN). We successfully expressed a suite of heterologous genes, including the bioluminescent lux operon, green fluorescent protein (GFP), and oxygen-independent fluorescent protein IFP2.0, in both strains. Optimization of IFP2.0 fluorescence was achieved under both aerobic and anaerobic conditions by coexpressing a heme oxygenase gene and/or supplementing the chromophore biliverdin or hemin. Additionally, we engineered these strains to biosynthesize the bioactive compounds naringenin and mycosporine-like amino acids. This work highlights the potential of native E. coli strains as versatile platforms for synthetic biology, paving the way for innovative applications in biomedical research and therapeutic development.

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

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

Engineering Escherichia coli Nissle 1917 Carrying PD1 Agonists Resolves Intestinal Inflammation via Local Immune Modulation

Immunological imbalance is a key factor in the progression of intestinal inflammation, yet effective treatments remain elusive. Using a radiation-induced intestinal injury model, we investigated the causes of inflammation at the single-cell level and identified abnormal T-cell activation as a major contributor. To address this, we targeted the PD1 signaling pathway to suppress T-cell activation and evaluated the anti-inflammatory and intestinal repair effects of the PD1 agonist displaying probiotic Escherichia coli Nissle 1917 (EcNMP1-M) in two mouse models. Encapsulated in Eudragit L100-55 for pH-dependent release, EcNMP1-M and its bacterial outer membrane vesicles (OMVs) expressed PD1 agonists, which inhibited excessive immune activation and reduced inflammatory cytokines. EcNMP1-M promoted the expression of proteins that maintain intestinal epithelial barrier integrity, improving gut function and immune responses in colitis mice. Furthermore, 16S rDNA microbiome sequencing revealed that EcNMP1-M enhanced intestinal microbiota diversity, increased beneficial bacteria, and reduced harmful bacteria. This study proposes a localized EcN-based immunosuppressive therapy for radiation-induced enteritis and inflammatory bowel disease with promising potential for clinical applications.

Escherichia coli Nissle 1917 efficiently expresses the RBD domain of SARS-CoV-2 spike protein without codon optimization

Bacterial outer membrane vesicles (OMVs) represent a promising and versatile platform for vaccine delivery. Their inherent self-adjuvant properties and the ability to be adorned with a wide range of heterogeneous antigens position them as a powerful tool in the fight against infectious diseases. Escherichia coli Nissle 1917 (EcN) stands out as a highly valuable probiotic strain because of its long history of safe use and proven clinical benefits in humans. The EcN strain was genetically engineered to derive OMVs displaying receptor binding domain (RBD) of SARS-CoV-2 spike protein on their surface. Although some research groups have previously expressed the SARS-CoV-2 viral spike protein or the RBD in E. coli, particularly in EcN, this study shows a maiden effort to utilize the gene encoding native RBD. The probiotic EcN exhibited a significant level of native RBD expression, demonstrating a more efficient codon usage pattern compared to commonly used bacterial expression systems such as BL21, and DH5α. EcN was engineered to display the native form of viral RBD on the surface using the Lpp-OmpA system. Cell fractionation studies clearly indicated the presence of RBD in the membrane fraction. OMVs displaying RBD on their surface were isolated using ultracentrifugation and the presence of RBD in the OMVs was confirmed by western blot followed by immunofluorescence analyses. Due to their preferential uptake by antigen presenting cells, OMVs derived from EcN bearing native form of RBD hold promise as a potential COVID-19 vaccine candidate.

Harnessing flavonoids to control probiotic function: in situ application of a naringenin-responsive genetic circuit

Efforts to improve probiotics' capabilities through synthetic biology have recently increased. Using naturally occurring plant-based compounds, such as flavonoids, as inputs of genetic circuits introduced in probiotics is a promising strategy to enhance or introduce a beneficial phenotype to the host. However, flavonoid-responsive genetic circuits have not yet been applied in host-microbe conditions. In this work, we have characterized the FdeR-based naringenin-responsive genetic circuit in the probiotic (Escherichia coli Nissle 1917) (EcN), both in vitro and in situ, applying the FdeR system in EcN colonizing mice guts. In culture, the circuit demonstrated a 131-fold activation upon naringenin exposure. In mice, circuit activity was monitored via luminescence produced by Nanoluc in fecal samples following oral gavage of naringenin (100 mg/kg), resulting in a 34-fold luminescence increase. This activation decreased over 24 hours but was reinduced after a second gavage with naringenin. These findings demonstrate the potential of naringenin-responsive genetic circuits to program probiotic phenotypes in vivo through external compound administration. Future studies should evaluate lower naringenin dosages and naringenin-rich foods as alternative inputs.

IMPORTANCE

Engineering probiotics is a rapidly advancing field in synthetic biology. Genetic circuits, which enable precise and predictable control of microbial phenotypes, are central to this effort. Leveraging natural, plant-based compounds like flavonoids to control gene expression offers a promising strategy for developing next-generation probiotics with enhanced capabilities. This study demonstrates the activity of a flavonoid-responsive genetic circuit during host-microbe interactions. The findings provide a foundation for using beneficial compounds like naringenin as inputs to drive desired phenotypes in vivo. In addition, this work expands the range of genetic circuit inputs, facilitating the design of more sophisticated, multi-input systems for probiotic engineering.

Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces

Among the emerging issues in probiotic safety, the possible presence of pks, a gene cluster synthetizing a genotoxin known as colibactin, is one of the most alarming. Indeed, indigenous E. coli strain pks-positive are found in 60% of patients with colorectal cancer, and the most widely used E. coli-based probiotic, known as E. coli Nissle 1917 (DSM 6601), is pks-positive. Starting from 25 potential candidates selected by screening 25 infant stool samples, we have selected an E. coli strain (named 5C, deposited as LMG S-33222) belonging to the phylotype A and having the serovar O173:H1. Having been previously completely sequenced by our group, we have further characterized this strain, demonstrating that it is (i) devoid of the most known potential pathogenic-related genes, (ii) devoid of possible plasmids, (iii) antibiotic-sensitive according to the EFSA panel, (iv) resistant in gastric and enteric juice, (v) significantly producing acetate, (vi) poorly producing histamine, (vii) endowed with a significant in vitro antipathogenic profile, (viii) promoting a significant in vitro immunological response based on IL-10 and IL-12, and (ix) devoid of the pks genes. A comparative genomics versus E. coli Nissle 1917 is also provided. Considering that the other two most commonly used E. coli-based probiotics (E. coli DSM 17252 and E. coli A0 34/86) are respectively pks-positive and alpha-hemolysin-(hly) and cytotoxic necrotizing factor-1-(cnf1) positive, this novel strain (E. coli 5C) is likely the probiotic E. coli strain with the best safety profile available to date for human use.

