Mohammadreza Rahimian, Elham Mohammadi, Mohammad Aghazadeh-Soltan-Ahmadi, Alireza Samari, Nosratollah Zarghami
{"title":"An update on experimental to large-scale production of bacteriophages against superbugs: a review.","authors":"Mohammadreza Rahimian, Elham Mohammadi, Mohammad Aghazadeh-Soltan-Ahmadi, Alireza Samari, Nosratollah Zarghami","doi":"10.1080/07388551.2025.2531446","DOIUrl":"https://doi.org/10.1080/07388551.2025.2531446","url":null,"abstract":"<p><p>The escalating problem of antibiotic resistance has sparked renewed interest in bacteriophages (phages) as potential substitutes for conventional antibiotics in treating infectious diseases, improving food safety, and advancing sustainable agriculture. The key phage research processes, such as host range, burst size, and environmental stability tests, strongly influence phage production processes. Hence, the standardization of the mentioned techniques must be prioritized. The introduction of high-throughput sequencing technologies with high accuracy and the emergence of novel bioinformatic tools to analyze the resulting raw molecular data provide comprehensive identification of phages and phage-verse (the universe of phage). While encapsulation of phages was studied comprehensively before, the production of encapsulated phages is still unclear. Moreover, recent advances in artificial intelligence (AI) contribute to phage research by increasing the accuracy of bioinformatic tools, improving resistance profiling, and facilitating phage host prediction. Incorporating AI promises a future of automated, precisely tailored phage applications. This review covers efficient techniques appropriate for industrial and agricultural applications as well as large-scale phage production methods, covering upstream and downstream processing. Also, encapsulated phage production and AI-based automated systems in various applications are proposed in this review. By covering both present issues and potential future uses of phages in the fight against antibiotic resistance, this review seeks to give academics and industry experts the fundamental information they need to advance phage-based solutions.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-20"},"PeriodicalIF":7.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Astaxanthin: nature's multifunctional molecule, natural sources, health benefits, and process advancements.","authors":"Vaibhav Sunil Tambat, Reeta Rani Singhania, Yamini Sumathi, Chiu-Wen Chen, Cheng-Di Dong, Philippe Michaud, Anil Kumar Patel","doi":"10.1080/07388551.2025.2537816","DOIUrl":"https://doi.org/10.1080/07388551.2025.2537816","url":null,"abstract":"<p><p>Astaxanthin, a natural di-keto carotenoid xanthophyll, is a highly valued nutraceutical and food ingredient due to its potent health benefits, including: anti-inflammatory, antioxidant, anti-cancer, cardiovascular, and anti-diabetic effects. This review examines the primary natural sources of: astaxanthin microalgae, yeast, bacteria, and plants, with a focus on microalgae due to their superior accumulation potential and bioactivity. It explores the growing prospects for large-scale astaxanthin production, highlighting advancements in both upstream and downstream processes. Upstream innovations include enhanced bioprocess designs that improve biomass yield, light and stress tolerance. Downstream, sustainable extraction methods such as aqueous two-phase systems with deep eutectic solvents (99.64% recovery) and high-pressure supercritical CO<sub>2</sub> extraction have improved efficiency and scalability. Additionally, eco-friendly techniques, such as bead milling and pulsed electric field permeabilization offer cost-effective solutions, among other cell disruption techniques, and ensure higher yields. This study provides a comprehensive overview of recent advances in astaxanthin production and extraction, aligned with the Sustainable Development Goals (SDGs) linked to health and well-being (SDG 3) and responsible consumption and production (SDG 12).</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-19"},"PeriodicalIF":7.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Whole recombinant yeast-based vaccines: concept, importance, issues, and future scope.","authors":"Ravinder Kumar, Vartika Srivastava, Aijaz Ahmad, Santi M Mandal, Piyush Baindara","doi":"10.1080/07388551.2025.2536808","DOIUrl":"https://doi.org/10.1080/07388551.2025.2536808","url":null,"abstract":"<p><p>Despite their tremendous benefits to society, currently licensed vaccines, including mRNA-based ones, are far from ideal and suffer several issues. Common problems associated with all types of vaccine formulations currently in clinical use include thermolabile nature, poor shelf life at ambient temperature, and the continuous need for cold chain and sometimes ultra-low