bims-livmat 2025-08-17 papers

bims-livmat

Biomed News

on Living materials

Issue of 2025–08–17
nine papers selected by
Sara Trujillo Muñoz, Leibniz-Institut für Neue Materialien

Unraveling the Constrained Cell Growth in Engineered Living Materials.
Polyelectrolyte Complex-Based Artificial Biofilms as Versatile Living Biomaterials.
Multilayered safety framework for living diagnostics in the colon.
Bioengineering of Probiotic Yeast Saccharomyces boulardii for Advanced Biotherapeutics.
Heterologous integration-assisted metabolic engineering in Escherichia coli for elevated D-pantothenic acid production.
Resynthesis of synthetic biology techniques: combining engineered bacteria with other antitumour therapies.
Evaluation of Engineering Potential in Undomesticated Microbes With VECTOR.
Advancing biomaterial innovation for tissue engineering through microbial synthetic biology: A review.
Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape.

ACS Synth Biol. 2025 Aug 14.

Unraveling the Constrained Cell Growth in Engineered Living Materials.

Shuang-Shuang Sun, Cheng-Cheng Ding, Hai-Yan Yu, Xian-Zheng Yuan, Shu-Guang Wang, Peng-Fei Xia.

  Engineered living materials (ELMs) leverage the integrative advantages of materials science and synthetic biology for advanced functionalities. Predicting and controlling cellular behavior are essential for designing and building ELMs, requiring a fundamental understanding of the growth dynamics of encapsulated cells. Here, we interrogate the interference of constrained growth with the engineered functionalities and cellular physiology of cyanobacteria and unveil the dynamic interaction between cell growth and spatial confinements within photosynthetic ELMs. We observed that engineered cyanobacteria within ELMs exhibited compromised performances in growth, uptake of nonutilizable substrate, and synthesis of customized products, while ELMs could protect encapsulated cells from external stresses. Besides commonly accepted external influences, we identified abnormally high levels of reactive oxygen species and impaired oxygen photosynthesis inside the cells encapsulated in the ELMs. Finally, we illustrated the dynamics of cell growth within the confined spaces enveloped by the material matrices, forming clustered cell aggregates and compressed growth bubbles until the spatial limits. Our study provides a fundamental yet often overlooked connection between cellular behavior and spatial confinement, consolidating the foundation for advanced ELM innovations.

Keywords:  confined growth; cyanobacteria; engineered living materials; hydrogel

DOI:  https://doi.org/10.1021/acssynbio.5c00378
ACS Appl Mater Interfaces. 2025 Aug 11.

Polyelectrolyte Complex-Based Artificial Biofilms as Versatile Living Biomaterials.

Yihao Cui, Zhe Wang, Haiyang Yu, Peng Fu, Changwei Shi, Ximing Xu, Lei Liu, Shuai Hou.

  Bacterial biofilms, while recognized as promising functional biomaterials, are constrained by intricate growth dynamics, complex extracellular polymer compositions, and limited processability. Here, we address these challenges by employing polyelectrolyte complexes (PECs) to create artificial biofilms via a one-step synthesis with predefined extracellular composition and enhanced processability, achieving natural biofilm-like bacterial density and properties across diverse bacterial species. The PEC matrix confers robust bacterial protection, resisting antibiotic concentrations 1000-fold above the minimal inhibitory level, lyophilization, and acidic environments. Its shear-thinning behavior enables versatile processing via extrusion, molding, or coating. As recyclable biocatalysts, these biofilms preserve the enzymatic activity at elevated temperatures (up to 80 °C). In simulated probiotic delivery, they enhance bacterial survival under gastrointestinal-like conditions and offer tunable, composition-dependent release profiles, achieving therapeutic efficacy in a murine colitis model. This platform combines flexible fabrication with customizable functionality, establishing a versatile strategy for engineered living biomaterials with broad applications in biotechnology and biomedicine.

Keywords:  bacterial encapsulation; biofilms; extracellular polymeric substances; living biomaterials; polyelectrolyte complexes

DOI:  https://doi.org/10.1021/acsami.5c06236
Front Syst Biol. 2023 ;3 1240040

Multilayered safety framework for living diagnostics in the colon.

Sonia Mecacci, Lucía Torregrosa-Barragán, Enrique Asin-Garcia, Robert W Smith.

