bims-biopma Biomed News
on Bioprogrammable materials
Issue of 2025–06–22
six papers selected by
Shrikrishnan Sankaran, Leibniz-Institut für Neue Materialien
  1. Applications of bacteriophages in precision engineering of the human gut microbiome.
  2. Drug-delivery strategies using biomaterials in the field of nerve regeneration.
  3. The Role of Artificial Intelligence in Advancing Biosensor Technology: Past, Present, and Future Perspectives.
  4. Dissecting the physics of bacterial biofilms with agent-based simulations.
  5. Addressing challenges in microbial manufacturing: Systematic microbial biotechnology.
  6. Investigating the Potential of Division of Labor in Synthetic Bacterial Communities for the Production of Violacein.
  1. Eng Microbiol. 2025 Mar;5(1): 100189
    Applications of bacteriophages in precision engineering of the human gut microbiome.
    Xiaoxian Kuang, Juntao Shen, Linggang Zheng, Yi Duan, Yingfei Ma, Elaine Lai-Han Leung, Lei Dai.
      As our understanding of the role of the gut microbiome in human diseases deepens, precision engineering of the gut microbiome using bacteriophages has gained significant attention. Herein, we review the recent advances in bacteriophage-mediated modulation of the gut microbiome, discuss approaches at the ecological and genetic levels, and summarize the challenges and strategies pertinent to each level of intervention. Drawing on the structural attributes of bacteriophages in the context of precision engineering, we examined the latest developments in the field of phage administration. Gaining a nuanced understanding of microbiome manipulation will yield tailored strategies and technologies. This could revolutionize the prevention and treatment of diseases linked to gut pathogens and offer new avenues for the therapeutic use of bacteriophages.
    Keywords:  Bacteriophages; Human gut microbiome; Microbiome engineering
    DOI:  https://doi.org/10.1016/j.engmic.2025.100189
  2. Neural Regen Res. 2025 Jun 19.
    Drug-delivery strategies using biomaterials in the field of nerve regeneration.
    Linbin Xu, Chao Zhou, Xu Wang, Cunyi Fan.
       ABSTRACT: Neural injuries can cause considerable functional impairments, and both central and peripheral nervous systems have limited regenerative capacity. The existing conventional pharmacological treatments in clinical practice show poor targeting, rapid drug clearance from the circulatory system, and low therapeutic efficiency. Therefore, in this review, we have first described the mechanisms underlying nerve regeneration, characterized the biomaterials used for drug delivery to facilitate nerve regeneration, and highlighted the functionalization strategies used for such drug-delivery systems. These systems mainly use natural and synthetic polymers, inorganic materials, and hybrid systems with advanced drug-delivery abilities, including nanoparticles, hydrogels, and scaffoldbased systems. Then, we focused on comparing the types of drug-delivery systems for neural regeneration as well as the mechanisms and challenges associated with targeted delivery of drugs to facilitate neural regeneration. Finally, we have summarized the clinical application research and limitations of targeted delivery of these drugs. These biomaterials and drug-delivery systems can provide mechanical support, sustained release of bioactive molecules, and enhanced intercellular contact, ultimately reducing cell apoptosis and enhancing functional recovery. Nevertheless, immune reactions, degradation regulation, and clinical translations remain major unresolved challenges. Future studies should focus on optimizing biomaterial properties, refining delivery precision, and overcoming translational barriers to advance these technologies toward clinical applications.
    Keywords:  RNA; biomaterials; clinical trial; drug; drug-delivery strategy; drug-loading strategy; drug-release strategy; nerve regeneration; peripheral nerve; tissue engineering
    DOI:  https://doi.org/10.4103/NRR.NRR-D-25-00027
  3. Adv Mater. 2025 Jun 16. e2504796
    The Role of Artificial Intelligence in Advancing Biosensor Technology: Past, Present, and Future Perspectives.
    Tuğba Akkaş, Mahshid Reshadsedghi, Mustafa Şen, Volkan Kılıç, Nesrin Horzum.
      Integrating artificial intelligence (AI) into biosensor technology enables data processing, quantitative analysis, real-time decision-making, and adaptive sensing capabilities through advanced pattern recognition and predictive modeling. In addition, AI has the potential to drive innovation in the design of advanced materials for biosensing applications by reducing the reliance on trial-and-error methods. This review explores the transformative impact of AI on biosensor technology in the context of historical development, current status, and future prospects. It begins with an overview of the evolution of AI, biosensor technology, and their integration. Comparative analysis of AI-driven innovations in optical, fluorometric, and electrochemical biosensors is presented, highlighting how AI can improve sensor performance. The role of advanced materials on the development of AI-assisted biosensors is also discussed as the choice of material has a profound effect on biosensor capabilities. Applications of AI-assisted biosensors are comprehensively explored across healthcare, environmental monitoring, food safety, and agriculture. This study concludes by addressing challenges, opportunities, ethical concerns, and future research directions, providing a comprehensive and up-to-date resource for researchers.