Gut microbiota and gastrointestinal tumors: insights from a bibliometric analysis

Introduction

Despite the growing number of studies on the role of gut microbiota in treating gastrointestinal tumors, the overall research trends in this field remain inadequately characterized.

Methods

A bibliometric analysis was conducted using publications retrieved from the Web of Science Core Collection (up to September 30, 2024). Analytical tools including VOSviewer, CiteSpace, and an online bibliometric platform were employed to evaluate trends and hotspots.

Results

Analysis of 1,421 publications revealed significant geographical disparities in research output, with China and the United States leading contributions. Institutionally, the University of Adelaide, Zhejiang University, and Shanghai Jiao Tong University were prominent contributors. Authorship analysis identified Hannah R. Wardill as the most prolific author, while the International Journal of Molecular Sciences emerged as a leading journal. Rapidly growing frontiers include "proliferation," "inhibition," "immunotherapy," "drug delivery," and "tumorigenesis."

Discussion

This study provides a comprehensive overview of research trends and highlights emerging directions, aiming to advance scientific and clinical applications of gut microbiota in gastrointestinal tumor therapy.

Enterococci for human health: A friend or foe?

Enterococci are widely distributed in nature and exhibit good temperature and pH tolerance, making them suitable for industrial fermentation. It can produce bacteriocins, natural antibacterial substances utilized in food preservation. Some Enterococci are employed as probiotics to regulate human immunity and maintain healthy intestinal environments. However, recent scientific studies have highlighted the pathogenicity and multidrug resistance of Enterococci, classifying it as an important pathogen in clinical infections. Moreover, increasing evidence has linked Enterococcus sp., particularly Enterococcus faecalis and Enterococcus faecium, to clinical diseases, raising concerns about their safety and posing the question, how should we approach the conflicting nature of the pathogenic and beneficial effects of Enterococci? This review provides the recent advancements in Enterococci research and incorporates the perspectives of international authoritative organizations and institutions to comprehensively analyze the beneficial and harmful characteristics of Enterococci in the fields of science, clinical and industrial applications, aiming to address three important questions: whether Enterococci are beneficial or harmful to humans, their potential use in medical treatments, and the criteria to evaluate their safety. The goal is to explore the feasibility of the standardized use of Enterococci and provide guidance on the scientific selection and utilization of probiotics.

Probiotics Exert Gut Immunomodulatory Effects by Regulating the Expression of Host miRNAs

Probiotics exert a diverse range of immunomodulatory effects on the human gut immune system. These mechanisms encompass strengthening the intestinal mucosal barrier, inhibiting pathogen adhesion and colonization, stimulating immune modulation, and fostering the production of beneficial substances. As a result, probiotics hold significant potential in the prevention and treatment of various conditions, including inflammatory bowel disease and colorectal cancer. A pivotal mechanism by which probiotics achieve these effects is through modulating the expression of host miRNAs. miRNAs, non-coding RNA molecules, are vital regulators of fundamental biological processes like cell growth, differentiation, and apoptosis. By interacting with mRNAs, miRNAs can either promote their degradation or repress their translation, thereby regulating gene expression post-transcriptionally and modulating the immune system. This review provides a comprehensive overview of how probiotics modulate gut immune responses by altering miRNA expression levels, both upregulating and downregulating specific miRNAs. It further delves into how this modulation impacts the host's resistance to pathogens and susceptibility to diseases, offering a theoretical foundation and practical insights for the clinical utilization of probiotics in disease prevention and therapy.

Anti-tumor activity of an αPD-L1-PE38 immunotoxin delivered by engineered Nissle 1917

Although immune checkpoint inhibitors specifically targeting the PD-1/PD-L1 axis have exhibited remarkable clinical success, they are not uniformly effective across all patient cohorts. Immunotoxins, a novel class of cancer therapeutics, offering a promising alternative. PD-L1, which is also present in certain normal tissues, limits its suitability as an ideal target for immunotoxins. The probiotic strain of E. coli Nissle 1917 (EcN) could target and colonize to solid tumors, which positions it as a promising candidate for tumor tissue-specific delivery of anti-tumor proteins. In this study, we constructed a PD-L1-targeted immunotoxin, designated as αPD-L1-PE38, by fusing an anti-PD-L1 nanobody and a clinically validated PE38 toxin. This immunotoxin exhibited potent cytotoxic activity against tumor cells while showed slightly cytotoxic activity against normal cells. To effectively deliver the αPD-L1-PE38 to tumor tissues, we engineered the EcN strain to release the immunotoxin induced by L-arabinose. Upon induction, the immunotoxin was efficiently secreted, and exhibited robust anti-tumor activity mainly by inducing cell apoptosis both in vitro and in vivo. Furthermore, we enhanced the immunotoxin's affinity for PD-L1 by optimizing the linker between the nanobody and PE38 toxin. The engineered EcN expressing the optimized immunotoxin, achieved superior anti-tumor activity. Collectively, our study suggests that the delivery of immunotoxins through live bacteria to improve safety and efficacy is a promising option in cancer therapeutics.

Bacterial Autonomous Intelligent Microrobots for Biomedical Applications

Micro/nanorobots are being increasingly utilized as new diagnostic and therapeutic platforms in the biomedical field, enabling remote navigation to hard-to-reach tissues and the execution of various medical procedures. Although significant progress has been made in the development of biomedical micro/nanorobots, how to achieve closed-loop control of them from sensing, memory, and precise trajectory planning to feedback to carry out biomedical tasks remains a challenge. Bacteria with self-propulsion and autonomous intelligence properties are well suited to be engineered as microrobots to achieve closed-loop control for biomedical applications. By virtue of synthetic biology, bacterial microrobots possess an expanded genetic toolbox, allowing them to load input sensors to respond or remember external signals. To achieve accurate control in the complex physiological environment, the development of bacterial microrobots should be matched with the corresponding control system design. In this review, a detailed summary of the sensing and control mechanisms of bacterial microrobots is presented. The engineering and applications of bacterial microrobots in the biomedical field are highlighted. Their future directions of bacterial autonomous intelligent microrobots for precision medicine are forecasted.

