Engineering Microbiology最新文献_第2页

Engineering Microbiology

Pub Date : 2026-01-01

引用次数: 0

Engineering Microbiology

Pub Date : 2026-01-01

引用次数: 0

Genetically encoded biosensors enabled high-throughput screening of microbial cell factories 基因编码的生物传感器实现了微生物细胞工厂的高通量筛选

Engineering Microbiology

Pub Date : 2025-12-24 DOI: 10.1016/j.engmic.2025.100258

Jin Wang , Xueyan Liu , Longqian Zhao , Yue Zhang , Meng Wang

Genetically encoded biosensors provide powerful tools for coupling desired phenotypes to detectable outputs and have been extensively developed to detect a wide range of natural and unnatural products. When integrated with diverse high-throughput screening (HTS) approaches, these biosensors enable efficient product-driven screening across various throughputs, thereby expediting the engineering and optimization of microbial cell factories to produce various target compounds. For effective HTS of microbial cell factories, biosensors need to possess certain crucial characteristics. The performance features of biosensors significantly influence their application potential in HTS and can be precisely engineered through synthetic biology strategies. Furthermore, to ensure biosensor-driven HTS, additional engineering and optimizations of the biosensors are often required to increase the success rate and reduce false positives in the screening process. This review discusses the essential features of genetically encoded biosensors designed for HTS and then summarizes the latest advances in biosensor engineering for HTS purposes via synthetic biology strategies. Following this, the challenges and optimization of biosensors to adapt to different HTS processes are also discussed and exemplified. Finally, the key concerns and research prospects of developing biosensors for HTS applications are highlighted. Overall, this review provides comprehensive guidance on the engineering of genetically encoded biosensors and their applications in HTS for developing microbial cell factories to produce diverse target compounds.

遗传编码的生物传感器为将所需表型与可检测输出相耦合提供了强大的工具，并已广泛开发用于检测各种天然和非天然产品。当与各种高通量筛选（HTS）方法集成时，这些生物传感器可以在各种吞吐量中实现高效的产品驱动筛选，从而加快微生物细胞工厂的工程和优化，以生产各种目标化合物。为了实现微生物细胞工厂的高效高温超导，生物传感器需要具备某些关键特性。生物传感器的性能特征显著影响其在高温超导领域的应用潜力，并可通过合成生物学策略进行精确设计。此外，为了确保生物传感器驱动的HTS，通常需要对生物传感器进行额外的工程和优化，以提高筛选过程中的成功率并减少误报。本文综述了用于HTS的基因编码生物传感器的基本特征，并从合成生物学的角度总结了用于HTS的生物传感器工程的最新进展。在此之后，还讨论并举例说明了适应不同高温高温过程的生物传感器的挑战和优化。最后，对高温超导应用生物传感器的研究前景进行了展望。综上所述，本文对基因编码生物传感器的工程设计及其在HTS中的应用提供了全面的指导，以开发微生物细胞工厂来生产多种目标化合物。

{"title":"Genetically encoded biosensors enabled high-throughput screening of microbial cell factories","authors":"Jin Wang , Xueyan Liu , Longqian Zhao , Yue Zhang , Meng Wang","doi":"10.1016/j.engmic.2025.100258","DOIUrl":"10.1016/j.engmic.2025.100258","url":null,"abstract":"<div><div>Genetically encoded biosensors provide powerful tools for coupling desired phenotypes to detectable outputs and have been extensively developed to detect a wide range of natural and unnatural products. When integrated with diverse high-throughput screening (HTS) approaches, these biosensors enable efficient product-driven screening across various throughputs, thereby expediting the engineering and optimization of microbial cell factories to produce various target compounds. For effective HTS of microbial cell factories, biosensors need to possess certain crucial characteristics. The performance features of biosensors significantly influence their application potential in HTS and can be precisely engineered through synthetic biology strategies. Furthermore, to ensure biosensor-driven HTS, additional engineering and optimizations of the biosensors are often required to increase the success rate and reduce false positives in the screening process. This review discusses the essential features of genetically encoded biosensors designed for HTS and then summarizes the latest advances in biosensor engineering for HTS purposes via synthetic biology strategies. Following this, the challenges and optimization of biosensors to adapt to different HTS processes are also discussed and exemplified. Finally, the key concerns and research prospects of developing biosensors for HTS applications are highlighted. Overall, this review provides comprehensive guidance on the engineering of genetically encoded biosensors and their applications in HTS for developing microbial cell factories to produce diverse target compounds.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100258"},"PeriodicalIF":0.0,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886453","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

