A de novo matrix for macroscopic living materials from bacteria

3D extrusion bioprinting of microbial inks for biomedical applications

In recent years, the field of 3D bioprinting has witnessed the intriguing development of a new type of bioink known as microbial inks. Bioinks, typically associated with mammalian cells, have been reimagined to involve microbes, enabling many new applications beyond tissue engineering and regenerative medicine. This review presents the latest advancements in microbial inks, including their definition, types, composition, salient characteristics, and biomedical applications. Herein, microbes are genetically engineered to produce 1) extrudable bioink and 2) life-like functionalities such as self-regeneration, self-healing, self-regulation, biosynthesis, biosensing, biosignaling, biosequestration, etc. We also discuss some of the promising applications of 3D extrusion printed microbial inks, such as 1) drugs and probiotics delivery, 2) metabolite production, 3) tissue engineering, 4) bioremediation, 5) biosensors and bioelectronics, 6) biominerals and biocomposites, and 7) infectious disease modeling. Finally, we describe some of the current challenges of microbial inks that needs to be addressed in the coming years, to make a greater impact in health science and technology and many other fields.

Living Porous Ceramics for Bacteria-Regulated Gas Sensing and Carbon Capture

Microorganisms hosted in abiotic structures have led to engineered living materials that can grow, sense, and adapt in ways that mimic biological systems. Although porous structures should favor colonization by microorganisms, they have not yet been exploited as abiotic scaffolds for the development of living materials. Here, porous ceramics are reported that are colonized by bacteria to form an engineered living material with self-regulated and genetically programmable carbon capture and gas-sensing functionalities. The carbon capture capability is achieved using wild-type photosynthetic cyanobacteria, whereas the gas-sensing function is generated utilizing genetically engineered E. coli. Hierarchical porous clay is used as a ceramic scaffold and evaluated in terms of bacterial growth, water uptake, and mechanical properties. Using state-of-the-art chemical analysis techniques, the ability of the living porous ceramics are demonstrated to capture CO2 directly from the air and to metabolically turn minute amounts of toxic gas into a benign scent detectable by humans.

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.

Genetically Modifying the Protein Matrix of Macroscopic Living Materials to Control Their Structure and Rheological Properties

The field of engineering living materials (ELMs) seeks to engineer cells to form macroscopic materials with tailorable structures and properties. While the rheological properties of ELMs have been altered using synthetic biology methodology, the relationships connecting their sequence, structural, and rheological properties remain to be elucidated. Recently, our lab created centimeter-scale ELMs from Caulobacter crescentus that offer a platform to investigate this paradigm. Here, we explore how changing the elastin-like polypeptide (ELP) length within the protein matrix of this ELM impacts its microstructure and viscoelastic behavior. We demonstrate that shortening ELP produces fibers almost 2× thicker than other variants, resulting in a stiffer material at rest. Interestingly, the midlength ELP forms a complex structure with globules and multidirectional fibers with increased yield stress under flow conditions. Lengthening ELP creates thinner strands between cells with similar storage and loss moduli to those of the midlength ELP. This study begins to elucidate sequence-structure-property relationships in these ELMs and shows that they are complex with few parallels to other biocomposite models. Furthermore, it highlights that fine-tuning genetic sequences can create significant differences in rheological properties, uncovering new design principles of ELMs.

Cohesive Living Bacterial Films with Tunable Mechanical Properties from Cell Surface Protein Display

Engineered living materials (ELMs) constitute a novel class of functional materials that contain living organisms. The mechanical properties of many such systems are dominated by the polymeric matrices used to encapsulate the cellular components of the material, making it hard to tune the mechanical behavior through genetic manipulation. To address this issue, we have developed living materials in which mechanical properties are controlled by the cell-surface display of engineered proteins. Here, we show that engineered Esherichia coli cells outfitted with surface-displayed elastin-like proteins (ELPs, designated E6) grow into soft, cohesive bacterial films with biaxial moduli around 14 kPa. When subjected to bulge-testing, such films yielded at strains of approximately 10%. Introduction of a single cysteine residue near the exposed N-terminus of the ELP (to afford a protein designated CE6) increases the film modulus 3-fold to 44 kPa and eliminates the yielding behavior. When subjected to oscillatory stress, films prepared from E. coli strains bearing CE6 exhibit modest hysteresis and full strain recovery; in E6 films much more significant hysteresis and substantial plastic deformation are observed. CE6 films heal autonomously after damage, with the biaxial modulus fully restored after a few hours. This work establishes an approach to living materials with genetically programmable mechanical properties and a capacity for self-healing. Such materials may find application in biomanufacturing, biosensing, and bioremediation.