Living Bacteria: A New Vehicle for Vaccine Delivery in Cancer Immunotherapy

Cancer vaccines, aimed at evolving the human immune system to eliminate tumor cells, have long been explored as a method of cancer treatment with significant clinical potential. Traditional delivery systems face significant challenges in directly targeting tumor cells and delivering adequate amounts of antigen due to the hostile tumor microenvironment. Emerging evidence suggests that certain bacteria naturally home in on tumors and modulate antitumor immunity, making bacterial vectors a promising vehicle for precision cancer vaccines. Live bacterial vehicles offer several advantages, including tumor colonization, precise drug delivery, and immune stimulation, making them a compelling option for cancer immunotherapy. In this review, we explore the mechanisms of action behind living bacteria-based vaccines, recent progress in popular bacterial chassis, and strategies for specific payload delivery and biocontainment to ensure safety. These approaches will lay the foundation for developing an affordable, widely applicable cancer vaccine delivery system. This review also discusses the challenges and future opportunities in harnessing bacterial-based vaccines for enhanced therapeutic outcomes in cancer treatment.

Genetically Engineered Bacteria as a Promising Therapeutic Strategy Against Cancer: A Comprehensive Review

As a significant cause of global mortality, the cancer has also economic impacts. In the era of cancer therapy, mitigating side effects and costs and overcoming drug resistance is crucial. Microbial species can grow inside the tumor microenvironment and inhibit cancer growth through direct killing of tumor cells and immunoregulatory effects. Although microbiota or their products have demonstrated anticancer effects, the possibility of acting as pathogens and exerting side effects in certain individuals is a risk. Hence, several genetically modified/engineered bacteria (GEB) have been developed to this aim with ability of diagnosing and selective targeting and destruction of cancers. Additionally, GEB are expected to be considerably more efficient, safer, more permeable, less costly, and less invasive theranostic approaches compared to wild types. Potential GEB strains such as Escherichia coli (Nissle 1917, and MG1655), Salmonella typhimurium YB1 SL7207 (aroA gene deletion), VNP20009 (∆msbB/∆purI) and ΔppGpp (PTet and PBAD), and Listeria monocytogenes Lmat-LLO have been developed to combat cancer cells. When used in tandem with conventional treatments, GEB substantially improve the efficacy of anticancer therapy outcomes. In addition, public acceptance, optimal timing (s), duration (s), dose (s), and strains identification, interactions with other strains and the host cells, efficacy, safety and quality, and potential risks and ethical dilemmas include major challenges.

Mechanisms Associated With Renal Injury in Hyperuricemia and Strategies for the Development of Natural Active Substances

Hyperuricemia (HUA) is a metabolic condition resulting from an abnormality in the process of purine metabolism. Its occurrence has been on the rise globally. The results of relevant studies show that 5% to 12% of HUA patients will eventually develop gout, and one-third of these patients may involve the kidneys and develop kidney disease. Although the severe renal health hazards associated with excessive uric acid levels are well known, the specific molecular mechanisms remain unknown. Therefore, this paper provides insights into the mechanisms and related chain reactions of HUA leading to renal injury from three perspectives: imbalance of intestinal homeostasis, oxidative stress response, and NLRP3 inflammasome. In addition, standing against the background of the strong side effects and high tolerability disadvantages of commercially available uric acid-lowering drugs such as allopurinol, benzbromarone, and febuxostat, the development of a new active anti-hyperuricemic drug with fewer side effects is justified. This article reviews the progress of research on natural actives (probiotics, dietary polyphenols, peptides) with a high safety profile, multi-targeting, and integrative modulatory effects, in an attempt to provide some ideas for drug developers.

A screening setup to streamline in vitro engineered living material cultures with the host

Engineered living materials (ELMs), which usually comprise bacteria, fungi, or animal cells entrapped in polymeric matrices, offer limitless possibilities in fields like drug delivery or biosensing. Determining the conditions that sustain ELM performance while ensuring compatibility with ELM hosts is essential before testing them in vivo. This is critical to reduce animal experimentation and can be achieved through in vitro investigations. Currently, there are no standards that ensure ELM compatibility with host tissues. Towards this goal, we designed a 96-well plate-based screening method to streamline ELM growth across culture conditions and determine their compatibility potential in vitro. We showed proliferation of three bacterial species encapsulated in hydrogels over time and screened six different cell culture media. We fabricated ELMs in bilayer and monolayer formats and tracked bacterial leakage as a measure of ELM biocontainment. After screening, an appropriate medium was selected that sustained growth of an ELM, and it was used to study cytocompatibility in vitro. ELM cytotoxicity on murine fibroblasts and human monocytes was studied by adding ELM supernatants and measuring cell membrane integrity and live/dead staining, respectively, proving ELM cytocompatibility. Our work illustrates a simple setup to streamline the screening of compatible environmental conditions of ELMs with the host.

Harnessing the polysaccharide production potential to optimize and expand the application of probiotics

Certain probiotic microorganisms can synthesize important bioproducts, including polysaccharides as components of cellular structure or extracellular matrix. Probiotic-derived polysaccharides have been widely applied in food, pharmaceutical, and medical fields due to their excellent properties and biological activities. The development of polysaccharide production potential has become a driving force for facilitating biotechnological applications of probiotics. Based on technical advances in synthetic biology, significant progress has recently been made in engineering probiotics with efficient biosynthesis of polysaccharides. Herein, this review summarizes probiotics chassis and genetic tools used for polysaccharide production. Then, probiotic polysaccharides and relevant biosynthesis mechanisms are also clearly described. Next, we introduce strategies for preparing high-yield, controllable molecular weight or non-native polysaccharides by adjusting metabolic pathways and integrating expression elements in probiotics. Finally, some prospective and well-established contributions of exogenous and in situ polysaccharides in probiotics' stability, bioactivity, and therapeutic effects are presented. Our viewpoints on advancing the efficient biomanufacturing of valuable biopolymers in probiotics and engineering probiotics with customized features are provided to exploit probiotics' industrial and biomedical applications.