Advances in microbial mevalonolactone production: from fermentative mevalonate accumulation to downstream lactonization 微生物甲羟戊酸内酯生产的进展：从发酵甲羟戊酸积累到下游内酯化

Engineering Microbiology

Pub Date : 2025-12-24 DOI: 10.1016/j.engmic.2025.100257

Hao Tang , Lihong Yin , Yiwen Jiang , Teng Xu , Ting Xue , Meimei Fu , Jianghao Chen , Jinshan Guo

Mevalonolactone (MVAL) is a high-value feedstock for the cosmetic industry, with (R)-(-)-MVAL as the sole bioactive enantiomer. Chemical synthesis, which is the traditional method for MVAL production, is hindered by cumbersome procedures, low chiral purity, and sensitivity to humidity. Microbial fermentation via fermentative mevalonate (MVA) accumulation followed by in vitro acid-catalyzed lactonization has emerged as a promising alternative for producing optically pure (R)-(-)-MVAL. Strategies for MVA overproduction in microbial systems are reviewed, including the selection of chassis strains and enzymes for the MVA biosynthetic pathway, metabolic engineering approaches for strain improvement, optimization of fermentation processes, and downstream processes for MVA-to-MVAL lactonization. Finally, prospects for advancing microbial MVAL production are discussed.

Mevalonolactone （MVAL）是化妆品行业的高价值原料，(R)-(-)-MVAL是唯一具有生物活性的对映体。化学合成是生产MVAL的传统方法，但由于程序繁琐、手性纯度低、对湿度敏感等问题，阻碍了MVAL的生产。微生物发酵通过发酵甲羟戊酸（MVA）积累，然后体外酸催化内酯化已成为生产光学纯(R)-(-)- mval的一种有前途的替代方法。综述了微生物系统中MVA过量生产的策略，包括MVA生物合成途径的基础菌株和酶的选择，菌株改良的代谢工程方法，发酵过程的优化以及MVA到mval内酯化的下游工艺。最后，对推进微生物MVAL生产的前景进行了展望。

引用次数: 0

Advances in polyethylene biodegradation and bioconversion: Microbial, enzymatic, and biotechnological insights 聚乙烯生物降解和生物转化的进展：微生物、酶和生物技术的见解

Engineering Microbiology

Pub Date : 2025-12-20 DOI: 10.1016/j.engmic.2025.100255

Jie Qiao , Luxuan Wu , Xiaoru Ma , Anni Li , Yannan Tian , Hailong Lin , Dongsheng Guo , Xiujuan Li

Polyethylene (PE) is one of the most widely used plastics worldwide and is valued for its versatility, durability, and cost-effectiveness. However, the chemical stability of PE combined with its widespread use makes it a persistent environmental pollutant that contributes to the accumulation of plastic waste in terrestrial and marine ecosystems. The escalating issue of plastic pollution has underscored the importance of developing sustainable solutions, of which PE biodegradation has emerged as a promising avenue for mitigating the environmental burden of recalcitrant polyolefins. This review systematically summarizes the recent advances in the biodegradation and bioconversion of PE, focusing on methods for evaluating degradation efficiency, the mechanisms by which microorganisms and enzymes contribute to PE degradation, and the microbial and enzymatic resources identified to date. In addition, we discuss physicochemical strategies that enhance degradation efficiency and their integration with biological approaches, as well as the potential applications of emerging biotechnological tools in PE degradation. The integration of cutting-edge biotechnological tools such as synthetic biology and machine learning with traditional biodegradation methods holds great potential for accelerating PE degradation rates and achieving more sustainable plastic waste management.

聚乙烯（PE）是世界上使用最广泛的塑料之一，因其多功能性、耐用性和成本效益而受到重视。然而，聚乙烯的化学稳定性及其广泛使用使其成为一种持久性环境污染物，有助于在陆地和海洋生态系统中积累塑料废物。不断升级的塑料污染问题强调了开发可持续解决方案的重要性，其中PE生物降解已成为减轻顽固性聚烯烃环境负担的有希望的途径。本文系统地综述了聚乙烯生物降解和生物转化的最新进展，重点介绍了降解效率的评价方法、微生物和酶对聚乙烯降解的作用机制以及迄今为止发现的微生物和酶资源。此外，我们还讨论了提高降解效率的物理化学策略及其与生物方法的结合，以及新兴生物技术工具在PE降解中的潜在应用。将合成生物学和机器学习等尖端生物技术工具与传统生物降解方法相结合，在加快PE降解速度和实现更可持续的塑料废物管理方面具有巨大潜力。

