Noah Remy , David Touboul , Edith Nicol , Séverine Humbert , Luminita Duma , Pedro Lameiras , Jean-Hugues Renault , Gabriel Paës
{"title":"Chemical imaging of lignocellulosic biomass: Mapping plant chemistry","authors":"Noah Remy , David Touboul , Edith Nicol , Séverine Humbert , Luminita Duma , Pedro Lameiras , Jean-Hugues Renault , Gabriel Paës","doi":"10.1016/j.biotechadv.2025.108696","DOIUrl":"10.1016/j.biotechadv.2025.108696","url":null,"abstract":"<div><div>Lignocellulosic biomass (LB), which encompasses various plant samples, requires thorough characterization to optimize its use as a carbon resource. Chemical imaging simultaneously provides chemical and spatial information, offering significant benefits for LB analysis. This review presents an overview of the most advanced techniques for achieving this goal. By combining spectrometry and microscopy, microspectroscopy enables chemical imaging using various irradiation sources (IR, Raman, fluorescence, among others), allowing for the quantitative mapping of key LB components such as lignins, cellulose, and hemicelluloses. Mass Spectrometry Imaging (MSI) generates a mass spectrum for each spot of a sample thereby creating a chemical image pixel-by-pixel. MSI techniques like Matrix-Assisted Laser Desorption/Ionization (MALDI), down to 2–5 μm spatial resolution, and Secondary Ion Mass Spectrometry (SIMS), down to 300 nm for molecular analysis, effectively map small molecules in LB. In contrast, Desorption ElectroSpray Ionization (DESI) has been applied to plant extracts but remains largely unexplored for LB applications. Nuclear Magnetic Resonance (NMR) provides insight into various LB properties too. Solid-state NMR (ssNMR) and Dynamic Nuclear Polarization (DNP) help elucidate the structure of LB, sometimes aided by 3D atomistic modeling, whereas micro–Magnetic Resonance Imaging (micro-MRI) and Time-Domain (TD-NMR) probe the impact of water on LB properties.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"85 ","pages":"Article 108696"},"PeriodicalIF":12.5,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kunlong Qi , Zheliang Liu , Felix Kwame Amevor , Dan Xu , Wei Zhu , Tong Li , Yingjie Wang , Liuting Wu , Gang Shu , Xiaoling Zhao
{"title":"Emerging research insights and future perspectives on the advancement of eccDNA: A comprehensive review","authors":"Kunlong Qi , Zheliang Liu , Felix Kwame Amevor , Dan Xu , Wei Zhu , Tong Li , Yingjie Wang , Liuting Wu , Gang Shu , Xiaoling Zhao","doi":"10.1016/j.biotechadv.2025.108693","DOIUrl":"10.1016/j.biotechadv.2025.108693","url":null,"abstract":"<div><div>Extrachromosomal circular DNA (eccDNA) is a class of chromosome-independent circular DNA molecules found in diverse organisms, including plants, animals, and microorganisms. Recent research has highlighted its roles in gene regulation, genome stability, and disease pathogenesis, with growing recognition of eccDNA as a valuable biomarker for cancer diagnosis, prognosis, and monitoring in precision medicine. Studies have also linked eccDNA to non-neoplastic diseases and normal tissue biology, broadening its biological significance beyond malignancies. Technological advancements have greatly enhanced the detection and characterization of eccDNA, enabling a better understanding of its formation, diversity, and functions. In agriculture, eccDNA research has shown potential applications for improving livestock productivity and health management. This review provides a comprehensive analysis of the current state of eccDNA research, focusing on its formation mechanisms, classification, biological functions, and implications in both disease and agriculture. Despite significant progress, challenges remain in fully understanding the biological roles, formation processes, and practical applications of eccDNA. Future research should adopt interdisciplinary approaches that integrate genomics, bioinformatics, and material science to further elucidate the complexities of eccDNA. By advancing our knowledge of eccDNA, researchers may unlock novel diagnostic, therapeutic, and biotechnological innovations, particularly in cancer treatment and livestock breeding programs.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108693"},"PeriodicalIF":12.5,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yeonju Lee , Bohyun Oh , Sumin Kang , Sumin Kim , Young-Pil Kim
