Engineering Microbiology最新文献

Advances in synthetic microbial ecosystems approach for studying ecological interactions and their influencing factors 合成微生物生态系统方法研究生态相互作用及其影响因素的进展

Engineering Microbiology Pub Date : 2025-03-26 DOI: 10.1016/j.engmic.2025.100205

Wei Jiang , Sumeng Wang , Fei Gu , Xiaoya Yang , Qingsheng Qi , Quanfeng Liang

{"title":"Advances in synthetic microbial ecosystems approach for studying ecological interactions and their influencing factors","authors":"Wei Jiang , Sumeng Wang , Fei Gu , Xiaoya Yang , Qingsheng Qi , Quanfeng Liang","doi":"10.1016/j.engmic.2025.100205","DOIUrl":"10.1016/j.engmic.2025.100205","url":null,"abstract":"<div><div>Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues, such as community stability, keystone species identification, and the manipulation of community structures. However, exploring these interactions proves challenging within complex natural ecosystems. With advances in synthetic biology, the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability. Various ecological relationships, including commensalism, amensalism, mutualism, competition, and predation have been established within synthetic ecosystems. These relationships are often context-dependent and shaped by physical and chemical environmental factors, as well as by interacting populations and surrounding species. This review consolidates current knowledge of synthetic microbial ecosystems and factors influencing their ecological dynamics. A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100205"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143881878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimizing the CRISPR/Cas9 system for gene editing in Yarrowia lipolytica 脂溶耶氏菌基因编辑CRISPR/Cas9系统的优化

Engineering Microbiology Pub Date : 2025-03-18 DOI: 10.1016/j.engmic.2025.100193

Jianhui Liu , Yamin Zhu , Jin Hou

{"title":"Optimizing the CRISPR/Cas9 system for gene editing in Yarrowia lipolytica","authors":"Jianhui Liu , Yamin Zhu , Jin Hou","doi":"10.1016/j.engmic.2025.100193","DOIUrl":"10.1016/j.engmic.2025.100193","url":null,"abstract":"<div><div><em>Yarrowia lipolytica</em> is a promising host for producing valuable chemicals owing to its robustness and metabolic versatility. Efficient genome editing tools are essential for advancing its biotechnological applications. Although CRISPR/Cas9 technology has been applied in <em>Y. lipolytica</em>, achieving a consistently high editing performance remains challenging owing to the low homologous recombination efficiency and variability in system components. In this study, we optimized CRISPR/Cas9-mediated genome editing in <em>Y. lipolytica</em> to enhance its editing efficiency. Using the RNA polymerase III promoter <em>SCR1-tRNA</em> for sgRNA expression, we achieved a gene disruption efficiency of 92.5 %. The tRNA-sgRNA architecture enabled a dual gene disruption efficiency of 57.5 %. <em>KU70</em> deletion in the Cas9 system increased the integration efficiency to 92.5 %, and <em>Rad52</em> and <em>Sae2</em> overexpression boosted homologous recombination. The introduction of Cas9<sup>D147Y, P411T</sup> (iCas9) enhanced the efficiency of both gene disruption and genome integration. This study provides a powerful tool for efficient gene editing in <em>Y. lipolytica</em>, which will accelerate the construction of yeast cell factories.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100193"},"PeriodicalIF":0.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carbon sequestration pathways in microorganisms: Advances, strategies, and applications 微生物中的碳固存途径：进展、策略和应用

Engineering Microbiology Pub Date : 2025-03-08 DOI: 10.1016/j.engmic.2025.100196

Shupeng Ruan , Yuchen Jiang , Aoxue Wang , Xinying Zhang , Ying Lin , Shuli Liang

