Pub Date : 2025-06-01DOI: 10.1016/j.engmic.2025.100206
Jing Li , Chengde Zhang , Shiwen Wu , Jiao Xue , Ke Chen , Zixin Deng , Dongqing Zhu
Pentalenolactone is a sesquiterpene antibiotic from Streptomyces. Its biosynthetic pathway has been elucidated, except for the oxidation of pentalen-13-al to 1-deoxypentalenic acid. In this study, we show that cytochrome P450 pentalenene oxygenase catalyzed the formation of 1-deoxypentalenic acid. Ferredoxin XNR_5179 and ferredoxin reductase XNR_4478 from S. albus are suitable redox proteins for pentalenene oxygenase. The biosynthetic pathway presented fills a gap in the biosynthetic pathway of pentalenolactone and provides an example of cytochrome P450 enzyme activity being affected by redox proteins.
{"title":"Cytochrome P450-catalyzed allylic oxidation of pentalenene to 1-deoxypentalenic acid in pentalenolactone biosynthesis","authors":"Jing Li , Chengde Zhang , Shiwen Wu , Jiao Xue , Ke Chen , Zixin Deng , Dongqing Zhu","doi":"10.1016/j.engmic.2025.100206","DOIUrl":"10.1016/j.engmic.2025.100206","url":null,"abstract":"<div><div>Pentalenolactone is a sesquiterpene antibiotic from <em>Streptomyces</em>. Its biosynthetic pathway has been elucidated, except for the oxidation of pentalen-13-al to 1-deoxypentalenic acid. In this study, we show that cytochrome P450 pentalenene oxygenase catalyzed the formation of 1-deoxypentalenic acid. Ferredoxin XNR_5179 and ferredoxin reductase XNR_4478 from <em>S. albus</em> are suitable redox proteins for pentalenene oxygenase. The biosynthetic pathway presented fills a gap in the biosynthetic pathway of pentalenolactone and provides an example of cytochrome P450 enzyme activity being affected by redox proteins.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 2","pages":"Article 100206"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144222263","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}
Pub Date : 2025-05-17DOI: 10.1016/j.engmic.2025.100210
Jinxin Yan , Hui Zhang , Hongxu Zhang , Hairong Yu , Wenjia Tian , Mingyuan Liu , Weikang Sun , Leilei Guo , Xiaoxu Tan , Kaiyu Gao , Tianyi Jiang , Chuanjuan Lü , Qianjin Kang , Wensi Meng , Cuiqing Ma , Chao Gao , Ping Xu
Dicarboxylates are valuable platform compounds with a broad range of applications. The in vitro biosynthetic system used to produce dicarboxylates from ω-amino acids via the natural pathway requires costly cofactors and co-substrates, which restricts its economic feasibility of use. In this study, we designed a cofactor- and co-substrate-free artificial pathway for the production of dicarboxylates from ω-amino acids. Only three enzymes (viz., amine oxidase from Kluyveromyces marxianus DMKU3-1042, xanthine oxidase from bovine milk, and catalase from Aspergillus niger) were required for dicarboxylate production. Succinate (0.79 g g-1), glutarate (0.83 g g-1), and adipate (0.77 g g-1) were produced in high yields from the corresponding ω-amino acids through the in vitro biosynthetic system with the artificial pathway. Glutarate could also be produced from l-lysine by further introducing l-lysine monooxygenase and 5-aminovaleramide amidohydrolase from Pseudomonas putida KT2440 into the in vitro biosynthetic system, with the cofactor- and co-substrate-free system achieving a product yield of 0.63 g g-1. Considering its desirable characteristics, this artificial pathway-based in vitro biosynthetic system may be a promising alternative for dicarboxylate production from biotechnologically produced ω-amino acids.