temperature. Several approaches have been tested in the past to surmount these shortcomings. This review discusses the advantages of whole yeast (WY) or whole recombinant yeast-based (WRY) vaccines compared to other vaccine formulations to overcome the above-mentioned issues. The interaction between yeast cells and the host immune system in relevance to the WRY vaccines has been discussed along with the importance of whole yeast cells in the development of anti-fungal vaccines by highlighting the bottlenecks hampering the use of WRY in vaccine formulation. Specifically, the present review highlighted the status of WRY vaccines, including those in clinical trials, and also summarized the guidelines, one should follow while conducting research or reporting the data related to WRY vaccines.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-16"},"PeriodicalIF":7.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microbiome on a chip: a promising technology for modeling of human organ microbiomes and their interactions.","authors":"Marzieh Ramezani Farani, Saber Saharkhiz, Kimia Feiz, Iraj Alipourfard, Yun Suk Huh","doi":"10.1080/07388551.2025.2531111","DOIUrl":"https://doi.org/10.1080/07388551.2025.2531111","url":null,"abstract":"<p><p>The increasing knowledge of the makeup and role of organ microbiomes has created new possibilities for understanding and managing human illnesses. The models used for animal studies conducted in laboratory settings and live animals may not always offer the necessary insights. One <i>in vitro</i> cell culture system known as organ-on-a-chip technology has garnered interest as a way to collect data that accurately reflects human responses. Organ-on-a-chip (OoC) technology, while accurately simulating the function of tissues and organs, has largely covered the differences between animal and human systems. Microbiome-on-a-chip (MoC) offers benefits over other <i>in vitro</i> procedures, permitting dimensional observation of ecological dynamics, microbial growth, and host-associated interactions while regulating and assessing relevant environmental parameters such as pH and O<sub>2</sub> in real-time. The fabricated MoC platforms can be designed to test microbiome-enabled therapies, to study culture and pharmacology, antibiotic resistance, and to model multi-organ interactions mediated by the microbiome. In the current overview, we provide a translational perspective and discuss different organs, such as: oral, skin, gut and vaginal microbiota on a chip and recently developed MoC-based devices. The commonly used MoC fabrication methods, such as microfluidics and 3D printing, have been explored, and the potential applications of MoC in microbiome engineering have been suggested.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-16"},"PeriodicalIF":7.7,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Min Li, Xue Yang, Di Zhang, Yuan Tian, Zi-Chang Jia, Wen-Hui Liu, Rui-Rui Hao, Yun-Sheng Chen, Mo-Xian Chen, Ying-Gao Liu
{"title":"A story of two kingdoms: unravelling the intricacies of protein phase separation in plants and animals.","authors":"Min Li, Xue Yang, Di Zhang, Yuan Tian, Zi-Chang Jia, Wen-Hui Liu, Rui-Rui Hao, Yun-Sheng Chen, Mo-Xian Chen, Ying-Gao Liu","doi":"10.1080/07388551.2024.2425989","DOIUrl":"10.1080/07388551.2024.2425989","url":null,"abstract":"<p><p>The biomolecular condensates (BCs) formed by proteins through phase separation provide the necessary space and raw materials for the orderly progression of cellular activities, and on this basis, various membraneless organelles (MLOs) are formed. The occurrence of eukaryotic phase separation is driven by multivalent interactions from intrinsically disordered regions (IDRs) and/or specific protein/nucleic acid binding domains and is regulated by various environmental factors. In plant and animal cells, the MLOs involved in gene expression regulation, stress response, and mitotic control display similar functions and mechanisms. In contrast, the phase separation related to reproductive development and immune regulation differs significantly between the two kingdoms owing to their distinct cell structures and nutritional patterns. In addition, animals and plants each exhibit unique protein phase separation activities, such as neural regulation and light signal response. By comparing the similarities and differences in the formation mechanism and functional regulation of known protein phase separation, we elucidated its importance in the evolution, differentiation, and environmental adaptation of both animals and plants. The significance of studying protein phase separation for enhancing biological quality of life has been further emphasized.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1019-1039"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142726727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mengshi Jia, Lei Shao, Jie Jiang, Wankui Jiang, Fengxue Xin, Wenming Zhang, Yujia Jiang, Min Jiang
