Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements

Advanced microbiome therapeutics for oral delivery of peptides and proteins: Advances, challenges, and opportunities

Peptide and protein medicines have changed the therapeutic landscape for many diseases, yet oral delivery remains a significant challenge due to enzymatic degradation, instability, and poor permeability in the gastrointestinal tract. Advanced Microbiome Therapeutics (AMTs) could overcome some of these barriers by producing and releasing therapeutic peptides directly in the gastrointestinal tract. AMTs can localize peptide production at the site of absorption, providing either sustained or controlled release while potentially reducing side effects associated with systemic administration. Here, this review assesses the status of AMTs for oral peptide delivery and discusses the potential integration of permeation enhancers, mucoadhesive systems, and receptor-mediated transport strategies to improve oral bioavailability further. Combining these approaches could pave the way for more widespread oral delivery strategies for peptide and protein medicines.

Leveraging the versatile properties of bacterial spores in materials

Inspired by biological functions of living systems, researchers have engineered cells as independent functional materials or integrated them within a natural or synthetic matrix to create engineered living materials (ELMs). However, the 'livingness' of cells in such materials poses serious drawbacks, such as a short lifespan and the need for cold-chain logistics. Bacterial spores have emerged as a game changer to bypass these shortcomings as a result of their intrinsic dormancy and resistance against harsh conditions. Emerging synthetic biology tools tailored for engineering spores and better understanding of their physical properties have led to novel applications of spore-based materials. Here, we review recent advances in such materials and discuss future challenges for the development of time- and cost-efficient spore-based materials with high performance.

Engineered microbial living matter for diagnostics, prevention, and therapy

Living therapeutic and diagnostic materials based on engineered microorganisms are emerging as a novel approach with the perspective of providing patient-tailored, sustainable, and cost-effective healthcare solutions. In this review, we focus on recent advances in using genetically or chemically engineered microorganisms as living diagnostics, therapeutics, and as a means of prevention for various diseases. We also highlight the applications of living therapeutics for acute and chronic diseases, and the role of micro/macro-encapsulation of the engineered microorganisms. We further showcase the current success of engineered living therapeutics in clinical trials and discuss challenges and future trends in the field.

A Nitrate/Nitrite Biosensor Designed with an Antiterminator for In Vivo Diagnosis of Colitis Based on Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a common microorganism in the human gut that has been linked to health benefits. Furthermore, it is an emerging synthetic biology chassis with the potential to be modified into diagnostic or therapeutic engineered probiotics. However, the absence of biological components limits its further applications. In this study, we developed an antiterminator microbial whole-cell biosensor (MWCB) based on B. thetaiotaomicron. The antiterminator-based element allows the chassis to detect colitis in mice by responding to nitrate and nitrite in an inflammatory environment. In particular, the nitrate/nitrite-inducible promoter was obtained by combining the constitutive promoter with the inducible terminator. Subsequently, the promoter and RBS were replaced to optimize a sensitive and specific response to nitrate/nitrite. A preliminary in vitro assessment was conducted to ascertain the functionality of the biosensor. Its in vivo sensing ability was evaluated in a chemically induced mouse model of ulcerative colitis (UC). The results demonstrated that the MWCB exhibited a robust response to colitis, with a notable positive correlation between the intensity of the response and the level of inflammation. This novel sensing element may provide a new avenue for the development of components for unconventional chassis, like B. thetaiotaomicron. It will also facilitate the development of engineered probiotics based on B. thetaiotaomicron, thereby providing patients with a wider range of medical treatment options.

Design and regulation of engineered bacteria for environmental release

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

Fabricating an advanced electrogenic chassis by activating microbial metabolism and fine-tuning extracellular electron transfer

Exploiting electrogenic microorganisms as unconventional chassis hosts offers potential solutions to global energy and environmental challenges. However, their limited electrogenic efficiency and metabolic versatility, due to genetic and metabolic constraints, hinder broader applications. Herein, we developed a multifaceted approach to fabricate an enhanced electrogenic chassis, starting with streamlining the genome by removing extrachromosomal genetic material. This reduction led to faster lactate consumption, higher intracellular NADH/NAD+ and ATP/ADP levels, and increased growth and biomass accumulation, as well as promoted electrogenic activity. Transcriptome profiling showed an overall activation of cellular metabolism. We further established a molecular toolkit with a vector vehicle incorporating native replication block and refined promoter components for precise gene expression control. This enabled engineered primary metabolism for greater environmental robustness and fine-tuned extracellular electron transfer (EET) for improved efficiency. The enhanced chassis demonstrated substantially improved pollutant biodegradation and radionuclide removal, establishing a new paradigm for utilizing electrogenic organisms as novel biotechnology chassis.