{"title":"Engineering cyclized biomolecules for advanced diagnostic and therapeutic applications","authors":"Yeonju Lee , Bohyun Oh , Sumin Kang , Sumin Kim , Young-Pil Kim","doi":"10.1016/j.biotechadv.2025.108694","DOIUrl":"10.1016/j.biotechadv.2025.108694","url":null,"abstract":"<div><div>Nucleic acids, peptides, and proteins demonstrate remarkable structural diversity and play essential roles in various biological processes. These biomolecules function as ligands, diagnostic agents, and therapeutic cargoes. However, their practical applications are often limited by inherent instability and inefficient delivery for targeted diagnosis and therapy. Cyclization has emerged as a promising solution, endowing these biomolecules with enhanced conformational rigidity, resistance to degradation, and a broader range of biological activities. Cyclic architectures not only enhance antitumor, anti-inflammatory, and anti-infective properties, but also eliminate the need for auxiliary carriers in some applications. This deliberate cyclization further enables precise control over binding affinity, stability, and membrane permeability. In this review, we cover diverse engineering methods for creating cyclized biomolecules and explore their applications in biosensing, targeted imaging, and delivery. Moving beyond naturally occurring forms, we highlight rationally engineered cyclized constructs that substantially expand their theranostic landscape in biology and biotechnology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108694"},"PeriodicalIF":12.5,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144900411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zehan Shi , Jiaxuan Li , Fengmei Zhu , Xiaojing Liu , Jiefang Zhou , Jun Li , Wentao Xu
{"title":"Multidimensional strategies for efficient heterologous protein expression in Aspergillus niger","authors":"Zehan Shi , Jiaxuan Li , Fengmei Zhu , Xiaojing Liu , Jiefang Zhou , Jun Li , Wentao Xu","doi":"10.1016/j.biotechadv.2025.108690","DOIUrl":"10.1016/j.biotechadv.2025.108690","url":null,"abstract":"<div><div>Microbial protein is a promising alternative to animal and plant proteins. <em>Aspergillus niger</em>, a generally recognized as safe (GRAS) microorganism, is frequently used for heterologous protein production, although its expression efficiency is constrained by multiple factors, including gene transcription, metabolic flux distribution, protein folding, and secretion pathways. However, constructing universal <em>Aspergillus niger</em> chassis cells for efficient protein production remains challenging due to the diverse properties of different proteins. With advancements in synthetic biology, numerous molecular biology tools and metabolic engineering strategies have been employed to address these issues. This article summarizes and discusses the latest progress in enhancing heterologous protein production from five dimensions: expression systems, secretion pathways, metabolic flux, intelligent fermentation, and systematic optimization through multi-omics integration. Additionally, it prospects the efficient and sustainable production of heterologous proteins by <em>Aspergillus niger</em>.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108690"},"PeriodicalIF":12.5,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144890812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Harnessing biological nitrogen fixation: Multi-scale engineering for self-sustaining agroecosystems","authors":"Wanjing Wu, Haiyang Hu, Weiwei Wang, Ping Xu, Hongzhi Tang","doi":"10.1016/j.biotechadv.2025.108687","DOIUrl":"10.1016/j.biotechadv.2025.108687","url":null,"abstract":"<div><div>Certain prokaryotic microorganisms possess the extraordinary ability to convert atmospheric nitrogen gas into ammonia in a process known as biological nitrogen fixation. Harnessing this process as a substitute for chemical nitrogen fertilizers offers substantial benefits for agricultural productivity. Improving the efficiency of nitrogen fixation and enabling crops to fix nitrogen biologically are crucial research goals. This review explores molecular mechanisms governing nitrogenase activity, engineering strategies for enhancing nitrogen fixation efficiency in non-diazotrophic hosts, and evaluates synthetic biology approaches for establishing robust nitrogen-fixing systems. We emphasize the integration of multi-scale engineering – from nitrogen fixation circuit design in microbial chassis to rhizosphere microbiome reprogramming to engineered nitrogen-fixing crops and field applications at the ecosystem level – as critical pathways toward creating self-sustaining agroecosystems. We conclude by discussing key challenges and identifying research priorities to expand the practical applications of biological nitrogen fixation. This review provides a framework for developing multi-layered bioengineering solutions that enhance crop productivity while reducing ecological impacts, ultimately advancing the realization of self-regulating agricultural ecosystems.