{"title":"Mitigating toxic formaldehyde to promote efficient utilization of C1 resources.","authors":"Mengshi Jia, Lei Shao, Jie Jiang, Wankui Jiang, Fengxue Xin, Wenming Zhang, Yujia Jiang, Min Jiang","doi":"10.1080/07388551.2024.2430476","DOIUrl":"10.1080/07388551.2024.2430476","url":null,"abstract":"<p><p>The C1 resource is widely considered because of its abundance and affordability. In the context of extensive utilization of C1 resources by methylotrophic microorganisms, especially for methanol, formaldehyde is an important intermediate metabolite that is at the crossroads of assimilation and dissimilation pathways. However, formaldehyde is an exceedingly reactive compound that can form covalent cross-linked complexes with amine and thiol groups in cells, which causes irreversible damage to the organism. Thus, it is important to balance the intensity of the assimilation and dissimilation pathways of formaldehyde, which can avoid formaldehyde toxicity and improve the full utilization of C1 resources. This review details the source of endogenous formaldehyde and its toxicity mechanism, explaining the harm of excessive accumulation of formaldehyde to metabolism. Importantly, the self-detoxification and various feasible strategies to mitigate formaldehyde toxicity are discussed and proposed. These strategies are meant to help appropriately handle formaldehyde toxicity and accelerate the effective use of C1 resources.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1175-1187"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gothandapani Sellamuthu, Amrita Chakraborty, Ramesh R Vetukuri, Saravanasakthi Sarath, Amit Roy
{"title":"RNAi-biofungicides: a quantum leap for tree fungal pathogen management.","authors":"Gothandapani Sellamuthu, Amrita Chakraborty, Ramesh R Vetukuri, Saravanasakthi Sarath, Amit Roy","doi":"10.1080/07388551.2024.2430478","DOIUrl":"10.1080/07388551.2024.2430478","url":null,"abstract":"<p><p>Fungal diseases threaten the forest ecosystem, impacting tree health, productivity, and biodiversity. Conventional approaches to combating diseases, such as biological control or fungicides, often reach limits regarding efficacy, resistance, non-target organisms, and environmental impact, enforcing alternative approaches. From an environmental and ecological standpoint, an RNA interference (RNAi) mediated double-stranded RNA (dsRNA)-based strategy can effectively manage forest fungal pathogens. The RNAi approach explicitly targets and suppresses gene expression through a conserved regulatory mechanism. Recently, it has evolved to be an effective tool in combating fungal diseases and promoting sustainable forest management approaches. RNAi bio-fungicides provide efficient and eco-friendly disease control alternatives using species-specific gene targeting, minimizing the off-target effects. With accessible data on fungal disease outbreaks, genomic resources, and effective delivery systems, RNAi-based biofungicides can be a promising tool for managing fungal pathogens in forests. However, concerns regarding the environmental fate of RNAi molecules and their potential impact on non-target organisms require an extensive investigation on a case-to-case basis. The current review critically evaluates the feasibility of RNAi bio-fungicides against forest pathogens by delving into the accessible delivery methods, environmental persistence, regulatory aspects, cost-effectiveness, community acceptance, and plausible future of RNAi-based forest protection products.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1131-1158"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142794534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marwa Hamdi, Bhanu Priya Kilari, Priti Mudgil, Nilesh Prakash Nirmal, Shreesh Ojha, Mohammed Akli Ayoub, Amr Amin, Sajid Maqsood
{"title":"Bioactive peptides with potential anticancer properties from various food protein sources: status of recent research, production technologies, and developments.","authors":"Marwa Hamdi, Bhanu Priya Kilari, Priti Mudgil, Nilesh Prakash Nirmal, Shreesh Ojha, Mohammed Akli Ayoub, Amr Amin, Sajid Maqsood","doi":"10.1080/07388551.2024.2435965","DOIUrl":"10.1080/07388551.2024.2435965","url":null,"abstract":"<p><p>Recently, bioactive peptides, from natural resources, have attracted remarkable attention as nutraceutical treasures and the health benefits of their consumption have extensively been studied. Therapies based on bioactive peptides have been recognized as an innovative and promising alternative method for dangerous diseases such as cancer. Indeed, there has been enormous interest in nutraceuticals and bioactive-based chemopreventive molecules as a potential