The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron

Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides are metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to the fluctuating levels of their cognate substrates is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. We demonstrate that RbpB interacts with numerous cellular transcripts, including a paralogous noncoding RNA family comprised of 14 members, the FopS (family of paralogous sRNAs). Through a series of in-vitro and in-vivo assays, we reveal that FopS sRNAs repress the translation of SusC-like glycan transporters when substrates are limited-an effect antagonized by RbpB. Ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut in a diet-dependent manner. Together, this study adds to our understanding of RNA-coordinated metabolic control as an important factor contributing to the in-vivo fitness of predominant microbiota species in dynamic nutrient landscapes.

Engineering Programmable Electroactive Living Materials for Highly Efficient Uranium Capture and Accumulation

Uranium is the primary fuel for nuclear energy, critical for sustainable, carbon-neutral energy transitions. However, limited terrestrial resources and environmental risks from uranium contamination require innovative immobilization and recovery solutions. In this work, we present a novel uranium recovery method using programmable electroactive living materials (ELMs). Utilizing Shewanella oneidensis, this approach leverages the intrinsic extracellular electron transfer capability of exoelectrogenic species, combining their adaptability and programmability with the robustness of engineered multicellular systems. These exoelectrogenic cells were endowed to selectively capture and enhance U(VI) reduction by expressing uranyl-binding proteins, coupled with a reconfigured transmembrane Mtr electron nanoconduit. By incorporating biofilm-promoting circuits, we improved cell-to-cell interactions and biofilm formation, enabling the stable assembly of ELMs with robust structural integrity. The ELMs demonstrated superior electrogenic activity, achieving a 3.30-fold increase in current density and a 3.15-fold increase in voltage output compared to controls in microbial electrochemical and fuel cells. When applied for uranium recovery, the ELMs exhibited robust U(VI) capture, reduction, and accumulation capabilities, with a maximum capacity of 808.42 μmol/g. This work not only provides a versatile and environmentally friendly solution for uranium recovery, but also highlights the potential of ELMs in sustainable environmental and energy technologies.

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

The field of Engineered Living Materials (ELMs) integrates engineered living organisms into natural biomaterials to achieve diverse objectives. Multiorganism consortia, prevalent in both naturally occurring and synthetic microbial cultures, exhibit complex functionalities and interrelationships, extending the scope of what can be achieved with individual engineered bacterial strains. However, the ELMs comprising microbial consortia are still in the developmental stage. In this Review, we introduce two strategies for designing ELMs constituted of microbial consortia: a top-down strategy, which involves characterizing microbial interactions and mimicking and reconstructing natural ecosystems, and a bottom-up strategy, which entails the rational design of synthetic consortia and their assembly with material substrates to achieve user-defined functions. Next, we summarize technologies from synthetic biology that facilitate the efficient engineering of microbial consortia for performing tasks more complex than those that can be done with single bacterial strains. Finally, we discuss essential challenges and future perspectives for microbial consortia-based ELMs.

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.

Xenobiology for the Biocontainment of Synthetic Organisms: Opportunities and Challenges

Since the development of recombinant DNA technologies, the need to establish biosafety and biosecurity measures to control genetically modified organisms has been clear. Auxotrophies, or conditional suicide switches, have been used as firewalls to avoid horizontal or vertical gene transfer, but their efficacy has important limitations. The use of xenobiological systems has been proposed as the ultimate biosafety tool to circumvent biosafety problems in genetically modified organisms. Xenobiology is a subfield of Synthetic Biology that aims to construct orthogonal biological systems based on alternative biochemistries. Establishing true orthogonality in cell-based or cell-free systems promises to improve and assure that we can progress in synthetic biology safely. Although a wide array of strategies for orthogonal genetic systems have been tested, the construction of a host harboring fully orthogonal genetic system, with all parts operating in an orchestrated, integrated, and controlled manner, still poses an extraordinary challenge for researchers. In this study, we have performed a thorough review of the current literature to present the main advances in the use of xenobiology as a strategy for biocontainment, expanding on the opportunities and challenges of this field of research.

Methods of DNA introduction for the engineering of commensal microbes

The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.