{"title":"Production of dicarboxylates from ω-amino acids using a cofactor- and co-substrate-free in vitro biosynthetic system","authors":"Jinxin Yan , Hui Zhang , Hongxu Zhang , Hairong Yu , Wenjia Tian , Mingyuan Liu , Weikang Sun , Leilei Guo , Xiaoxu Tan , Kaiyu Gao , Tianyi Jiang , Chuanjuan Lü , Qianjin Kang , Wensi Meng , Cuiqing Ma , Chao Gao , Ping Xu","doi":"10.1016/j.engmic.2025.100210","DOIUrl":"10.1016/j.engmic.2025.100210","url":null,"abstract":"<div><div>Dicarboxylates are valuable platform compounds with a broad range of applications. The <em>in vitro</em> biosynthetic system used to produce dicarboxylates from ω-amino acids via the natural pathway requires costly cofactors and co-substrates, which restricts its economic feasibility of use. In this study, we designed a cofactor- and co-substrate-free artificial pathway for the production of dicarboxylates from ω-amino acids. Only three enzymes (viz., amine oxidase from <em>Kluyveromyces marxianus</em> DMKU3-1042, xanthine oxidase from bovine milk, and catalase from <em>Aspergillus niger</em>) were required for dicarboxylate production. Succinate (0.79 g g<sup>-1</sup>), glutarate (0.83 g g<sup>-1</sup>), and adipate (0.77 g g<sup>-1</sup>) were produced in high yields from the corresponding ω-amino acids through the <em>in vitro</em> biosynthetic system with the artificial pathway. Glutarate could also be produced from <span>l</span>-lysine by further introducing <span>l</span>-lysine monooxygenase and 5-aminovaleramide amidohydrolase from <em>Pseudomonas putida</em> KT2440 into the <em>in vitro</em> biosynthetic system, with the cofactor- and co-substrate-free system achieving a product yield of 0.63 g g<sup>-1</sup>. Considering its desirable characteristics, this artificial pathway-based <em>in vitro</em> biosynthetic system may be a promising alternative for dicarboxylate production from biotechnologically produced ω-amino acids.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100210"},"PeriodicalIF":0.0,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272099","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}
Pub Date : 2025-05-09DOI: 10.1016/j.engmic.2025.100208
Minmin Hu , Shiyang Xu , Ruofei Xu , Xiangjie Qi , Xiaofeng Yu , Jinqi Wang , Yige Li , Yangyang Liu , Guiran Xi , Junbao Yu , Mei Shi
Gastric cancer (GC) is the fifth most prevalent malignancy globally. However, its heterogeneity and asymptomatic early-stage development hinder timely diagnosis and effective treatment. Here, we employed single-cell RNA sequencing to delineate the transitional features of pit mucous cells (PMCs) during the gastritis-to-cancer transition and identified 100 core genes. Characterization of the gene set revealed the role of ribosomal protein small subunit and ribosomal protein large subunit in inflammation-to-cancer transition, which promoted ribonucleoprotein complex biogenesis and cytoplasmic translation. External validation using independent cohorts confirmed that this core gene set discriminated disease progression (AUC > 0.7) and was significantly enriched in GC tissues (p < 0.01). Moreover, we evaluated the therapeutic intervention effects of C. butyricum and synbiotics (Weichanghao®) using a rat model of gastritis and demonstrated the targeted suppression of inflammation-to-cancer transition genes. Our findings establish the basis for early diagnosis of GC through PMC-driven molecular dynamics. Additionally, we propose microbiota-based strategies to prevent the inflammation-to-cancer transition in preneoplastic stages. Furthermore, our results highlight that dysbiosis of the gastric microbiome can be addressed using probiotic supplementations and the core gene set may provide labeling for the evaluation of probiotics-based treatment.
