bims-biopma 2025-06-15 papers

bims-biopma

Biomed News

on Bioprogrammable materials

Issue of 2025–06–15
eight papers selected by
Shrikrishnan Sankaran, Leibniz-Institut für Neue Materialien

The Challenge of the Yuck Factor in Public Acceptance of Engineered Living Materials.
Tuning viscoelasticity and fine structure of living materials via synthetic adhesion logic and rheological perturbations.
Mechanics control the proliferation of diatoms entrapped in hydrogels.
Living Kombucha Electronics with Proteinoids.
DNA-programmed responsive microorganism assembly with controlled patterns and behaviors.
From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing.
A discovery platform for identification of host-induced bacterial biosensors from diverse sources.
Bioactive DNA hydrogel interfacing with living cells and extracellular vesicles.

Glob Chall. 2025 Jun;9(6): 2400384

The Challenge of the Yuck Factor in Public Acceptance of Engineered Living Materials.

Kristen K Intemann, Hannah R Lavoie, Kirke D A Elsass, Brandon G Scott, Robin Gerlach.

  Engineered Living Materials (or ELMs) are an emerging class of materials that utilize microorganisms that can either generate their own structure (such as biofilms) or that can be incorporated into synthetic matrices using technologies (such as 3D printing). ELMs can be designed to have multiple functions, such as biosensing, self-repair, or bioremediation. Such materials have the potential to address a variety of problems related to sustainability, including water security, energy, and health. One major challenge to widescale social acceptance and adoption of these materials is the so-called yuck factor, or the propensity these materials may have to elicit disgust reactions. This Perspective provides an overview of social science research directed at the yuck factor to identify the drivers and demographics of disgust experiences and to examine how each of these are likely to arise in relation to ELMs. Strategies for overcoming these challenges are also addressed. Finally, areas where future empirical research is needed to better understand disgust toward ELMs, or particular ELM applications, are identified.

Keywords:  disgust; living materials; social acceptance of materials; yuck factor

DOI:  https://doi.org/10.1002/gch2.202400384
bioRxiv. 2025 Jun 04. pii: 2025.06.04.657808. [Epub ahead of print]

Tuning viscoelasticity and fine structure of living materials via synthetic adhesion logic and rheological perturbations.

Stefana A Costan, Kira Hallerbach, Samuel Y Kim, Chris Camp, Minkyu Kim, Ingmar H Riedel-Kruse.

Engineered living materials (ELMs) at the multicelluar level represent an innovation that promises programmable properties for biomedical, environmental, and consumer applications. However, the rational tuning of the mechanical properties of such ELMs from first principles remains a challenge. Here we use synthetic cell-cell adhesins to systematically characterize how rheological and viscoelastic properties of multicellular materials made from living bacteria can be tuned via adhesin strength, cell size and shape, and adhesion logic. We confirmed that the previous results obtained for non-living materials also apply to bacterial ELMs. Additionally, the incorporation of synthetic adhesins, combined with the adaptability of bacterial cells in modifying various cellular parameters, now enables novel and precise control over material properties. Furthermore, we demonstrate that rheology is a powerful tool for actively shaping the microscopic structure of ELMs, enabling control over cell aggregation and particle rearrangement, a key feature for complex material design. These results deepen our understanding of tuning the viscoelastic properties and fine structure of ELMs for applications like bioprinting and microbial consortia design including natural systems.

DOI: https://doi.org/10.1101/2025.06.04.657808
Soft Matter. 2025 Jun 11.

Mechanics control the proliferation of diatoms entrapped in hydrogels.

Rani Boons, Dominic Gerber, Robert W Style, Anouk Droux, Tanja Zimmermann, Gustav Nyström, Gilberto Siqueira, André R Studart.

The proliferation of microorganisms in hydrogels is crucial for the design of engineered living materials and biotechnological processes, and may provide insights into cellular growth in aquatic environments. While the mechanical properties of the gel have been shown to affect the division of entrapped cells, research is still needed to understand the impact and the origin of mechanical forces controlling the growth of microorganisms inside hydrogels. Using diatoms as model microorganisms, we investigate the viability, time to division and growth dynamics of cells entrapped in agar hydrogels with tuneable mechanical properties. Cell culture experiments, confocal optical microscopy and particle tracking velocimetry are performed to uncover the role of stress relaxation and residual stresses in the gel and how these affect diatom proliferation. Our experiments reveal that the interplay between the internal pressure of the dividing cell and the mechanical response of the hydrogel control the proliferation behaviour of the entrapped diatoms. By providing quantitative guidelines for the selection of hydrogels for the entrapment and growth of microorganisms, this study offers new insights on the design of living materials for established and emerging biotechnologies.

DOI: https://doi.org/10.1039/d5sm00391a
ACS Omega. 2025 Jun 03. 10(21): 21128-21146

Living Kombucha Electronics with Proteinoids.

Anna Nikolaidou, Panagiotis Mougkogiannis, Andrew Adamatzky.

The work introduces a composite material that combines Kombucha cellulose mats with synthetic thermal proteinoids to create electroactive biofilms, capable of sensing and computation. The synthesis of proteinoids involves heating amino acid mixtures, which leads to the formation of proto-cell structures capable of biological electrical signaling. We demonstrate that these hybrid biofilms exhibit adjustable memristive and memfractance properties, which can be utilized for unconventional computing tasks. The potential applications of living biofilms extend beyond neural interfaces, encompassing bioinspired robotics, smart wearables, adaptive biorobotic systems, and other technologies that rely on dynamic bioelectronic materials. The composite films offer a wide range of options for synthesis and performance customization. Current research is dedicated to customizing the composition, nanostructure, and integration of proteinoids in hybrid circuits to achieve specific electronic functionalities. Overall, these cross-kingdom biofilms are an intriguing category of materials that combine the unique properties of biological organisms and smart polymers. The Kombucha-proteinoid composites are a significant step forward in the development of future technologies that bridge the gap between living and artificial life systems. These composites have the remarkable ability to support cellular systems and demonstrate adaptive bioelectronic behavior.