Genetically engineered bacteria expressing IL-34 alleviate DSS-induced experimental colitis by promoting tight junction protein expression in intestinal mucosal epithelial cells

BACKGROUND

The intestinal mucosa of ulcerative colitis patients expresses high levels of interleukin 34, and mice lacking IL-34 have more severe DSS-induced experimental colitis. There are no studies on the effects of directly upregulating intestinal IL-34 on experimental colitis in mice.

METHODS

The bacteria EcN/CSF-1 and EcN/IL-34, which express CSF-1 and IL-34, respectively, were genetically engineered from Escherichia coli Nissle 1917 (EcN). Colitis mice received daily gavage of sterile PBS buffer, empty plasmid E. coli (EcN/WT), EcN/CSF-1, or EcN/IL-34. Each group of mice was assessed for body mass, clinical signs, DAI, intestinal mucosal permeability, pathological, and immunohistological changes. In vitro, NCM460 cells were treated with CSF-1 or IL-34 recombinant proteins in the presence of signaling pathway inhibitors to evaluate tight junction protein expression. Additionally, intestinal mucosal epithelial cells isolated from active UC patients were analyzed for IL-34 and tight junction protein levels.

RESULTS

DSS-induced colitis mice are protected by EcN/IL-34 gavage. Pathological results showed that EcN/IL-34 group colonic histological injury was significantly improved and tight junction protein ZO-1 and Occludin expression increased. In NCM460 cells, IL-34 also increased tight junction protein expression. More importantly, expression of IL-34 was positively correlated with the level of tight junction protein expression in epithelial cells of UC patients.

CONCLUSION

EcN/IL-34 can directly act on damaged intestinal mucosa, up-regulate IL-34 expression, and promote tight junction protein expression in intestinal mucosal epithelial cells to alleviate experimental colitis in mice. IL-34 may be a potential therapeutic target for ulcerative colitis, and genetically engineered bacteria carrying the cytokine may offer new ideas for treating UC.

Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes

Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native Escherichia coli strains. We found that competition outcomes are context-dependent, modulated by microbiome complexity, LBT transgene expression, intestinal inflammation, and host diet. Furthermore, we demonstrated that native LBTs can establish long-term engraftment in the gut alongside a parental strain, with transgene-associated fitness effects influencing competition. We identified various interventions, including strategic dosing and dietary modulation, that significantly enhanced LBT colonization levels by 2 to 3 orders of magnitude. These insights provide a framework for optimizing LBT engraftment and efficacy, supporting their potential translation for human therapeutic applications.

A CRISPR-Cas9 system protecting E. coli against acquisition of antibiotic resistance genes

Antimicrobial resistance (AMR) is an increasing problem worldwide, and new treatment options for bacterial infections are direly needed. Engineered probiotics show strong potential in treating or preventing bacterial infections. However, one concern with the use of live bacteria is the risk of the bacteria acquiring genes encoding for AMR or virulence factors through horizontal gene transfer (HGT), and the transformation of the probiotic into a superbug. Therefore, we developed an engineered CRISPR-Cas9 system that protects bacteria from horizontal gene transfer. We synthesized a CRISPR locus targeting eight AMR genes and cloned this with the Cas9 and transacting tracrRNA on a medium copy plasmid. We next evaluated the efficiency of the system to block HGT through transformation, transduction, and conjugation. Our results show that expression of the CRISPR-Cas9 system successfully protects E. coli MG1655 from acquiring the targeted resistance genes by transformation or transduction with 2-3 logs of protection depending on the system for transfer and the target gene. Furthermore, we show that the system blocks conjugation of a set of clinical plasmids, and that the system is also able to protect the probiotic bacterium E. coli Nissle 1917 from acquiring AMR genes.

Quantifying Metagenomic Strain Associations from Microbiomes with Anpan

Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpan's methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.

Bacteria as Precision Tools for Cancer Therapy

The discovery at the end of the 20th century of genes that induce cell death revolutionised the biocontaintment of genetically manipulated bacteria for environmental or agricultural applications. These bacterial 'killer' genes were then assayed for their potential to target and control malignant cells in human cancers. The identification of the bacteriomes in different human organs and tissues, coupled with the observation that bacteria tend to accumulate near tumours, has opened new avenues for anti-cancer strategies. This progress, along with recent insights into how cancer cells evade immune response, has prompted innovative therapeutic approaches. Tumour microenvironments are typically nutrient-rich, characterised by low oxygen tensions and very resistant to immune responses. Two recent studies in MBT highlight the promise of using Salmonella typhimurium and Escherichia coli as vectors in novel cancer treatments. Engineered S. typhimurium strains can generate adjuvant flagellin-antigen complexes that function as in situ vaccines, hence increasing the immunogenic responses within tumour environment. Similarly, gut E. coli can be used as vectors to targert tumour cells in colon cancer, enabling both diagnostic applications and localised treatments. Both approaches hold significant potential to improve patient survival outcomes.

Gut‑liver axis in liver disease: From basic science to clinical treatment (Review)

Incidence of a number of liver diseases has increased. Gut microbiota serves a role in the pathogenesis of hepatitis, cirrhosis and liver cancer. Gut microbiota is considered 'a new virtual metabolic organ'. The interaction between the gut microbiota and liver is termed the gut‑liver axis. The gut‑liver axis provides a novel research direction for mechanism of liver disease development. The present review discusses the role of the gut‑liver axis and how this can be targeted by novel treatments for common liver diseases.

One-for-all gene inactivation via PAM-independent base editing in bacteria

Base editing is preferable for bacterial gene inactivation without generating double-strand breaks, requiring homology recombination, or highly efficient DNA delivery capability. However, the potential of base editing is limited by the adjoined dependence on the editing window and protospacer adjacent motif. Herein, we report an unconstrained base-editing system to enable the inactivation of any genes of interest in bacteria. We employed a dCas9 derivative, dSpRY, and activation-induced cytidine deaminase to build a protospacer adjacent motif-independent base editor. Then, we programmed the base editor to exclude the START codon of a gene of interest instead of introducing premature STOP codons to obtain a universal approach for gene inactivation, namely XSTART, with an overall efficiency approaching 100%. By using XSTART, we successfully manipulated the amino acid metabolisms in Escherichia coli, generating glutamine, arginine, and aspartate auxotrophic strains. While we observed a high frequency of off-target events as a trade-off for increased efficiency, refining the regulatory system of XSTART to limit expression levels reduced off-target events by over 60% without sacrificing efficiency, aligning our results with previously reported levels. Finally, the effectiveness of XSTART was also demonstrated in probiotic E. coli Nissle 1917 and photoautotrophic cyanobacterium Synechococcus elongatus, illustrating its potential in reprogramming diverse bacteria.