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108687"},"PeriodicalIF":12.5,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bio-upcycling PET waste: Advances in enzymatic hydrolysis and biosynthesis of value-added products","authors":"Yu Zhou , Jiaxing Zhang , Shengping You , Congqiang Zhang , Wei Qi","doi":"10.1016/j.biotechadv.2025.108685","DOIUrl":"10.1016/j.biotechadv.2025.108685","url":null,"abstract":"<div><div>With excellent mechanical properties and chemical stability, poly (ethylene terephthalate) (PET), an engineering plastic, is widely applied in textiles and packaging. However, the widespread use and low biodegradability of PET have resulted in significant environmental pollution. Recent advances in PET hydrolase discovery and engineering have driven the rapid advancement of PET bio-recycling, while efficient PET hydrolases can depolymerize PET into monomers under mild conditions, providing a sustainable approach to potentially addressing the plastic pollution issue. However, PET enzymatic hydrolysis still faces some technical challenges, such as poor stability of the hydrolases and low efficiency in degrading high-crystalline PET. Thus, this review summarizes recent advances in strategies to enhance the efficiency of PET enzymatic hydrolysis and explores the interplay of factors affecting PET hydrolysis efficiency. Furthermore, we highlight the progress in metabolic engineering approaches for the biotransformation of PET degradation products into higher value chemicals, providing insights into achieving efficient PET bio-recycling. This review systematically integrates key factors for enhancing the PET enzymatic hydrolysis efficiency and showcases successful examples of PET waste further valorization, providing valuable references and insights for the industrialization of PET bio-upcycling.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108685"},"PeriodicalIF":12.5,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tae-Eui Lee , Kyung-Chul Shin , Jin-Byung Park , Deok-Kun Oh
{"title":"Specialized pro-resolving mediators: Biosynthetic pathways, biocatalytic synthesis, and applications","authors":"Tae-Eui Lee , Kyung-Chul Shin , Jin-Byung Park , Deok-Kun Oh","doi":"10.1016/j.biotechadv.2025.108682","DOIUrl":"10.1016/j.biotechadv.2025.108682","url":null,"abstract":"<div><div>Specialized pro-resolving mediators (SPMs), a class of di- and trihydroxy fatty acids derived from C20- and C22-polyunsaturated fatty acids, are endogenously produced by human M2 macrophages, polymorphonuclear leukocytes, and other immune and structural cells. They play crucial roles in the resolution of inflammation and infection. Owing to their potent bioactivities, SPMs have attracted considerable interest for applications in food, cosmetics, and clinical therapeutics. Therefore, achieving high concentrations of these mediators is essential. This review provides a comprehensive overview of the nomenclature, classification, biological functions, biosynthetic pathways, and recent advances in the biocatalytic synthesis of SPMs, including lipoxins, resolvins, protectins, and maresins. We examine the biosynthetic pathways: from arachidonic acid to lipoxins; from eicosapentaenoic acid, docosahexaenoic acid, and n-3 docosapentaenoic acid to resolvin E, D, and T series, respectively; and from docosahexaenoic acid to protectins, and maresins. These pathways are catalyzed by fatty acid oxygenases, such as lipoxygenases (LOXs), aspirin-triggered cyclooxygenases, and cytochrome P450 monooxygenases, in combination with hydrolases and peroxidases. Recent advances in microbial biocatalysis, particularly through the use of recombinant cells expressing microbial LOXs, have enabled the efficient synthesis of SPMs. The discovery of microbial double‑oxygenating LOXs has significantly improved production yields, achieving gram-per-liter scale. To further enhance the biocatalytic synthesis, this review discusses enzyme discovery, protein engineering, and biocatalysis optimization strategies aimed at enhancing SPM production. Notably, computational and artificial intelligence-driven approaches are emerging as powerful tools for the discovery and engineering of high-efficiency LOXs, providing a promising route to improve the biocatalytic synthesis of SPMs.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108682"},"PeriodicalIF":12.5,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Farhan Ahmad , Kasun H. Bodawatta , Michael Poulsen , Daochen Zhu
{"title":"Advancing approaches to cultivate industrially and ecologically relevant microorganisms from termite guts","authors":"Farhan Ahmad , Kasun H. Bodawatta , Michael Poulsen , Daochen Zhu","doi":"10.1016/j.biotechadv.2025.108676","DOIUrl":"10.1016/j.biotechadv.2025.108676","url":null,"abstract":"<div><div>The termite gut harbours a remarkably dense and diverse consortium of symbiotic microbes, encompassing archaeal, bacterial, and eukaryotic taxa. These symbiotic communities hold intricate ecological processes and a pronounced potential for exploitation across multifaceted domains, including industrially important enzymes, biofuels, pharmaceuticals, and bioremediation. Despite the conspicuous richness, a substantial portion of microbial assemblages inhabiting the termite gut remains undiscovered and inadequately characterized. Although traditional culture-based and culture-independent molecular-based technologies are broadly used to study termite gut microbiota, they more recent frequently encounter limitations in the isolation, culturing, and characterization of less prevalent microbial lineages and are biased toward certain taxa. The rapid development of molecular techniques has greatly promoted the identification and genomic potential of microbes in termite guts, revealing hidden diversity and application potential. However, limitations in culture-based approaches to build on genomic insights have hampered our understanding of the ecology of most of these microbes and the capitalisation on their properties. To help improve culturomics approaches for termite gut microbes, we provide an overview of past and emerging methodologies for isolation and cultivation of symbiotic microbes. In doing so, we highlight future directions and current challenges that need to be overcome to advance these approaches.