{"title":"Carbon sequestration pathways in microorganisms: Advances, strategies, and applications","authors":"Shupeng Ruan , Yuchen Jiang , Aoxue Wang , Xinying Zhang , Ying Lin , Shuli Liang","doi":"10.1016/j.engmic.2025.100196","DOIUrl":"10.1016/j.engmic.2025.100196","url":null,"abstract":"<div><div>In recent years, industrial activities have significantly increased atmospheric CO<sub>2</sub> levels, exacerbating global warming. Carbon reduction involves implementing measures to minimize CO<sub>2</sub> emissions from human activities and achieve a balance between carbon absorption and emissions. Therefore, effective reduction of CO<sub>2</sub> emissions is crucial. Conventional physical and chemical methods for CO₂ fixation frequently cause secondary environmental pollution. As a result, utilizing microorganisms for CO<sub>2</sub> fixation has gained considerable interest. This review provides an overview of the natural pathways for microbial CO<sub>2</sub> fixation, recent advancements in artificial CO<sub>2</sub> fixation, and strategies for enhancing the efficiency of microbial CO<sub>2</sub> fixation. We also discuss the conversion of CO<sub>2</sub> into diverse metabolic products and high-value chemicals. By identifying efficient carbon fixation pathways for microorganisms, this review aims to lay the foundation for the biological production of high-value chemicals using CO<sub>2</sub> as a raw material.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100196"},"PeriodicalIF":0.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143642867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modification of essential factors mediating post-translational processing for high-quality protein expression in Penicillium 介导青霉高质量蛋白表达翻译后加工的关键因子的修饰

Engineering Microbiology Pub Date : 2025-03-01 DOI: 10.1016/j.engmic.2025.100194

Demin Guo , Shengfang Zhao , Jie Chen, Shuhui Han, Yangtao Li, Yu Chen, Shengbiao Hu, Yibo Hu

{"title":"Modification of essential factors mediating post-translational processing for high-quality protein expression in Penicillium","authors":"Demin Guo , Shengfang Zhao , Jie Chen, Shuhui Han, Yangtao Li, Yu Chen, Shengbiao Hu, Yibo Hu","doi":"10.1016/j.engmic.2025.100194","DOIUrl":"10.1016/j.engmic.2025.100194","url":null,"abstract":"<div><div>The formation of mature proteins requires complex post-translational modification and processing. Efficient post-translational processing machinery is beneficial for the high-quality expression of proteins. To comprehensively evaluate the role of post-translational mediating factors (PTMFs) in protein synthesis, two reporter strains expressing a homologous protein, Amy15A, and a heterologous protein, TaEG, were constructed in <em>Penicillium oxalicum</em>. Three PTMFs including a conserved basic leucine zipper transcription factor, HacA; an endoplasmic reticulum chaperone-binding protein, BipA; and a protein disulfide isomerase, PdiA, were individually overexpressed in the both reporter strains. The findings showed that overexpression of these PTMFs enhanced the enzymatic activity of both homologous and heterologous proteins. However, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed that, upon overexpression of the PTMFs, heterologous protein secretion remained stable or slightly increased, whereas that of homologous proteins remained unchanged or decreased. Neither the vegetative growth rate nor reporter transcription levels accounted for these variations in protein production or enzymatic activity. Conclusively, this study suggests that PTMFs play a positive role in protein expression and can be leveraged to optimize filamentous fungal chassis cells in the future.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100194"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143610266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Erratum to “In vitro characterization of a nitro-forming oxygenase involved in 3-(trans-2’-aminocyclopropyl)alanine biosynthesis” [Engineering Microbiology 2 (2022) 100007] 对“参与3-（反式-2 ' -氨基环丙基）丙氨酸生物合成的一种造氮加氧酶的体外表征”的勘误[工程微生物学2 (2022)100007]

Engineering Microbiology Pub Date : 2025-03-01 DOI: 10.1016/j.engmic.2025.100195

Linlin Pang , Weijing Niu , Yuwei Duan , Liujie Huo , Aiying Li , Jiequn Wu , Youming Zhang , Xiaoying Bian , Guannan Zhong