    Keywords:  Internet of Things (IoT); artificial intelligence; biosensors; wearable devices
    DOI:  https://doi.org/10.1002/adma.202504796
  4. Curr Opin Solid State Mater Sci. 2025 Jul;pii: 101228. [Epub ahead of print]37
    Dissecting the physics of bacterial biofilms with agent-based simulations.
    Kee-Myoung Nam, Changhao Li, Bastiaan J R Cockx, Danh T Nguyen, Ying Li, Jan-Ulrich Kreft, Jing Yan.
      Biofilms are surface-attached bacterial communities encased within extracellular matrices (ECMs) of biopolymers that play many significant roles in health and society. Biofilms are versatile, living biomaterials that are resilient to a wide range of external perturbations, primarily due to the ECM, which consists of a complex network of polymeric macromolecules. Newly established platforms for live biofilm imaging at single-cell resolution have revealed a wealth of novel insights into the emergence of cellular organization within a developing biofilm. This has, in turn, necessitated the development of modeling approaches that can pinpoint the mechanistic origins of this organization. In this review, we discuss the use of agent-based models (ABMs) as a general framework for simulating the development of bacterial colonies and biofilms. We describe the ingredients that are typically included in an ABM, together with the biological entity or process that each such ingredient represents, and the assumptions that underlie its precise formulation within the model. We then discuss a selection of recent studies in which ABMs have been used to investigate the physical mechanisms that govern biofilm development, focusing on our recent work on orientational ordering within Vibrio cholerae biofilms. Finally, we describe the numerous ways in which we foresee that ABMs can be leveraged to further our understanding of biofilm development.
    Keywords:  Bacterial biofilms; agent-based models; bacterial communities; extracellular matrix; individual-based models; mechanical interactions; simulations
    DOI:  https://doi.org/10.1016/j.cossms.2025.101228
  5. Innovation (Camb). 2025 Jun 02. 6(6): 100871
    Addressing challenges in microbial manufacturing: Systematic microbial biotechnology.
    Lijuan Liu, Fan Wang, Lei Wang, Xinglin Jiang, Haibo Zhang.
      Microbial manufacturing offers an alternative approach to producing chemicals and materials in a sustainable and environmentally friendly manner. Despite its significance and widespread attention, various challenges persist in its industrial application. We propose a systematic approach to microbial biotechnology-a comprehensive framework for developing customized technologies tailored to the unique characteristics of the entire process for specific products. It utilizes approaches such as simplifying the process, sequential rearrangement, and coupling steps to systematically and holistically address the bottlenecks of the entire process in microbial manufacturing, aiming to achieve optimal economic and environmental benefits. This method involves the integration of multiple disciplines, including enzymology, synthetic biology, metabolic engineering, fermentation, separation engineering, and artificial intelligence (AI) technology. Here, we present several cases involving various stages of product bioproduction, developed under the concept of systematic microbial biotechnology, to demonstrate its effectiveness and advantages. The development and application of these technological concepts hold significant potential to shape the future of a sustainable circular bioeconomy driven by microbial manufacturing.
    DOI:  https://doi.org/10.1016/j.xinn.2025.100871
  6. ACS Synth Biol. 2025 Jun 17.
    Investigating the Potential of Division of Labor in Synthetic Bacterial Communities for the Production of Violacein.
    Harman Mehta, Jose Jimenez, Rodrigo Ledesma-Amaro, Guy-Bart Stan.
      With advancements in synthetic biology and metabolic engineering, microorganisms can now be engineered to perform increasingly complex functions, which may be limited by the resources available in individual cells. Introducing heterologous metabolic pathways introduces both genetic burden due to the competition for cellular transcription and translational machinery, as well as metabolic burden due to the redirection of metabolic flux from the native metabolic pathways. Division of labor in synthetic microbial communities offers a promising approach to enhance metabolic efficiency and resilience in bioproduction. By distributing complex metabolic pathways across multiple subpopulations, the resource competition and metabolic burden imposed on an individual cell are reduced, potentially enabling more efficient production of target compounds. Violacein is a high-value pigment with antitumor properties that exemplifies such a challenge due to its complex bioproduction pathway, imposing a significant metabolic burden on host cells. In this study, we investigated the benefits of division of labor for violacein production by splitting the violacein bioproduction pathway between two subpopulations of Escherichia coli-based synthetic communities. We tested several pathway splitting strategies and reported that splitting the pathway into two subpopulations expressing VioABE and VioDC at a final composition of 60:40 yields a 2.5-fold increase in violacein production as compared to a monoculture. We demonstrated that the coculture outperforms the monoculture when both subpopulations exhibit similar metabolic burden levels, resulting in comparable growth rates, and when both subpopulations are present in sufficiently high proportions.
    Keywords:  division of labor; metabolic engineering; precision fermentation; synthetic biology; synthetic microbial communities; violacein biosynthesis
    DOI:  https://doi.org/10.1021/acssynbio.5c00120
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