{"title":"Analysis of single-cell RNA sequencing data to examine the gastric inflammation-to-cancer transition and evaluation of the effect of probiotic on precancerous lesions","authors":"Minmin Hu , Shiyang Xu , Ruofei Xu , Xiangjie Qi , Xiaofeng Yu , Jinqi Wang , Yige Li , Yangyang Liu , Guiran Xi , Junbao Yu , Mei Shi","doi":"10.1016/j.engmic.2025.100208","DOIUrl":"10.1016/j.engmic.2025.100208","url":null,"abstract":"<div><div>Gastric cancer (GC) is the fifth most prevalent malignancy globally. However, its heterogeneity and asymptomatic early-stage development hinder timely diagnosis and effective treatment. Here, we employed single-cell RNA sequencing to delineate the transitional features of pit mucous cells (PMCs) during the gastritis-to-cancer transition and identified 100 core genes. Characterization of the gene set revealed the role of ribosomal protein small subunit and ribosomal protein large subunit in inflammation-to-cancer transition, which promoted ribonucleoprotein complex biogenesis and cytoplasmic translation. External validation using independent cohorts confirmed that this core gene set discriminated disease progression (AUC > 0.7) and was significantly enriched in GC tissues (<em>p</em> < 0.01). Moreover, we evaluated the therapeutic intervention effects of <em>C. butyricum</em> and synbiotics (Weichanghao®) using a rat model of gastritis and demonstrated the targeted suppression of inflammation-to-cancer transition genes. Our findings establish the basis for early diagnosis of GC through PMC-driven molecular dynamics. Additionally, we propose microbiota-based strategies to prevent the inflammation-to-cancer transition in preneoplastic stages. Furthermore, our results highlight that dysbiosis of the gastric microbiome can be addressed using probiotic supplementations and the core gene set may provide labeling for the evaluation of probiotics-based treatment.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"5 3","pages":"Article 100208"},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144205430","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}
Pub Date : 2025-03-26DOI: 10.1016/j.engmic.2025.100205
Wei Jiang , Sumeng Wang , Fei Gu , Xiaoya Yang , Qingsheng Qi , Quanfeng Liang
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.
{"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}
Pub Date : 2025-03-18DOI: 10.1016/j.engmic.2025.100193
Jianhui Liu , Yamin Zhu , Jin Hou
Yarrowia lipolytica 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 Y. lipolytica, 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 Y. lipolytica to enhance its editing efficiency. Using the RNA polymerase III promoter SCR1-tRNA 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 %. KU70 deletion in the Cas9 system increased the integration efficiency to 92.5 %, and Rad52 and Sae2 overexpression boosted homologous recombination. The introduction of Cas9D147Y, P411T (iCas9) enhanced the efficiency of both gene disruption and genome integration. This study provides a powerful tool for efficient gene editing in Y. lipolytica, which will accelerate the construction of yeast cell factories.
{"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}
Pub Date : 2025-03-08DOI: 10.1016/j.engmic.2025.100196
Shupeng Ruan , Yuchen Jiang , Aoxue Wang , Xinying Zhang , Ying Lin , Shuli Liang
In recent years, industrial activities have significantly increased atmospheric CO2 levels, exacerbating global warming. Carbon reduction involves implementing measures to minimize CO2 emissions from human activities and achieve a balance between carbon absorption and emissions. Therefore, effective reduction of CO2 emissions is crucial. Conventional physical and chemical methods for CO₂ fixation frequently cause secondary environmental pollution. As a result, utilizing microorganisms for CO2 fixation has gained considerable interest. This review provides an overview of the natural pathways for microbial CO2 fixation, recent advancements in artificial CO2 fixation, and strategies for enhancing the efficiency of microbial CO2 fixation. We also discuss the conversion of CO2 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 CO2 as a raw material.
{"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}
Pub Date : 2025-03-01DOI: 10.1016/j.engmic.2025.100194
Demin Guo , Shengfang Zhao , Jie Chen, Shuhui Han, Yangtao Li, Yu Chen, Shengbiao Hu, Yibo Hu
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 Penicillium oxalicum. 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.
{"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}
Pub Date : 2025-02-08DOI: 10.1016/j.engmic.2025.100192
Zhiwei Guan , Hailong Wang , Qiang Feng
An imbalance in oral microbial homeostasis is significantly associated with the onset and progression of several systemic diseases. Fusobacterium nucleatum, 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). F. nucleatum is one of the few oral anaerobes that can be cultured purely in vitro and is a ‘model species’ for studying the impact of oral health on systemic health. The establishment and development of genetic manipulation tools for F. nucleatum and the construction of pathogenic gene-disrupted strains are important strategies for studying the pathogenicity of F. nucleatum. Here, we review the establishment and development of the genetic manipulation systems for F. nucleatum 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 F. nucleatum. We hope to provide reference information and ideas for future research on genetic manipulation tools and the pathogenic mechanisms of F. nucleatum and other Fusobacterium species.
{"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}
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.
{"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}
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