DOI: https://doi.org/10.1021/acsomega.4c09743
Sci Adv. 2025 Jun 13. 11(24): eads8651

DNA-programmed responsive microorganism assembly with controlled patterns and behaviors.

Yuhan Kong, Qi Du, Dan Zhao, Yujian Wen, Tianqing Zhang, Zhiwang Geng, Maben Ying, Bryan Wei, Tong Si, Ye Tian, Feng Li, Zhou Nie, Hang Xing.

Programming microorganism adhesions to engineer multicellular microbial communities holds promise for synthetic biology and medicine. Current chemical and genetic engineering approaches often lack specificity or require engineered bacteria, making the design of responsive interactions challenging. Here, we demonstrate the use of functional DNA as programmable surface receptors to regulate the patterns and behaviors of microbial communities. Using metabolic labeling and hydrophobic insertion, we modified various microorganisms with DNA, including Gram-positive and Gram-negative bacteria, and dormant spores. By incorporating distinct sequences, we achieved precise spatial control of bi- and tricomponent microbial assemblies, forming diverse morphologies like core-shell and selective clusters. Stimuli-responsive clustering was successfully realized using aptamers, strand displacement, and reverse-Hoogsteen base pairing, with oligonucleotides or small molecules as exogenous cues. This work extends the use of functional DNA to control microbial interactions, enabling living communities with dynamic biofunctions, such as biofilm formation, antibiotic sensitivity, and quorum sensing, in response to biological triggers.

DOI: https://doi.org/10.1126/sciadv.ads8651
Curr Opin Biotechnol. 2025 Jun 11. pii: S0958-1669(25)00064-3. [Epub ahead of print]94 103320

From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing.

Christopher J Petzold, Aindrila Mukhopadhyay.

Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy. Here, we review the current state of the art, some key challenges and possible solutions. We see a critical role of automation, high-throughput technologies, self-driving and cloud labs, and data management to enable Artificial Intelligence/Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel bio-based solutions. Accurate models will expedite the development and scale-up of engineered microbes for a range of final products from many starting materials.

DOI: https://doi.org/10.1016/j.copbio.2025.103320
Mol Syst Biol. 2025 Jun 09.

A discovery platform for identification of host-induced bacterial biosensors from diverse sources.

Clare M Robinson, David Carreño, Tim Weber, Yangyumeng Chen, David T Riglar.

  Synthetic biology approaches such as whole-cell biosensing and 'sense-and-respond' therapeutics aim to enlist the vast sensing repertoire of gut microbes to drive cutting-edge clinical and research applications. However, well-characterised circuit components that sense health- and disease-relevant conditions within the gut remain limited. Here, we extend the flexibility and power of a biosensor screening platform using bacterial memory circuits. We construct libraries of sensory components sourced from diverse gut bacteria using a bespoke two-component system identification and cloning pipeline. Tagging unique strains using a hypervariable DNA barcode enables parallel tracking of thousands of unique clones, corresponding to ~150 putative biosensors, in a single experiment. Evaluating sensor activity and performance heterogeneity across various in vitro and in vivo conditions using mouse models, we identify several biosensors of interest. Validated hits include biosensors with relevance for autonomous control of synthetic functions within the mammalian gut and for non-invasive monitoring of inflammatory disease using faecal sampling. This approach will promote rapid biosensor engineering to advance the development of synthetic biology tools for deployment within complex environments.

Keywords:  Bacterial Biosensor; Gut Microbiome; Inflammation; Synthetic Biology

DOI:  https://doi.org/10.1038/s44320-025-00123-3
Biomater Sci. 2025 Jun 11.

Bioactive DNA hydrogel interfacing with living cells and extracellular vesicles.

Rui Zhang, Mingxing Liu, Hongjin Li, Yan Huang, Coo Yee Nah, Chi Yao, Dayong Yang.

Biological vesicles, such as living cells and extracellular vesicles (EVs) in biological systems, are important agents and regulators of life functions and play an irreplaceable role in physiological processes and disease progression. The maintenance of high bioactivity and structural integrity as well as selective isolation of target biological vesicles from complex biological systems are of great significance for downstream applications, such as early diagnosis, treatment and prognostic monitoring of major diseases. Bioactive hydrogel is a material made of hydrogel containing bioactive molecules that simulate living systems in vitro. By exploiting the unique molecular recognition and sequence programmability of deoxyribonucleic acid (DNA), DNA containing multifunctional modules serves as the material chemistry basis. Through molecular design and functional unit incorporation, these strategies enable the construction of DNA hydrogels capable of targeted vesicle recognition. This review discusses interactions between DNA hydrogels and biological vesicles, focuses on controllable release mechanisms of vesicles, and highlights recent advances in biomedical applications boosted by bioactive DNA hydrogels, including cell and EV isolation, cell engineering and three-dimensional (3D) culture, disease detection, and disease treatments. First, the interaction and controllable release mechanisms of bioactive DNA hydrogels are summarized, and relevant research based on these mechanisms is reviewed. Second, pioneering work in biomaterial applications is summarized. Finally, it is concluded with the challenges faced by DNA hydrogels and the future prospects of bioactive DNA hydrogels.

DOI: https://doi.org/10.1039/d5bm00690b