Time-Responsive Activity of Engineered Bacteria for Local Sterilization and Biofilm Removal in Periodontitis

Periodontitis is a highly prevalent and common condition in people of all ages, however, existing drugs to treat periodontitis have difficulty penetrating complex biofilms. Here, we report a biofilm-penetrating probiotic hybrid strategy for the treatment of periodontitis. It consists of therapeutic probiotics of E. coli Nissle 1917, which can produce antimicrobial peptides and hydrogen, and is coated with D-amino acids that can penetrate biofilms. After the fusion of D-amino acids with the biofilm, EcN entered the plaque biofilm and produced antimicrobial peptides to kill porphyromonas gingivalis and eliminate periodontitis under the action of hydrogen. The efficacy of EcN@DA-D in biofilm penetration and treatment of periodontitis was demonstrated in a rat model of periodontitis. In addition, the clinical combination to construct a rat periodontitis model by using clinical tissue has a significant therapeutic effect. In conclusion, EcN@DA-D offers a promising topical treatment for periodontitis without developing detectable pathogen resistance and side effects.

Rewiring Tryptophan Metabolism via Programmable Probiotic Integrated by Dual-Layered Microcapsule Protects against Inflammatory Bowel Disease in Mice

Intestinal dysbiosis and the associated l-tryptophan metabolic disorder are pivotal in inflammatory bowel disease progression, leading to a compromised intestinal barrier integrity. Remedying the dysfunction in tryptophan metabolism has emerged as a promising therapeutic strategy. Herein, we reprogram the tryptophan metabolism in situ by EcN-TRP@A/G, encapsulating the engineered probiotic, EcN-TRP, with enhanced tryptophan synthesis capacity, for sustained modulation, thereby restoring intestinal barrier function and microbial homeostasis. The pH-responsive dual-layered EcN-TRP@A/G microcapsule developed via high-voltage electrospraying and liquid interface self-assembly, preserved probiotic viability in the harsh gastrointestinal milieu, and facilitated targeted colon release. Bioluminescent tracking in mice reveals a 22.84-fold increase in EcN-TRP@A/G viability and distribution compared to naked EcN-TRP. Targeted metabolomics highlights EcN-TRP@A/G's modulation of the tryptophan-indole pathway. Oral administration of EcN-TRP@A/G sustained elevates indole metabolites, particularly indole-3-acetic acid and indole-3-propionic acid, in colon tissue for up to 7 days. In IBD mice, EcN-TRP@A/G improves intestinal permeability, reduces inflammation, and recovers the gut microbiome by enhancing beneficial bacteria abundance like Prevotellaceae_UCG-001 and Anaerostipes while suppressing pathogenic strains like Escherichia-Shigella. Our findings offer a cost-effective approach, harnessing the probiotic metabolic potential in situ through engineered modifications for effective IBD treatment.

Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation

Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.

New insight into acid-resistant enzymes from natural mutations of Escherichia coli Nissle 1917

The probiotic Escherichia coli Nissle 1917 (EcN), known for its superior acid resistance (AR), serves as a promising chassis for live therapeutics due to the effective colonization capabilities. However, the enzymatic activity regarding AR in EcN remains poorly understood. First, we investigated the AR systems of EcN by measuring cell growth under acidic stress and exploring the relationship of mutations to their corresponding enzymatic activities. As a result, the catalytic activity of inducible decarboxylases of GadB, AdiA and CadA, responsible for metabolizing glutamate, arginine, and lysine, exhibited an average 2-fold increase in EcN compared to the reference strain MG1655. Furthermore, we discovered that the glutamate-dependent AR2 system in EcN was meticulously regulated by specific regulons such as GadW. This study not only revealed the physiology of EcN under acidic conditions, but also highlighted that the mutated core enzymes in the AR system of EcN exhibit improved activities.

A Review of Clinical Trials Involving Genetically Modified Bacteria, Bacteriophages and Their Associated Risk Assessments

Introduction

Discussion of gene-modified investigational products (IPs) in clinical trials has largely focused on nucleic acid-based vectors, viral vectors, and gene-modified cellular products involving mammalian cells. Use of bacteria and bacteriophages as IPs is resurgent, and discussion of the risks associated with genetic modification of these organisms has become pertinent to the biosafety community.

Methods

This review article summarizes the United States Food and Drug Administration classification for IPs comprising bacteria or bacteriophages and provides an overview of clinical trials conducted to date involving genetically modified bacteria. The risk assessment for bacterial or bacteriophage-based IPs is discussed.

Conclusion

The risk assessment process for bacterial or bacteriophage-based IPs is different from that of gene expression vectors and mammalian cells. Greater consideration must be given to the attenuating mutations affecting virulence, replication competency, antibiotic susceptibility, and persistence in the environment. With the recent growth in clinical trials involving genetically modified bacteria, biosafety professionals and Institutional Biosafety Committees with responsibilities including oversight of clinical trials must become familiar with the associated risk assessment.

Living Engineered Bacterial Therapeutics: Emerging Affordable Precision Interventions

Live biotherapeutic products (LBPs), including engineered bacteria, are rapidly emerging as potential therapeutic interventions. These innovative therapies can serve as live in situ drug delivery platforms for the direct deposition of therapeutic payloads, including complex biologics, at sites of disease. This approach offers a platform likely to enhance therapeutic efficacy and decrease off-target side effects. LBPs also can likely be distributed at a relatively low price point, as their production can be economically scaled up. LBPs represent an exciting new means for ensuring healthy lives and promoting well-being for all ages, aligning with the World Health Organization's sustainable development goal 3.