引用次数: 0

Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum 核梭杆菌基因操作工具的建立与改进

Engineering Microbiology Pub Date : 2025-02-08 DOI: 10.1016/j.engmic.2025.100192

Zhiwei Guan , Hailong Wang , Qiang Feng

{"title":"Establishment and improvement of genetic manipulation tools for Fusobacterium nucleatum","authors":"Zhiwei Guan , Hailong Wang , Qiang Feng","doi":"10.1016/j.engmic.2025.100192","DOIUrl":"10.1016/j.engmic.2025.100192","url":null,"abstract":"<div><div>An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases. <em>Fusobacterium nucleatum</em>, a ubiquitous periodontitis-causing bacterium in the oral cavity, is frequently detected in focal sites and contributes to the pathogenesis of many extraoral diseases, including cancers, cardiovascular diseases, and adverse pregnancy outcomes (APOs). <em>F. nucleatum</em> is one of the few oral anaerobes that can be cultured purely <em>in vitro</em> and is a ‘model species’ for studying the impact of oral health on systemic health. The establishment and development of genetic manipulation tools for <em>F. nucleatum</em> and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of <em>F. nucleatum</em>. Here, we review the establishment and development of the genetic manipulation systems for <em>F. nucleatum</em> and summarize the characteristics of various genetic manipulation tools, such as suicide plasmid-based systems for gene inactivation, replicable plasmid-based systems controlling gene expression, and transposon-based random mutagenesis systems. Notably, we summarize and analyze their applications in the study of the pathogenic mechanisms of <em>F. nucleatum</em>. We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of <em>F. nucleatum</em> and other <em>Fusobacterium</em> species.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100192"},"PeriodicalIF":0.0,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143421876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The gut virome and human health: From diversity to personalized medicine 肠道病毒与人类健康：从多样性到个性化医疗

Engineering Microbiology Pub Date : 2025-02-07 DOI: 10.1016/j.engmic.2025.100191

Rahul Harikumar Lathakumari, Leela Kakithakara Vajravelu, Anusha Gopinathan, Poornima Baskar Vimala, Vishnupriya Panneerselvam, Sujith Sri Surya Ravi, Jayaprakash Thulukanam

{"title":"The gut virome and human health: From diversity to personalized medicine","authors":"Rahul Harikumar Lathakumari, Leela Kakithakara Vajravelu, Anusha Gopinathan, Poornima Baskar Vimala, Vishnupriya Panneerselvam, Sujith Sri Surya Ravi, Jayaprakash Thulukanam","doi":"10.1016/j.engmic.2025.100191","DOIUrl":"10.1016/j.engmic.2025.100191","url":null,"abstract":"<div><div>The human gut virome plays a crucial role in the gut and overall health; its diversity and regulatory functions influence bacterial populations, metabolism, and immune responses. Bacteriophages (phages) and eukaryotic viruses within the gut microbiome contribute to these processes, and recent advancements in sequencing technologies and bioinformatics have greatly expanded our understanding of the gut virome. These advances have led to the development of phage-based therapeutics, diagnostics, and artificial intelligence-driven precision medicine. The emerging field of phageomics shows promise for delivering personalized phage therapies that combat antimicrobial resistance by specifically targeting pathogenic bacteria while preserving beneficial microbes. Moreover, CRISPR-Cas systems delivered via phages have shown success in selectively targeting antibiotic resistance genes and enhancing treatment effectiveness. Phage-based diagnostics are highly sensitive in detecting bacterial pathogens, offering significant benefits for human health and zoonotic disease surveillance. This synthesis of the current knowledge highlights the pivotal role of the gut virome in regulating microbial communities and its transformative potential in personalized medicine, emphasizing its importance in advancing therapeutic and diagnostic strategies for improving health outcomes.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 1","pages":"Article 100191"},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Activating cryptic biosynthetic gene clusters via ACTIMOT 通过ACTIMOT激活隐生生物合成基因簇

Engineering Microbiology Pub Date : 2025-01-24 DOI: 10.1016/j.engmic.2025.100190

Xiaoying Bian

引用次数: 0

Applications of bacteriophages in precision engineering of the human gut microbiome 噬菌体在人体肠道微生物群精密工程中的应用

Engineering Microbiology Pub Date : 2025-01-06 DOI: 10.1016/j.engmic.2025.100189

Xiaoxian Kuang , Juntao Shen , Linggang Zheng , Yi Duan , Yingfei Ma , Elaine Lai-Han Leung , Lei Dai

引用次数: 0

Engineering Microbiology Pub Date : 2025-01-01 DOI: 10.1016/j.engmic.2024.100188

Zhiwei Deng, Zhenbo Yuan, Zhengshan Luo, Yijian Rao

引用次数: 0