opportunity to manage chronic diseases, including cancer at different stages, rather than the traditionally used therapies. The relative safety and efficacy of these peptides in targeting only the tumor cells without affecting the normal cells make them attractive alternatives to existing pharmaceuticals for the treatment, management, and prevention of cancer, being able to act as potential physiological modulators of metabolism during their intestinal digestion. Novel bioactive peptides derived from food sources can be beneficial as anticancer nutraceuticals and provide a basis for the pharmaceutical development of food-derived bioactive peptides. Bioactive peptides can be generated through different protein hydrolysis methods and purified using advanced chromatographic techniques. Moreover, establishing bioactive peptides' efficacy and mechanism of action can provide alternative methods for cancer prevention and management. Most of the research on anticancer peptides is carried out on cell lines with very limited research being investigated in animal models or human clinical models. In this context, this review article comprehensively discusses anticancer peptides': production, isolation, therapeutic strategies, mechanism of action, and application in cancer therapy.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1076-1097"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Haoyi Yang, Xiaoyu Lin, Xianen Zhong, Mingfeng Cao, Jifeng Yuan, Zhipeng Li, Xueping Ling, Ning He
{"title":"Current status and advances in the green synthesis of muconic acid.","authors":"Haoyi Yang, Xiaoyu Lin, Xianen Zhong, Mingfeng Cao, Jifeng Yuan, Zhipeng Li, Xueping Ling, Ning He","doi":"10.1080/07388551.2024.2433998","DOIUrl":"10.1080/07388551.2024.2433998","url":null,"abstract":"<p><p>Muconic acid (MA) is a valuable dicarboxylic acid with three isomers that are extensively utilized in textile and chemical industries. Traditionally, the chemical synthesis of MA consumes nonrenewable petrochemical raw materials and causes significant environmental problems. With the rapid increase in demand for MA, eco-friendly biosynthetic technologies with renewable sources are becoming ideal alternative solutions. This paper systematically reviews recent advances in the biosynthesis of MA isomers, describing not only the mechanism for MA biosynthesis in different microorganisms, including wild and engineered strains, but also focuses on MA production from various renewable resources, especially lignin hydrolysate and lignin-derived aromatics hydrocarbons, such as: benzoic acid, isoeugenol, vanillic acid and phenol. Moreover, <i>cis,cis</i>-muconic acid production from xylose, PET, methane, and glycerol are discussed in detail, providing a much broader substrate spectra and further possibilities for MA large scale industrialization economically. Challenges facing biosynthesis of cis, trans muconic acid and trans, trans muconic acid are discussed finally.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1040-1057"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vishal Kumar, Ashutosh Bahuguna, Subhash Kumar, Myunghee Kim
{"title":"Xylooligosaccharides mediated gut microbiome modulation: prebiotics to postbiotics.","authors":"Vishal Kumar, Ashutosh Bahuguna, Subhash Kumar, Myunghee Kim","doi":"10.1080/07388551.2025.2460852","DOIUrl":"10.1080/07388551.2025.2460852","url":null,"abstract":"<p><p>An increasing trend toward harnessing nutraceuticals as food supplements rather than pharmaceuticals as curative and preventive agents against various ailments has been observed. Owing to their health benefits, prebiotics have received notable attention from the pharmaceutical and food industries. Among the different prebiotic oligosaccharides, xylooligosaccharides (XOS) exhibited a remarkable capacity to stimulate the growth of the gut microbiota and benefit individuals with metabolic abnormalities. Additionally, XOS can be produced from various renewable agricultural wastes, which supports their economic feasibility for use as prebiotics at the industrial level. This review explains gut microbiome modulation based on <i>in vivo</i>, <i>in vitro</i>, and clinical findings. Gut microbiome modulation leads to the production of postbiotics that stimulate various beneficial health effects. The current review entails the mechanisms of different health-promoting activities mediated by XOS, including immunomodulation and anticancer effects. Additionally, the concept of converting prebiotics to synbiotics using XOS has been established for nutraceutical applications. Synbiotics based on XOS and probiotics may be good alternatives to nutraceuticals for improving human health.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1098-1116"},"PeriodicalIF":8.1,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}