bims-livmat 2025-08-03 papers

bims-livmat

Biomed News

on Living materials

Issue of 2025–08–03
nine papers selected by
Sara Trujillo Muñoz, Leibniz-Institut für Neue Materialien

Ingestible optoelectronic capsules enable bidirectional communication with engineered microbes for controllable therapeutic interventions.
Genetic engineering of Saccharomyces boulardii: Tools, strategies and advances for enhanced probiotic and therapeutic applications.
How many plasmids can bacteria carry? A synthetic biology perspective.
Mathematical Modeling of Salmonella Cancer Therapies Demonstrates the Necessity of Both Bacterial Cytotoxicity and Immune Activation.
Synthetic biology approaches for restoring gut microbial balance and engineering disease-specific microbiome therapeutics.
Multiplex Genome Editing and Regulation in Bacillus subtilis with CRISPR-MAD7.
Activation of NF-κB Signaling by Optogenetic Clustering of IKKα and β.
Orchestrating Gut Disorders by Oral Delivery of a Living-Synthetic Hybrid Hydrogel.
Safety evaluation of Lactiplantibacillus plantarum N13: genomic, phenotypic, and toxicological assessment for probiotic applications.

Nat Microbiol. 2025 Aug;10(8): 1841-1853

Ingestible optoelectronic capsules enable bidirectional communication with engineered microbes for controllable therapeutic interventions.

Xinyu Zhang, Zhijie Feng, Hongxiang Li, Haoyan Yang, Lianyue Li, Chao Zhang, Pengxiu Dai, Hanxin Wang, Huimin Xue, Yaxin Wang, Dawei Sun, Xinyu Liu, Mingshan Li, Shenjunjie Lu, Jing Liu, Taofeng Du, Duo Liu, Hanjie Wang.

Engineered microbes can be used for biomolecular sensing and therapeutic interventions. However, they cannot be monitored and controlled while in vivo. Here we combine optogenetically engineered Escherichia coli Nissle 1917, an ingestible optoelectronic capsule and a wireless smartphone to establish a bidirectional biological-optical-electronic signal processing chain for diagnostic or therapeutic capabilities under user control. As a proof of concept, we engineered E. coli Nissle 1917 to detect inflammation-associated nitric oxide in the pig gut and generate a bioluminescent signal for diagnosis of colitis. This signal is transduced by the optoelectronic capsule into a wireless electrical signal and remotely monitored by a smartphone. Smartphone wireless signals activate LED irradiation in the optoelectronic capsule, in turn activating the microbial expression and secretion of an anti-inflammatory nanobody to alleviate colitis in pigs. This approach highlights the potential for integrating synthetic biology and optoelectronics for digital health monitoring and controllable intervention.

DOI: https://doi.org/10.1038/s41564-025-02057-w
Biotechnol Adv. 2025 Jul 30. pii: S0734-9750(25)00149-1. [Epub ahead of print] 108663

Genetic engineering of Saccharomyces boulardii: Tools, strategies and advances for enhanced probiotic and therapeutic applications.

João Paulo Carvalho, David Sáez Moreno, Lucília Domingues.

  Saccharomyces boulardii is a probiotic yeast that has been extensively studied in clinical trials, and it is used to treat several gut disorders. Its high survivability and the ability of secreting recombinant proteins, make S. boulardii an attractive delivery vessel for molecules of interest in the gut. Despite its natural mechanisms of action still not being fully understood, genetic engineering offers the advantage of rationally design the delivery of molecules of interest to the gut. As a yeast, S. boulardii can produce complex proteins with post translational modifications, an advantage when compared with bacterial probiotics. In addition, antibiotics can be co-administered with this yeast, increasing gut residence times and improving the positive effects on human health. This review aims to cover the genetic engineering advances and applications of genetically engineered S. boulardii. The similarity of this yeast with S. cerevisiae has made it possible to develop tools like CRISPR-Cas9, plasmid expression systems and gene integration techniques that have allowed the modification of S. boulardii. These genetic tools and modifications are discussed in detail according to the state of the art highlighting the most effective ones. Genetic engineering has increased the possible applications of S. boulardii, including immune response modulation, enhanced pathogen neutralization, anti-obesity strategies, vitamin production. Others have used these tools to tackle its limitations as probiotic compared to others commonly used such as lactic acid bacteria, increasing its residence times and allowing the development of biocontainment strategies. Current limitations and future directions of the field such as scalability, standardization and the lack of clinical data are also highlighted and discussed.