Macroscopic Assembly of Materials with Engineered Bacterial Spores via Coiled-Coil Interaction

Herein, we report macroscopic materials formed by the assembly of engineered bacterial spores. Spores were engineered by using a T7-driven expression system to display a high density of pH-responsive self-associating proteins on their surface. The engineered surface protein on the spore surface enabled pH-dependent binding at the protein level and enabled the assembly of granular materials. Mechanical properties remained largely constant with changing pH, but erosion stability was pH-dependent in a manner consistent with the pH-dependent interaction between the engineered surface proteins. Our finding utilizes synthetic biology for the design of macroscopic materials and illuminates the impact of coiled-coil interaction across various length scales.

Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials

Advanced design strategies are essential to realize the full potential of engineered living materials, including their biodegradability, manufacturability, sustainability, and ability to tailor functional properties. Toward these goals, we present mechanically engineered living material with compostability, healability, and scalability - a material that integrates these features in the form of a stretchable plastic that is simultaneously flushable, compostable, and exhibits the characteristics of paper. This plastic/paper-like material is produced in scalable quantities (0.5-1 g L-1), directly from cultured bacterial biomass (40%) containing engineered curli protein nanofibers. The elongation at break (1-160%) and Young's modulus (6-450 MPa) is tuned to more than two orders of magnitude. By genetically encoded covalent crosslinking of curli nanofibers, we increase the Young's modulus by two times. The designed engineered living materials biodegrade completely in 15-75 days, while its mechanical properties are comparable to petrochemical plastics and thus may find use as compostable materials for primary packaging.

Transcriptional regulation of living materials via extracellular electron transfer

Engineered living materials combine the advantages of biological and synthetic systems by leveraging genetic and metabolic programming to control material-wide properties. Here, we demonstrate that extracellular electron transfer (EET), a microbial respiration process, can serve as a tunable bridge between live cell metabolism and synthetic material properties. In this system, EET flux from Shewanella oneidensis to a copper catalyst controls hydrogel cross-linking via two distinct chemistries to form living synthetic polymer networks. We first demonstrate that synthetic biology-inspired design rules derived from fluorescence parameterization can be applied toward EET-based regulation of polymer network mechanics. We then program transcriptional Boolean logic gates to govern EET gene expression, which enables design of computational polymer networks that mechanically respond to combinations of molecular inputs. Finally, we control fibroblast morphology using EET as a bridge for programmed material properties. Our results demonstrate how rational genetic circuit design can emulate physiological behavior in engineered living materials.

Directed evolution of material-producing microorganisms

Nature is home to a variety of microorganisms that create materials under environmentally friendly conditions. While this offers an attractive approach for sustainable manufacturing, the production of materials by native microorganisms is usually slow and synthetic biology tools to engineer faster microorganisms are only available when prior knowledge of genotype-phenotype links is available. Here, we utilize a high-throughput directed evolution platform to enhance the fitness of whole microorganisms under selection pressure and identify genetic pathways to enhance the material production capabilities of native species. Using Komagataeibacter sucrofermentans as a model cellulose-producing microorganism, we show that our droplet-based microfluidic platform enables the directed evolution of these bacteria toward a small number of cellulose overproducers from an initial pool of 40,000 random mutants. Sequencing of the evolved strains reveals an unexpected link between the cellulose-forming ability of the bacteria and a gene encoding a protease complex responsible for protein turnover in the cell. The ability to enhance the fitness of microorganisms toward a specific phenotype and to unravel genotype-phenotype links makes this high-throughput directed evolution platform a promising tool for the development of new strains for the sustainable manufacturing of materials.