Design of probiotic delivery systems and their therapeutic effects on targeted tissues

The microbiota at different sites in the body is closely related to disease. The intake of probiotics is an effective strategy to alleviate diseases and be adjuvant in their treatment. However, probiotics may suffer from harsh environments and colonization resistance, making it difficult to maintain a sufficient number of live probiotics to reach the target sites and exert their original probiotic effects. Encapsulation of probiotics is an effective strategy. Therefore, probiotic delivery systems, as effective methods, have been continuously developed and innovated to ensure that probiotics are effectively delivered to the targeted site. In this review, initially, the design of probiotic delivery systems is reviewed from four aspects: probiotic characteristics, processing technologies, cell-derived wall materials, and interactions between wall materials. Subsequently, the review focuses on the effects of probiotic delivery systems that target four main microbial colonization sites: the oral cavity, skin, intestine, and vagina, as well as disease sites such as tumors. Finally, this review also discusses the safety concerns of probiotic delivery systems in the treatment of disease and the challenges and limitations of implementing this method in clinical studies. It is necessary to conduct more clinical studies to evaluate the effectiveness of different probiotic delivery systems in the treatment of diseases.

Engineering probiotic Escherichia coli Nissle 1917 to block transfer of multiple antibiotic resistance genes by exploiting a type I CRISPR-Cas system

Many multidrug-resistant (MDR) bacteria have evolved through the accumulation of antibiotic resistance genes (ARGs). Although the potential risk of probiotics as reservoirs of ARGs has been recognized, strategies for blocking the transfer of ARGs while using probiotics have rarely been explored. The probiotic Escherichia coli Nissle 1917 (EcN) has long been used for treating intestinal diseases. Here, we demonstrate frequent transfer of ARGs into EcN both in vitro and in vivo, raising concerns about its potential risk of accumulating antibiotic resistance. Given that no CRISPR-Cas system was found in natural EcN, we integrated the type I-E CRISPR-Cas3 system derived from E. coli BW25113 into EcN. The engineered EcN was able to efficiently cleave multiple ARGs [i.e., mcr-1, blaNDM-1, and tet(X)] encoding enzymes for degrading last-resort antibiotics. Through co-incubation of EcN expressing Cas3-Cascade and that expressing Cas9, we showed that the growth of the former strain outcompeted the latter strain, demonstrating a better clinical application prospect of EcN expressing the type I-E CRISPR-Cas3 system. In the intestine of a model animal (i.e., zebrafish), the engineered EcN exhibited immunity against the transfer of CRISPR-targeted ARGs. Our work equips EcN with immunity against the transfer of multiple ARGs by exploiting the exogenous type I-E CRISPR-Cas3 system, thereby reducing the risk of the spread of ARGs while using it as a probiotic chassis for generating living therapeutics.

IMPORTANCE

To reduce the development of antibiotic resistance, probiotics have been considered as a substitute for antibiotics. However, probiotics themselves are reservoirs of antibiotic resistance genes (ARGs). This study introduces a new strategy for limiting the spread of ARGs by engineering the typical probiotic strain Escherichia coli Nissle 1917 (EcN), which has been used for treating intestinal diseases and developed as living therapeutics. We also demonstrate that the type I CRISPR-Cas system imposes a lower growth burden than the type II CRISPR-Cas system, highlighting its promising clinical application potential. Our work not only provides a new strategy for restricting the transfer of ARGs while using probiotics but also enriches the genetic engineering toolbox of EcN, paving the way for the safe use and development of probiotics as living therapeutics.

US/PA/MR multimodal imaging-guided multifunctional genetically engineered bio-targeted synergistic agent for tumor therapy

Focused ultrasound ablation surgery (FUAS) is a minimally invasive treatment option that has been utilized in various tumors. However, its clinical advancement has been hindered by issues such as low safety and efficiency, single image guidance mode, and postoperative tumor residue. To address these limitations, this study aimed to develop a novel multi-functional gas-producing engineering bacteria biological targeting cooperative system. Pulse-focused ultrasound (PFUS) could adjust the ratio of thermal effect to non-thermal effect by adjusting the duty cycle, and improve the safety and effectiveness of treatment.The genetic modification of Escherichia coli (E.coli) involved the insertion of an acoustic reporter gene to encode gas vesicles (GVs), resulting in gas-producing E.coli (GVs-E.coli) capable of targeting tumor anoxia. GVs-E.coli colonized and proliferated within the tumor while the GVs facilitated ultrasound imaging and cooperative PFUS. Additionally, multifunctional cationic polyethyleneimine (PEI)-poly (lactic-co-glycolic acid) (PLGA) nanoparticles (PEI-PLGA/EPI/PFH@Fe3O4) containing superparamagnetic iron oxide (SPIO, Fe3O4), perfluorohexane (PFH), and epirubicin (EPI) were developed. These nanoparticles offered synergistic PFUS, supplementary chemotherapy, and multimodal imaging capabilities.GVs-E.coli effectively directed the PEI-PLGA/EPI/PFH@Fe3O4 to accumulate within the tumor target area by means of electrostatic adsorption, resulting in a synergistic therapeutic impact on tumor eradication.In conclusion, GVs-E.coli-mediated multi-functional nanoparticles can synergize with PFUS and chemotherapy to effectively treat tumors, overcoming the limitations of current FUAS therapy and improving safety and efficacy. This approach presents a promising new strategy for tumor therapy.

Escherichia coli on colorectal cancer: A two-edged sword

Escherichia coli (E. coli) is a ubiquitous symbiotic bacterium in the gut, and the diversity of E. coli genes determines the diversity of its functions. In this review, the two-edged sword theory was innovatively proposed. For the question 'how can we harness the ambivalent nature of E. coli to screen and treat CRC?', in terms of CRC screening, the variations in the abundance and subtypes of E. coli across different populations present an opportunity to utilise it as a biomarker, while in terms of CRC treatment, the natural beneficial effect of E. coli on CRC may be limited, and engineered E. coli, particularly certain subtypes with probiotic potential, can indeed play a significant role in CRC treatment. It seems that the favourable role of E. coli as a genetic tool lies not in its direct impact on CRC but its potential as a research platform that can be integrated with various technologies such as nanoparticles, imaging methods, and synthetic biology modification. The relationship between gut microflora and CRC remains unclear due to the complex diversity and interaction of gut microflora. Therefore, the application of E. coli should be based on the 'One Health' view and take the interactions between E. coli and other microorganisms, host, and environmental factors, as well as its own changes into account. In this paper, the two-edged sword role of E. coli in CRC is emphasised to realise the great potential of E. coli in CRC screening and treatment.