Keywords:  CRISPR-Cas9; Probiotic engineering; Probiotics; Saccharomyces boulardii

DOI:  https://doi.org/10.1016/j.biotechadv.2025.108663
Open Biol. 2025 Jul;15(7): 240378

How many plasmids can bacteria carry? A synthetic biology perspective.

Cholpisit Kiattisewee.

  Plasmids are pinnacle tools in synthetic biology and other biotechnological applications. They serve as the simplest approach to introduce recombinant DNA, which is then transcribed into RNA that functions as is or is translated into a protein of interest. Despite their widespread utility, the question 'how many plasmids can be used in this bacterium?' remains underexplored in the existing literature. In this article, I discuss the maintenance of multiple unique plasmids in bacteria through a microbial synthetic biology perspective, both in theoretical and practical aspects. I delve into the existing evidence of multi-plasmid systems, aiming to pinpoint the possible maximum number of unique plasmids a single microbe can carry. Finally, I highlight how the existing applications of multi-plasmid systems drive novel discovery and development in metabolic engineering, synthetic biology and other relevant areas in comparison to other non-plasmid strategies.

Keywords:  bacteria; plasmids; synthetic biology

DOI:  https://doi.org/10.1098/rsob.240378
Bioengineering (Basel). 2025 Jul 10. pii: 751. [Epub ahead of print]12(7):

Mathematical Modeling of Salmonella Cancer Therapies Demonstrates the Necessity of Both Bacterial Cytotoxicity and Immune Activation.

Lars M Howell, Neil S Forbes.

  Salmonella therapies are a promising tool for the treatment of solid tumors. Salmonella can be engineered to increase their tumor infiltration, cell killing abilities, and immunostimulatory properties. However, bacterial therapies have often failed in clinical trials due to poor characterization. Mathematical models are useful for predicting the immune response to cancer treatments and characterizing the properties of bacterial invasion. Herein we develop an ordinary differential equation-based model that combines bacterial therapies with classical anti-tumor immunotherapies. Our modeling results suggest that increasing bacterial localization to the tumor is key for therapeutic efficacy; however, increased intracellular invasion and direct bacterial mediated cytotoxicity does not reduce tumor growth. Further, the model suggests that enhancing T cell-mediated cell death by both bacterial stimulation of pro-inflammatory cytokines and activation of T cells via antigen cascade is critical for therapeutic efficacy. A balance of intracellular and extracellular Salmonella leads to more effective therapeutic response, which suggests a strategy for strain design to be tested in vivo. Overall, this model provides a system to predict which engineered features of Salmonella therapies lead to effective treatment outcomes.

Keywords:  Salmonella therapies; T cell cytotoxicity; cancer; immunoengineering; ordinary differential equation model

DOI:  https://doi.org/10.3390/bioengineering12070751
Microb Pathog. 2025 Jul 25. pii: S0882-4010(25)00656-4. [Epub ahead of print]207 107931

Synthetic biology approaches for restoring gut microbial balance and engineering disease-specific microbiome therapeutics.

Timoth Mkilima.