  Introduction: Colorectal cancer is the second most deadly cancer worldwide. Current screening methods have low detection rates and frequently provide false positive results, leading to missed diagnoses or unnecessary colonoscopies. To tackle this issue, the Wageningen UR iGEM team from 2022 developed "Colourectal", a living diagnostic tool for colorectal cancer. Following a synthetic biology approach, the project used an engineered Escherichia coli Nissle 1917 strain capable of binding to tumour cells that detects two distinct cancer biomarkers, and secretes a coloured protein observable in stool. Due to the utilization of genetically modified bacteria in vivo, precautionary biosafety measures were included within a three level safe-by-design strategy. Results: The first genetic safeguard ensured confinement of the living diagnostic to the colon environment by implementing auxotrophy to mucin that is abundant in the colon lining. For this, a synthetic chimeric receptor was generated to ensure expression of essential genes in the presence of mucin. The second strategy limited the viability of the engineered bacteria to the human body, preventing proliferation in open environments. The use of a temperature sensitive kill switch induced bacterial cell death at temperatures below 37°C. The third biocontainment strategy was installed as an emergency kill switch to stop the Colourectal test at any point. By inducing a highly genotoxic response through CRISPR-Cas-mediated DNA degradation, cell death of E. coli Nissle is triggered. Discussion: While the use of engineered microorganisms in human applications is not yet a reality, the safety considerations of our multi-layered strategy provide a framework for the development of future living diagnostic tools.

Keywords:  auxotrophy; biocontainment; biosafety; colorectal cancer; diagnostic tool; genetic circuits; inducible kill switches; safe-by-design

DOI:  https://doi.org/10.3389/fsysb.2023.1240040
ACS Synth Biol. 2025 Aug 14.

Bioengineering of Probiotic Yeast Saccharomyces boulardii for Advanced Biotherapeutics.

Tiew-Yik Ting, Wei-Jing Lee, Hoe-Han Goh.

  Saccharomyces cerevisiae var. boulardii (Sb), a subspecies of S. cerevisiae (Sc), is widely recognized for its probiotic properties. Recently, Sb has attracted growing interest as a chassis organism for engineered live biotherapeutics and advanced microbiome therapies. Traditional genetic manipulation techniques developed for Sc are now being successfully adapted for Sb, facilitating diverse genome integration strategies to enable the in situ biomanufacturing of functional molecules for disease intervention. Concurrently, research efforts are advancing Sb's potential as a platform for biosensing applications and diagnostic tools through the development of disease-responsive biosensors. Biosafety concerns are also being addressed through the design of biocontainment strains that ensure controlled application. To the best of our knowledge, earlier reviews have largely emphasized its clinical applications, safety profile, and probiotic mechanisms. This review uniquely consolidates recent advances in genetic modification, metabolic engineering, and synthetic biology strategies applied to Sb for therapeutic use. Together, these synthetic biology advancements position Sb as a promising and versatile platform for next-generation microbiome-based therapeutics and expanding applications in human health and food biotechnology.

Keywords:  Saccharomyces cerevisiae var. boulardii, systems biology; advanced microbiome therapies (AMTs); engineered live biotherapeutics (eLBPs); probiotics; synthetic biology

DOI:  https://doi.org/10.1021/acssynbio.5c00236
Metab Eng. 2025 Aug 11. pii: S1096-7176(25)00122-3. [Epub ahead of print]

Heterologous integration-assisted metabolic engineering in Escherichia coli for elevated D-pantothenic acid production.

Kuo Zhao, Hailin Gao, Mengnan Han, Bo Zhang, Zhiqiang Liu, Shuping Zou, Yuguo Zheng.