Advancements in gene editing technologies for probiotic-enabled disease therapy

Probiotics typically refer to microorganisms that have been identified for their health benefits, and they are added to foods or supplements to promote the health of the host. A growing number of probiotic strains have been identified lately and developed into valuable regulatory pharmaceuticals for nutritional and medical applications. Gene editing technologies play a crucial role in addressing the need for safe and therapeutic probiotics in disease treatment. These technologies offer valuable assistance in comprehending the underlying mechanisms of probiotic bioactivity and in the development of advanced probiotics. This review aims to offer a comprehensive overview of gene editing technologies applied in the engineering of both traditional and next-generation probiotics. It further explores the potential for on-demand production of customized products derived from enhanced probiotics, with a particular emphasis on the future of gene editing in the development of live biotherapeutics.

In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli

Engineered smart microbes that deliver therapeutic payloads are emerging as treatment modalities, particularly for diseases with links to the gastrointestinal tract. Enterohemorrhagic Escherichia coli (EHEC) is a causative agent of potentially lethal hemolytic uremic syndrome. Given concerns that antibiotic treatment increases EHEC production of Shiga toxin (Stx), which is responsible for systemic disease, novel remedies are needed. EHEC encodes a type III secretion system (T3SS) that injects Tir into enterocytes. Tir inserts into the host cell membrane, exposing an extracellular domain that subsequently binds intimin, one of its outer membrane proteins, triggering the formation of attaching and effacing (A/E) lesions that promote EHEC mucosal colonization. Citrobacter rodentium (Cr), a natural A/E mouse pathogen, similarly requires Tir and intimin for its pathogenesis. Mice infected with Cr(ΦStx2dact), a variant lysogenized with an EHEC-derived phage that produces Stx2dact, develop intestinal A/E lesions and toxin-dependent disease. Stx2a is more closely associated with human disease. By developing an efficient approach to seamlessly modify the C. rodentium genome, we generated Cr_Tir-MEHEC(ΦStx2a), a variant that expresses Stx2a and the EHEC extracellular Tir domain. We found that mouse precolonization with HS-PROT3EcT-TD4, a human commensal E. coli strain (E. coli HS) engineered to efficiently secrete an anti-EHEC Tir nanobody, delayed bacterial colonization and improved survival after challenge with Cr_Tir-MEHEC(ΦStx2a). This study suggests that commensal E. coli engineered to deliver payloads that block essential virulence determinants can be developed as a new means to prevent and potentially treat infections including those due to antibiotic resistant microbes.

Propionate-producing engineered probiotics ameliorated murine ulcerative colitis by restoring anti-inflammatory macrophage via the GPR43/HDAC1/IL-10 axis

Inflammatory bowel disease (IBD) is a chronic and unspecific inflammatory disorder of the gastrointestinal tract, and current treatment options often fail to maintain long-term remission. Studies have shown that propionate level is reduced in fecal samples from patients with IBD. Propionate can ameliorate IBD through intestinal epithelial cells and immune regulation, but its effects on the inflammatory microenvironment and macrophage differentiation have not been widely studied. To address this, we constructed an engineered propionate-producing probiotic (EcNP3) to achieve sustained restoration of propionate levels in the gut and increase its bioavailability. DSS-induced experimental intestinal inflammation model was used to evaluate the effect of EcNP3 on improving the intestinal mucosal barrier and increasing the proportion of anti-inflammatory macrophages. It was found that EcNP3 exhibited a restorative effect on the depletion of peritoneal anti-inflammatory macrophages (F4/80hiCD11bhi) and significantly improved the expression level of IL-10. Simultaneously, the expression of IL-1β, IL-6, and CXCL1 was downregulated while inhibiting apoptosis of tissue-resident macrophages ex vivo. Further investigation revealed that EcNP3 regulates IL-10 expression through G protein-coupled receptor 43 and histone deacetylase. Furthermore, EcNP3 significantly inhibited the protein expression of HDAC1 and promoted the histone acetylation level of cells. Finally, EcNP3 significantly improved DSS-induced colitis in mice by increasing mucus production and reducing inflammatory infiltration. Our results suggest that the engineered live biotherapeutic product EcNP3 is a safe and potently efficacious treatment for IBD, which defines a novel strategy in IBD therapy through macrophage IL-10 signaling.

Intratumoral Microbiota as a Target for Advanced Cancer Therapeutics

In recent years, advancements in microbial sequencing technology have sparked an increasing interest in the bacteria residing within solid tumors and its distribution and functions in various tumors. Intratumoral bacteria critically modulate tumor oncogenesis and development through DNA damage induction, chronic inflammation, epigenetic alterations, and metabolic and immune regulation, while also influencing cancer treatment efficacy by affecting drug metabolism. In response to these discoveries, a variety of anti-cancer therapies targeting these microorganisms have emerged. These approaches encompass oncolytic therapy utilizing tumor-associated bacteria, the design of biomaterials based on intratumoral bacteria, the use of intratumoral bacterial components for drug delivery systems, and comprehensive strategies aimed at the eradication of tumor-promoting bacteria. Herein, this review article summarizes the distribution patterns of bacteria in different solid tumors, examines their impact on tumors, and evaluates current therapeutic strategies centered on tumor-associated bacteria. Furthermore, the challenges and prospects for developing drugs that target these bacterial communities are also explored, promising new directions for cancer treatment.

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.