  The human gut microbiome plays a pivotal role in regulating digestion, immune function, and metabolic homeostasis. Disruption of this microbial equilibrium, known as dysbiosis, is increasingly linked to chronic conditions including inflammatory bowel disease (IBD), obesity, diabetes, and neurodegenerative disorders. Conventional interventions, such as probiotics and faecal microbiota transplantation (FMT), often yield inconsistent results due to individual microbiome variability and limited ecological stability. Engineered artificial microbial consortia (AMCs) have emerged as a next-generation strategy for precision modulation of the gut microbiome. This review critically examines cutting-edge advances in synthetic biology, CRISPR-based genome editing, metabolic engineering, and multi-omics integration that underpin the rational design of AMCs targeted to disease-specific microbial dysfunctions. Notably, this work presents an ecological precision engineering framework that integrates regional microbiome ecotypes, diet-responsive modular design, and adaptive metabolic modelling to ensure cross-population compatibility and stability. Enabling technologies, such as gut-on-a-chip platforms, high-throughput co-culture screening, and ecological modelling, are explored in the context of optimizing AMC performance across diverse host environments. Furthermore, the review highlights the potential for AMC-based therapeutics to be equitably scaled through regionally adapted templates, thereby extending microbiome-based healthcare to low-resource settings. By bridging ecological diversity and therapeutic specificity, this review presents a globally relevant roadmap for developing reproducible, adaptable, and inclusive microbiome interventions within the broader framework of precision medicine.

Keywords:  CRISPR genome editing; Gut dysbiosis; Metabolic engineering; Multi-omics integration; Precision medicine

DOI:  https://doi.org/10.1016/j.micpath.2025.107931
ACS Synth Biol. 2025 Jul 29.

Multiplex Genome Editing and Regulation in Bacillus subtilis with CRISPR-MAD7.

Nathalie Laforge, Magali Calabre, Matthieu Jules, Anne-Gaëlle Planson.

  With the advent of MAD7, a Cpf1-like nuclease, there has been a renewed focus on the development of CRISPR-based genome engineering tools in recent years. To improve genome engineering methodologies in B. subtilis, we revisited the potential of MAD7 for gene modification and expression interference. A key challenge in these endeavors is the limited transformation efficiency. To overcome this, we developed an efficient transformation protocol using strains overexpressing competence genes. Our results showed that although MAD7 together with a B. subtilis chromosome-targeting gRNA is lethal, enabling robust counterselection, we successfully engineered a strain carrying the MAD7-gRNA machinery in a reversibly inactivated state, marking a significant advance in the field. We demonstrated that both MAD7 and its catalytically inactive variant (dMAD7) can be conditionally regulated by inactivation at elevated temperatures. In addition, the MAD7-gRNA complex is effective for multiplex genome editing, allowing for the simultaneous deletion, mutation, or insertion of up to four loci, and enabling the combination of gene deletion, gene insertion, and point mutations. Furthermore, we established a strategy that achieves the simultaneous removal of MAD7 and the gRNA along with the desired genome edits. Altogether, this comprehensive study underscores the versatility of MAD7 for complex, scarless genome engineering and lays a strong foundation for further advancing genetic manipulation in B. subtilis.

Keywords:  Bacillus subtilis; CRISPR; Cas12; MAD7; genome editing

DOI:  https://doi.org/10.1021/acssynbio.5c00274
Adv Biol (Weinh). 2025 Jul 29. e00384

Activation of NF-κB Signaling by Optogenetic Clustering of IKKα and β.

Alexandra Anna Maria Fischer, Markus Michael Kramer, Miguel Baños, Merlin Moritz Grimm, Manfred Fliegauf, Bodo Grimbacher, Gerald Radziwill, Sven Rahmann, Wilfried Weber.

  Molecular optogenetics allows the control of molecular signaling pathways in response to light. This enables the analysis of the kinetics of signal activation and propagation in a spatially and temporally resolved manner. A key strategy for such control is the light-inducible clustering of signaling molecules, which leads to their activation and subsequent downstream signaling. In this work, an optogenetic approach is developed for inducing graded clustering of different proteins that are fused to eGFP, a widely used protein tag. To this aim, an eGFP-specific nanobody is fused to Cryptochrome 2 variants engineered for different orders of cluster formation. This is exemplified by clustering eGFP-IKKα and eGFP-IKKβ, thereby achieving potent and reversible activation of NF-κB signaling. It is demonstrated that this approach can activate downstream signaling via the endogenous NF-κB pathway and is thereby capable of activating both an NF-κB-responsive reporter construct as well as endogenous NF-κB-responsive target genes as analyzed by RNA sequencing. The generic design of this system is likely transferable to other signaling pathways to analyze the kinetics of signal activation and propagation.