  D-pantothenic acid (D-PA) is a vital water-soluble vitamin with diverse industrial applications, driving the demand for efficient microbial production. Here, we rationally engineered an Escherichia coli strain to enhance D-PA production through metabolic engineering. First, to enhance carbon utilization efficiency, competing byproduct pathways were deleted and the pentose phosphate pathway was downregulated. Next, the glucose and β-alanine transport systems were strategically enhanced, and cofactor availability was improved through engineering NADPH regeneration and ATP recycling pathways. Subsequently, pathway engineering was applied to fine-tune the expression of heterologous enzymes, thereby enhancing the metabolic pull toward D-PA biosynthesis. To enhance the supply of one-carbon donor required by the rate-limiting enzyme ketopantoate hydroxymethyltransferase (KPHMT), a heterologous 5,10-methylenetetrahydrofolate biosynthesis module was introduced. Finally, dynamic regulation of isocitrate synthase and pantothenate kinase was implemented to balance cell growth and D-PA production. As a result of the integrated metabolic engineering strategies, the final strain DPZ28/P31 achieved a D-PA titer of 98.6 g/L and a yield of 0.44 g/g glucose in a two-stage fed-batch fermentation. These findings provide valuable insights for industrial-scale production of D-PA and related compounds.

Keywords:  Cofactor regeneration; D-pantothenic acid; Dynamic regulation; Escherichia coli; One-carbon donor; Substrate transport

DOI:  https://doi.org/10.1016/j.ymben.2025.08.003
Front Microbiol. 2025 ;16 1545334

Resynthesis of synthetic biology techniques: combining engineered bacteria with other antitumour therapies.

Xueke Chang, Xiaolin Liu, Xiumei Wang, Lin Ma, Jing Liang, Yan Li.

  Worldwide cancer mortality rates underscore the pressing need to identify and develop novel anticancer therapies to supplement traditional cancer treatments. Naturally occurring bacteria are ideal for cancer therapy owing to their autonomous propulsion and hypoxia-targeting properties, but their poor tumour targeting ability and weak tumour penetration limit their use. Bacteria can be modified by bioengineering and nanotechnology methods to improve their physiological activity and therapeutic effect. Furthermore, engineering allows for refined spatiotemporal control, precise functional recombination, and direct genetic reprogramming. These engineered bacteria can produce synergistic anticancer effects upon coadministration with anticancer drug-containing nanomaterials or other therapeutic payloads. In this paper, the use of engineered bacteria combined with other antitumour therapies, such as radiotherapy (RT), chemotherapy, immunotherapy, light therapy and life technology, is reviewed to aid in improving antitumour therapy efficacy. In addition, we provide an overview of the current state of spatiotemporally regulated bacterial gene expression and drug release, discuss the drawbacks and difficulties of employing engineered bacteria for tumour therapy, and explore potential research avenues on the basis of current advancements.

Keywords:  antitumour therapy; engineered bacteria; spatiotemporal manipulation; synthetic biology; therapeutic effect

DOI:  https://doi.org/10.3389/fmicb.2025.1545334
Microb Biotechnol. 2025 Aug;18(8): e70215

Evaluation of Engineering Potential in Undomesticated Microbes With VECTOR.

Riley Williamson, Nicholas Dusek, Eglantina Lopez-Echartea, Megan K Townsend Ramsett, Barney A Geddes.

  Genetic engineering research has predominantly focused on well-characterised organisms like Escherichia coli and Bacillus subtilis, with methods that often fail to translate to other microorganisms. This limitation presents a significant challenge, particularly given the increasing isolation of large microbial collections through high-throughput culturomics. In response, we developed a scalable, high-throughput pipeline to evaluate the engineerability of diverse microbial community members we named VECTOR (Versatile Engineering and Characterisation of Transferable Origins and Resistance). We utilised a library of vectors with the Bacterial Expression Vector Archive (BEVA) architecture that included combinations of three antibiotic resistance genes and three broad host-range origins of replication (pBBR1, RK2 and RSF1010) or the restricted host-range R6K with an integrative mariner transposon. We tagged each vector with green fluorescent protein and a unique nucleotide barcode. The resulting plasmids were delivered en masse to libraries of undomesticated microbes from plant microbiomes in workflows designed to evaluate their ability to be engineered. Utilising OD600 and relative fluorescence measurements, we were able to monitor genetic cargo transfer in real time, indicating successfully engineered strains. Next-generation sequencing of plasmid molecular barcodes allowed us to identify specific vector architectures that worked well in particular bacterial strains from a large community. Modifications to the procedure facilitated isolation of engineered microbes.

Keywords:  barcodes; genetic engineering; plasmid; synthetic biology

DOI:  https://doi.org/10.1111/1751-7915.70215
Int J Biol Macromol. 2025 Aug 11. pii: S0141-8130(25)07328-3. [Epub ahead of print] 146771

Advancing biomaterial innovation for tissue engineering through microbial synthetic biology: A review.