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108676"},"PeriodicalIF":12.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dana B. Griffiths , Ravi P. Tiwari , Daniel V. Murphy , Colin Scott
{"title":"Haloferax and the Haloferacaceae: Potential role in bioindustry","authors":"Dana B. Griffiths , Ravi P. Tiwari , Daniel V. Murphy , Colin Scott","doi":"10.1016/j.biotechadv.2025.108666","DOIUrl":"10.1016/j.biotechadv.2025.108666","url":null,"abstract":"<div><div>Members of the <em>Haloferacaceae</em>, a family of extremely halophilic archaea, exhibit unique physiological and genetic traits that make them promising candidates for biotechnological applications. These organisms thrive in hypersaline environments and tolerate a wide range of stresses, including high temperatures, UV radiation, and toxic metals. Their ability to grow on agro-industrial waste, coupled with their inherent resistance to contamination and the simplicity of downstream processing via osmotic shock, makes them ideal for sustainable bioproduction. Species such as <em>Haloferax mediterranei</em> have been explored for the biosynthesis of polyhydroxyalkanoates, carotenoids, halocins, and enzymes functional under extreme conditions. Species of <em>Haloferacaceae</em> can also bioremediate saline environments contaminated with hydrocarbons, heavy metals, and nitrogenous waste. Advances in genetic tools, including CRISPR interference, inducible promoters, and knock-in/knock-out systems, particularly in <em>H. volcanii</em>, have significantly expanded the engineering potential of these archaea. However, there remains a need for further innovation in genetic tools for this family. This review highlights the expanding potential of the <em>Haloferacaceae</em> for circular bioeconomy applications and identifies key technological gaps limiting their broader industrial adoption.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108666"},"PeriodicalIF":12.5,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rahul Mahadev Shelake , Muhammad Abdullah Khalid , Jae-Yean Kim
{"title":"Microalgal bioengineering for futuristic applications in synthetic and space biology","authors":"Rahul Mahadev Shelake , Muhammad Abdullah Khalid , Jae-Yean Kim","doi":"10.1016/j.biotechadv.2025.108665","DOIUrl":"10.1016/j.biotechadv.2025.108665","url":null,"abstract":"<div><div>Extreme environmental conditions on Earth and in space pose significant challenges to sustaining life. As global population growth exacerbates issues such as climate change, food security, and resource depletion, innovative solutions are needed. Similarly, confined and isolated environments on Earth and in space lack essential life-supporting resources such as oxygen, water, and food. Combined with the challenges of microgravity and radiation exposure, these factors present substantial obstacles to advancing human space exploration. Biotechnological innovations are essential to enable long-term habitation in extraterrestrial environments. Microalgae, with their high photosynthetic efficiency, diverse metabolic capabilities, omnipresence in the natural world, and adaptability to extreme conditions, have emerged as promising candidates for synthetic biology (SynBio) applications. Recent advancements in genetic engineering, particularly CRISPR-based genome editing (GE), provide unprecedented opportunities to enhance microalgal traits for the sustainable bioproduction of oxygen, water, and nutrition in space missions. Engineered microalgae hold immense potential for bioregenerative life support systems (BLSS), supplying essential resources while reducing logistical constraints. This review examines the integration of SynBio and GE in microalgae, highlighting their role in space research and environmental sustainability. We discuss key advancements in CRISPR and innovative (omics, synthetic gene circuits, artificial cells, nanotechnology, and artificial intelligence) technologies relevant to metabolic pathway engineering and space-adapted microalgal systems, underscoring their transformative potential in addressing both terrestrial and extraterrestrial challenges.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"84 ","pages":"Article 108665"},"PeriodicalIF":12.5,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144738156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}