Fabrication of Living Entangled Network Composites Enabled by Mycelium

Organic polymer-based composite materials with favorable mechanical performance and functionalities are keystones to various modern industries; however, the environmental pollution stemming from their processing poses a great challenge. In this study, by finding an autonomous phase separating ability of fungal mycelium, a new material fabrication approach is introduced that leverages such biological metabolism-driven, mycelial growth-induced phase separation to bypass high-energy cost and labor-intensive synthetic methods. The resulting self-regenerative composites, featuring an entangled network structure of mycelium and assembled organic polymers, exhibit remarkable self-healing properties, being capable of reversing complete separation and restoring ≈90% of the original strength. These composites further show exceptional mechanical strength, with a high specific strength of 8.15 MPa g.cm-3, and low water absorption properties (≈33% after 15 days of immersion). This approach spearheads the development of state-of-the-art living composites, which directly utilize bioactive materials to "self-grow" into materials endowed with exceptional mechanical and functional properties.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Engineered Living Material Bioreactors with Tunable Mechanical Properties using Vat Photopolymerization

3D-printed engineered living materials (ELM) are promising bioproduction platforms for agriculture, biotechnology, sustainable energy, and green technology applications. However, the design of these platforms faces several challenges, such as the processability of these materials into complex form factors and control over their mechanical properties. Herein, ELM are presented as 3D-printed bioreactors with arbitrary shape geometries and tunable mechanical properties (moduli and toughness). Poly(ethylene glycol) diacrylate (PEGDA) is used as the precursor to create polymer networks that encapsulate the microorganisms during the vat photopolymerization process. A major limitation of PEGDA networks is their propensity to swell and fracture when submerged in water. The authors overcame this issue by adding glycerol to the resin formulation to 3D print mechanically tough ELM hydrogels. While polymer concentration affects the modulus and reduces bioproduction, ELM bioreactors still maintain their metabolic activity regardless of polymer concentration. These ELM bioreactors have the potential to be used in different applications for sustainable architecture, food production, and biomedical devices that require different mechanical properties from soft to stiff.

Cell-Free Protein Expression in Polymer Materials

While synthetic biology has advanced complex capabilities such as sensing and molecular synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics make the incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over the cellular viability or release of genetically modified organisms. Here, we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable biofunctionality in a ubiquitous class of synthetic materials.

Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus

Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.

Engineering functional materials through bacteria-assisted living grafting

Functionalizing materials with biomacromolecules such as enzymes has broad applications in biotechnology and biomedicine. Here, we introduce a grafting method mediated by living cells to functionalize materials. We use polymeric scaffolds to trap engineered bacteria and micron-sized particles with chemical groups serving as active sites for grafting. The bacteria synthesize the desired protein for grafting and autonomously lyse to release it. The released functional moieties are locally grafted onto the active sites, generating the materials engineered by living grafting (MELGs). MELGs are resilient to perturbations because of both the bonding and the regeneration of functional domains synthesized by living cells. The programmability of the bacteria enables us to fabricate MELGs that can respond to external input, decompose a pollutant, reconstitute synthetic pathways for natural product synthesis, and purify mismatched DNA. Our work establishes a bacteria-assisted grafting strategy to functionalize materials with a broad range of biological activities in an integrated, flexible, and modular manner. A record of this paper's transparent peer review process is included in the supplemental information.

Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface

Protein-based biomaterials have played a key role in tissue engineering, and additional exciting applications as self-healing materials and sustainable polymers are emerging. Over the past few decades, recombinant expression and production of various fibrous proteins from microbes have been demonstrated; however, the resulting proteins typically must then be purified and processed by humans to form usable fibers and materials. Here, we show that the Gram-positive bacterium Bacillus subtilis can be programmed to secrete silk through its translocon via an orthogonal signal peptide/peptidase pair. Surprisingly, we discover that this translocation mechanism drives the silk proteins to assemble into fibers spontaneously on the cell surface, in a process we call secretion-catalyzed assembly (SCA). Secreted silk fibers form self-healing hydrogels with minimal processing. Alternatively, the fibers retained on the membrane provide a facile route to create engineered living materials from Bacillus cells. This work provides a blueprint to achieve autonomous assembly of protein biomaterials in useful morphologies directly from microbial factories.