Keywords:  NF‐κB signaling; oligomerization; optogenetics; phase separation; synthetic biology

DOI:  https://doi.org/10.1002/adbi.202400384
ACS Nano. 2025 Jul 25.

Orchestrating Gut Disorders by Oral Delivery of a Living-Synthetic Hybrid Hydrogel.

Kun Zhang, Yi Liang, Qiao Chen, Shirong Zhang, Yanbing Liu, Wei Wu, Li Zhu, Kai Qu, Xian Qin, Yidan Chen, Da Sun, Xu Qiu, Minjun Ye, Jiawei Li, Fei Yan, Chunhui Lang, Lixin Xu, Bo Xiao, Jinyao Liu, Wei Wu.

  Elevated intestinal inflammation, reactive oxygen species (ROS), and gut microbiota dysbiosis are prominent features of various intestinal disorders. In this work, we develop an oral inulin-based hydrogel delivery system (LICH) containing living probiotics and hyaluronic acid (HA)-modified carbon dot (CD) nanoenzymes to orchestrate gut disorders. Utilizing the hydrophobic properties of HA under acidic conditions, LICH contracts its network to safeguard probiotics during gastric transit. Upon reaching the intestine, HA-modified CD enables spatiotemporal targeting of lesion sites, achieving anti-inflammatory and ROS-scavenging effects. Concurrently, probiotics and inulin synergistically restore a balanced gut microbiota. In a murine model of ulcerative colitis, LICH exhibits prolonged intestinal retention and significantly ameliorates the pathological microenvironment. Transcriptomic and metabolomic analyses further reveal that LICH exerts its therapeutic effects primarily by modulating inflammation, scavenging ROS, and promoting intestinal barrier repair. This study provides a versatile oral platform to regulate multifaceted pathological characteristics for the treatment of intestinal disorders.

Keywords:  carbon dot nanoenzymes; gut microbiota; hybrid hydrogel; intestinal disorders; pH-responsive pore contraction

DOI:  https://doi.org/10.1021/acsnano.5c08982
Benef Microbes. 2025 Jul 28. 1-20

Safety evaluation of Lactiplantibacillus plantarum N13: genomic, phenotypic, and toxicological assessment for probiotic applications.

Y Qi, W Si, Y Fan, Y Dong, Z Gai, Y Zhang.

Probiotics offer numerous health benefits and are increasingly incorporated into dietary supplements and food products. Rigorous safety evaluations are essential to ensure their suitability for human consumption. This study evaluates the safety profile of Lactiplantibacillus plantarum N13, isolated from traditional fermented dairy products, through genomic and phenotypic analyses. Whole-genome sequencing confirmed general length of strain N13 (containing three plasmids) is about 3,318,516 bp, GC content is 44.4% and the absence of antibiotic resistance and virulence genes. Antibiotic susceptibility tests demonstrated that N13 is sensitive to ampicillin (1 μg/ml), gentamycin (4 μg/ml), kanamycin (32 μg/ml), erythromycin (0.5 μg/ml), clindamycin (0.25 μg/ml), tetracycline (32 μg/ml), and chloramphenicol (8 μg/ml), meeting the European Food Safety Authority (EFSA) guidelines. Additionally, genome analysis confirmed that N13 lacks genes related to biogenic amine biosynthesis, indicating its low risk of biogenic amine production. Scanning electron microscopy confirmed that N13 cells exhibited typical L. plantarum morphology. Phenotypic assays demonstrated that N13 is non-hemolytic and lacks harmful enzyme activity, including α-galactosidase, β-glucuronidase, and α-mannosidase. Acute and 28-day oral toxicity tests demonstrated that N13 was well tolerated in both Immunocompetent Research mice and Sprague Dawley rats, with no observable toxic effects or adverse changes even at high doses. At the recommended dose (0.5 × 1010 CFU/kg), N13 exhibited good oral safety. These findings establish L. plantarum N13 as a safe and promising probiotic strain, paving the way for its further application in dietary and functional food products.

DOI: https://doi.org/10.1163/18762891-bja00093