Ruikai Ma, Shuao Zhao, Yesheng Jin, Yinhao Li, Huxin Tang, Mingyang Hu, Xinyu Hu, Yong Xu, Wenge Ding.

  Microbial synthetic biology is a burgeoning discipline of resplendent innovation. Its primary objective is to enable microorganisms to synthesize specific substances or acquire diverse biological functions by modifying microbial genomes or regulating metabolic processes. With the ceaseless advancement of synthetic biology technology and the continuous deepening of research, microbial synthetic biology has achieved remarkable breakthroughs in the realm of biomaterial science, offering a new direction for designing advanced biomaterials for tissue engineering. In this review, we first outline commonly used microbial hosts and synthetic biology approaches related to biomaterials production. Then we focus on the classification of biomaterials produced by engineered microbes, explaining the production strategies for these different categories of biomaterials and the specific advantages of producing them using engineered microbes. We discuss the advancements and profound impacts of these innovative microbial-synthesized materials in the field of tissue engineering. Despite the challenges that lie ahead, the prospects for the application of these biomaterials in the field of tissue engineering remain exceedingly vast. In the future, microbial synthesized materials are expected to bring more innovations and breakthroughs to the field of tissue engineering.

Keywords:  Biomaterials; Microbial synthetic biology; Tissue engineering

DOI:  https://doi.org/10.1016/j.ijbiomac.2025.146771
Appl Environ Microbiol. 2025 Aug 13. e0074125

Secure biosystems design in Saccharomyces cerevisiae establishes effective biocontainment strategies and mechanisms of escape.

Natalie A Lamb, Kimberly A Rosenbach, Thomas J Musselwhite, Kathleen L Arnolds, Riley C Higgins, Gabriella A Li, Jeffrey G Linger, Michael T Guarnieri.

  The widespread application of recombinant DNA and synthetic biology approaches for microbial metabolic engineering pursuits has motivated the development of biocontainment strategies, targeting safe and secure deployment of genetically modified microorganisms (GMMs). However, the design rules and mechanistic drivers governing biocontainment efficacy, as well as impacts of biocontainment upon microbial fitness, remain to be comprehensively evaluated, hindering predictive design and application of these strategies. We have developed a platform for high-resolution analysis of a transactivated kill switch in laboratory and industrial strains of Saccharomyces cerevisiae to assess modes of biocontainment escape and establish design rules for development of kill switch systems in diverse microbes. A camphor-regulated, RelE toxin system was systematically deployed to assess the impacts of differential kill switch copy number and ploidy in laboratory vs industrial strains. CRISPR-mediated integration of the biocontainment system at various loci revealed rapid escape events driven, in part, by mutations to both the Cam-transactivator (cam-TA) and RelE toxin. Genetic engineering enabled recapitulation of escape phenotypes, confirming mechanisms of escape and establishing structure-function relationships in the cam-TA system. Interestingly, genomic resequencing of escape mutants also revealed a series of off-target mutations, implicating additional modes of kill switch escape. Multi-copy integration of the kill switch system mitigated these effects by orders of magnitude, without compromising the biosynthetic capacity of the microbes, but proved insufficient to establish sustained biocontainment. The resultant data define a series of key design rules for next-generation biocontainment strategies and add to a growing foundational knowledge base targeting establishment of secure biosystems designs.IMPORTANCEThe development of biocontainment mechanisms is essential for safe deployment of microbes in industrial processes and to minimize escape into the natural environment. To achieve secure biosystems designs, a deeper understanding of the mechanistic drivers governing biocontainment efficacy and associated impacts of biocontainment upon microbial fitness are needed. This study uncovers successful biocontainment strategies for kill switch deployment in addition to mechanistic information conferring kill switch escape. Additionally, differential effects were observed in laboratory vs industrial yeasts, implicating auxotrophies and heterothallism as additional drivers of biocontainment. These learnings can inform iterative designs, with the goal of improving the efficacy of biocontainment while maintaining fitness in engineered microbes.

Keywords:  biocontainment; bioproduction; biotechnology; escape mechanisms; genetically modified microorganisms; secure biosystems; whole genome sequencing; yeast genetics

DOI:  https://doi.org/10.1128/aem.00741-25