Engineering Tissue-Scale Properties with Synthetic Cells: Forging One from Many

In metazoans, living cells achieve capabilities beyond individual cell functionality by assembling into multicellular tissue structures. These higher-order structures represent dynamic, heterogeneous, and responsive systems that have evolved to regenerate and coordinate their actions over large distances. Recent advances in constructing micrometer-sized vesicles, or synthetic cells, now point to a future where construction of synthetic tissue can be pursued, a boon to pressing material needs in biomedical implants, drug delivery systems, adhesives, filters, and storage devices, among others. To fully realize the potential of synthetic tissue, inspiration has been and will continue to be drawn from new molecular findings on its natural counterpart. In this review, we describe advances in introducing tissue-scale features into synthetic cell assemblies. Beyond mere complexation, synthetic cells have been fashioned with a variety of natural and engineered molecular components that serve as initial steps toward morphological control and patterning, intercellular communication, replication, and responsiveness in synthetic tissue. Particular attention has been paid to the dynamics, spatial constraints, and mechanical strengths of interactions that drive the synthesis of this next-generation material, describing how multiple synthetic cells can act as one.

Engineered Living Materials For Sustainability

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

Synchronized Swarmers and Sticky Stalks: Caulobacter crescentus as a Model for Bacterial Cell Biology

First isolated and classified in the 1960s, Caulobacter crescentus has been instrumental in the study of bacterial cell biology and differentiation. C. crescentus is a Gram-negative alphaproteobacterium that exhibits a dimorphic life cycle composed of two distinct cell types: a motile swarmer cell and a nonmotile, division-competent stalked cell. Progression through the cell cycle is accentuated by tightly controlled biogenesis of appendages, morphological transitions, and distinct localization of developmental regulators. These features as well as the ability to synchronize populations of cells and follow their progression make C. crescentus an ideal model for answering questions relevant to how development and differentiation are achieved at the single-cell level. This review will explore the discovery and development of C. crescentus as a model organism before diving into several key features and discoveries that have made it such a powerful organism to study. Finally, we will summarize a few of the ongoing areas of research that are leveraging knowledge gained over the last century with C. crescentus to highlight its continuing role at the forefront of cell and developmental biology.

Intracellular Experimental Evolution of Francisella tularensis Subsp. holarctica Live Vaccine Strain (LVS) to Antimicrobial Resistance

In vitro experimental evolution has complemented clinical studies as an excellent tool to identify genetic changes responsible for the de novo evolution of antimicrobial resistance. However, the in vivo context for adaptation contributes to the success of particular evolutionary trajectories, especially in intracellular niches where the adaptive landscape of virulence and resistance are strongly coupled. In this work, we designed an ex vivo evolution approach to identify evolutionary trajectories responsible for antibiotic resistance in the Live Vaccine Strain (LVS) of Francisella tularensis subsp. holarctica while being passaged to increasing ciprofloxacin (CIP) and doxycycline (DOX) concentrations within macrophages. Overall, adaptation within macrophages advanced much slower when compared to previous in vitro evolution studies reflecting a limiting capacity for the expansion of adaptive mutations within the macrophage. Longitudinal genomic analysis identified resistance conferring gyrase mutations outside the Quinolone Resistance Determining Region. Strikingly, FupA/B mutations that are uniquely associated with in vitro CIP resistance in Francisella were not observed ex vivo, reflecting the coupling of intracellular survival and resistance during intracellular adaptation. To our knowledge, this is the first experimental study demonstrating the ability to conduct experimental evolution to antimicrobial resistance within macrophages. The results provide evidence of differences in mutational profiles of populations adapted to the same antibiotic in different environments/cellular compartments and underscore the significance of host mediated stress during resistance evolution.

Complex Living Materials Made by Light-Based Printing of Genetically Programmed Bacteria

Living materials with embedded microorganisms can genetically encode attractive sensing, self-repairing, and responsive functionalities for applications in medicine, robotics, and infrastructure. While the synthetic toolbox for genetically engineering bacteria continues to expand, technologies to shape bacteria-laden living materials into complex 3D geometries are still rather limited. Here, it is shown that bacteria-laden hydrogels can be shaped into living materials with unusual architectures and functionalities using readily available light-based printing techniques. Bioluminescent and melanin-producing bacteria are used to create complex materials with autonomous chemical-sensing capabilities by harnessing the metabolic activity of wild-type and engineered microorganisms. The shaping freedom offered by printing technologies and the rich biochemical diversity available in bacteria provides ample design space for the creation and exploration of complex living materials with programmable functionalities for a broad range of applications.