Engineering Cells for Cancer Therapy

Cells, particularly living cells, serve as natural carriers of bioactive substances. Their inherent low immunogenicity and multifunctionality have garnered significant attention in the realm of disease treatment applications, specifically within the domains of cancer immunotherapy and regenerative tissue repair. Nevertheless, several prominent challenges impede their swift translation into clinical applications, including obstacles related to large-scale production feasibility and high utilization costs. To address these issues comprehensively, researchers have proposed the notion of bionic cells that are synthetically generated through chemical or biosynthetic means to emulate cellular functions and behaviors. However, artificial cell strategies encounter difficulties in fully replicating the intricate functionalities exhibited by living cells while also grappling with the complexities associated with design implementation for clinical translation purposes. The convergence of disciplines has facilitated the reform of living cells through a range of approaches, including chemical-, biological-, genetic-, and materials-based methods. These techniques can be employed to impart specific functions to cells or enhance the efficacy of therapy. For example, cells are engineered through gene transduction, surface modifications, endocytosis of drugs as delivery systems, and membrane fusion. The concept of engineered cells presents a promising avenue for enhancing control over living cells, thereby enhancing therapeutic efficacy while concurrently mitigating toxic side effects and ultimately facilitating the realization of precision medicine.In this Account, we present a comprehensive overview of our recent research advancements in the field of engineered cells. Our work involves the application of biological or chemical engineering techniques to manipulate endogenous cells for therapeutics or drug delivery purposes. For instance, to avoid the laborious process of isolating, modifying, and expanding engineered cells in vitro, we proposed the concept of in situ engineered cells. By applying a hydrogel loaded with nanoparticles carrying edited chimeric antigen receptor (CAR) plasmids within the postoperative cavity of glioma, we successfully targeted tumor-associated macrophages for gene editing, leading to effective tumor recurrence inhibition. Furthermore, leveraging platelet's ability to release microparticles upon activation at injury sites, we modified antiprogrammed death 1 (PD-1) antibodies on their surface to suppress postoperative tumor recurrence and provide immunotherapy for inoperable tumors. Similarly, by exploiting bacteria's active tropism toward sites of inflammation and hypoxia, we delivered protein drugs by engineered bacteria to induce cancer cell death through pyroptosis initiation and immunotherapy strategies. In the final section, we summarize our aforementioned research progress while providing an outlook on cancer therapy and the hurdles for clinical translation with potential solutions or future directions based on the concept of engineered cells.

Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases

Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation with no cure and limited treatment options that often have systemic side effects. In this study, we developed a target-specific system to potentially treat IBD by engineering the probiotic bacterium Escherichia coli Nissle 1917 (EcN). Our modular system comprises three components: a transcription factor-based sensor (NorR) capable of detecting the inflammation biomarker nitric oxide (NO), a type 1 hemolysin secretion system, and a therapeutic cargo consisting of a library of humanized anti-TNFα nanobodies. Despite a reduction in sensitivity, our system demonstrated a concentration-dependent response to NO, successfully secreting functional nanobodies with binding affinities comparable to the commonly used drug Adalimumab, as confirmed by enzyme-linked immunosorbent assay and in vitro assays. This newly validated nanobody library expands EcN therapeutic capabilities. The adopted secretion system, also characterized for the first time in EcN, can be further adapted as a platform for screening and purifying proteins of interest. Additionally, we provided a mathematical framework to assess critical parameters in engineering probiotic systems, including the production and diffusion of relevant molecules, bacterial colonization rates, and particle interactions. This integrated approach expands the synthetic biology toolbox for EcN-based therapies, providing novel parts, circuits, and a model for tunable responses at inflammatory hotspots.

Systems Metabolic Engineering to Elucidate and Enhance Intestinal Metabolic Activities of Escherichia coli Nissle 1917

Escherichia coli Nissle 1917 (EcN) is one of the most widely used probiotics to treat gastrointestinal diseases. Recently, many studies have engineered EcN to release therapeutic proteins to treat specific diseases. However, because EcN exhibits intestinal metabolic activities, it is difficult to predict outcomes after administration. In silico and fermentation profiles revealed mucin metabolism of EcN. Multiomics revealed that fucose metabolism contributes to the intestinal colonization of EcN by enhancing the synthesis of flagella and nutrient uptake. The multiomics results also revealed that excessive intracellular trehalose synthesis in EcN, which is responsible for galactose metabolism, acts as a metabolic bottleneck, adversely affecting growth. To improve the ability of EcN to metabolize galactose, otsAB genes for trehalose synthesis were deleted, resulting in the ΔotsAB strain; the ΔotsAB strain exhibited a 1.47-fold increase in the growth rate and a 1.37-fold increase in the substrate consumption rate relative to wild-type EcN.

Functional modification of gut bacteria for disease diagnosis and treatment

Intestinal bacteria help keep humans healthy by regulating lipid and glucose metabolism as well as the immunological and neurological systems. Oral treatment using intestinal bacteria is limited by the high acidity of stomach fluids and the immune system's attack on foreign bacteria. Scientists have created coatings and workarounds to overcome these limitations and improve bacterial therapy. These preparations have demonstrated promising outcomes, with advances in synthetic biology and optogenetics improving their focused colonization and controlled release. Engineering bacteria preparations have become a revolutionary therapeutic approach that converts intestinal bacteria into cellular factories for medicinal chemical synthesis. The present paper discusses various aspects of engineering bacteria preparations, including wrapping materials, biomedical uses, and future developments.

Tumor Pre-Targeting System Using Streptavidin-Expressing Bacteria

PURPOSE

A major obstacle to targeted cancer therapy is identifying suitable targets that are specifically and abundantly expressed by solid tumors. Certain bacterial strains selectively colonize solid tumors and can deliver genetically encoded cargo molecules to the tumor cells. Here, we engineered bacteria to express monomeric streptavidin (mSA) in tumors, and developed a novel tumor pre-targeting system by visualizing the presence of tumor-associated mSA using a biotinylated imaging probe.

PROCEDURES

We constructed a plasmid expressing mSA fused to maltose-binding protein and optimized the ribosome binding site sequence to increase solubility and expression levels. E. coli MG1655 was transformed with the recombinant plasmid, expression of which is driven by the pBAD promotor. Expression of mSA was induced by L-arabinose 4 days after injection of bacteria into mice bearing CT26 mouse colon carcinoma cells. Selective accumulation of mSA in tumor tissues was visualized by optical imaging after administration of a biotinylated fluorescent dye. Counting of viable bacterial cells was also performed.

RESULTS

Compared with a conventional system, the novel expression system resulted in significantly higher expression of mSA and sustained binding to biotin. Imaging signals in tumor tissues were significantly stronger in the mSA-expressing group than in non-expressing group (P = 0.0005). Furthermore, the fluorescent signal in tumor tissues became detectable again after multiple inductions with L-arabinose. The bacterial counts in tumor tissues showed no significant differences between conditions with and without L-arabinose (P = 0.45). Western blot analysis of tumor tissues confirmed expression and binding of mSA to biotin.

CONCLUSIONS

We successfully engineered tumor-targeting bacteria carrying a recombinant plasmid expressing mSA, which was targeted to, and expressed in, tumor tissues. These data demonstrate the potential of this novel tumor pre-targeting system when combined with biotinylated imaging probes or therapeutic agents.

Directed Evolution of Escherichia coli Nissle 1917 to Utilize Allulose as Sole Carbon Source

Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.

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.