{"title":"Advances in polyethylene biodegradation and bioconversion: Microbial, enzymatic, and biotechnological insights","authors":"Jie Qiao , Luxuan Wu , Xiaoru Ma , Anni Li , Yannan Tian , Hailong Lin , Dongsheng Guo , Xiujuan Li","doi":"10.1016/j.engmic.2025.100255","DOIUrl":"10.1016/j.engmic.2025.100255","url":null,"abstract":"<div><div>Polyethylene (PE) is one of the most widely used plastics worldwide and is valued for its versatility, durability, and cost-effectiveness. However, the chemical stability of PE combined with its widespread use makes it a persistent environmental pollutant that contributes to the accumulation of plastic waste in terrestrial and marine ecosystems. The escalating issue of plastic pollution has underscored the importance of developing sustainable solutions, of which PE biodegradation has emerged as a promising avenue for mitigating the environmental burden of recalcitrant polyolefins. This review systematically summarizes the recent advances in the biodegradation and bioconversion of PE, focusing on methods for evaluating degradation efficiency, the mechanisms by which microorganisms and enzymes contribute to PE degradation, and the microbial and enzymatic resources identified to date. In addition, we discuss physicochemical strategies that enhance degradation efficiency and their integration with biological approaches, as well as the potential applications of emerging biotechnological tools in PE degradation. The integration of cutting-edge biotechnological tools such as synthetic biology and machine learning with traditional biodegradation methods holds great potential for accelerating PE degradation rates and achieving more sustainable plastic waste management.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100255"},"PeriodicalIF":0.0,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928178","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

Modulation of Hachiman defence by a type II toxin-antitoxin system via balancing trade-off between the fitness cost and antiphage activity II型毒素-抗毒素系统通过适应成本和抗噬菌体活性之间的平衡权衡来调节Hachiman防御

Engineering Microbiology

Pub Date : 2025-12-19 DOI: 10.1016/j.engmic.2025.100254

Xuhui Tian, Ruyi Zheng, Xin Li, Suping Jiang, Fang Wang, Yulong Shen, Qunxin She

Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the Streptococcus genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a S. thermophilus Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in Escherichia coli, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.

Hachiman系统提供跨原核结构域的先天性抗噬菌体免疫。该系统编码一个HamB核酸酶和一个HamB解旋酶，这两个酶在序列上都表现出很大的多样性。对HamA和HamB蛋白的系统发育分析显示，这两种蛋白的系统发育树相似，可分为三种主要类型。对其中一个亚分支的仔细检查发现了一个独特的亚家族，其中大多数Hachiman系统是单独存在的，然而，链球菌属的Hachiman与PezAT（一种独特的肺炎球菌epsilon zeta毒素-抗毒素系统）结合在一起，产生了PezAT - ham系统。对嗜热链球菌Pez-Ham系统的研究表明，只有Hachiman系统是介导抗噬菌体防御所必需的。对编码蛋白（即HamA或HamB单独或在蛋白质复合物中）的生化表征表明，HamA核酸酶单独无活性，但当与HamB形成异源二聚体时，所产生的蛋白质复合物能以广泛的特异性（5 ' -CNNNG-3 '）有效地切割各种形式的dna，并且HamB中的ATP结合极大地促进了核酸酶的活性，而ATP水解则在较小程度上促进了酶的活性。遗传学研究进一步表明，虽然Pez系统在大肠杆菌的抗噬菌体免疫中不起作用，但该系统抑制了Hachiman的表达，从而平衡了适应度成本和抗噬菌体防御效果之间的权衡。

{"title":"Modulation of Hachiman defence by a type II toxin-antitoxin system via balancing trade-off between the fitness cost and antiphage activity","authors":"Xuhui Tian, Ruyi Zheng, Xin Li, Suping Jiang, Fang Wang, Yulong Shen, Qunxin She","doi":"10.1016/j.engmic.2025.100254","DOIUrl":"10.1016/j.engmic.2025.100254","url":null,"abstract":"<div><div>Hachiman systems provide innate antiphage immunity across prokaryotic domains. The system encodes a HamA nuclease and a HamB helicase both of which exhibit great diversity in sequence. Phylogenetic analyses of HamA and HamB proteins revealed similar phylogenetic trees for both proteins, falling into three major types. Close examination of one of the subclades identified a distinct subfamily in which most of these Hachiman systems stands alone, however, Hachiman in the <em>Streptococcus</em> genus is combined with PezAT, a distinct pneumococcal epsilon zeta toxin-antitoxin system, yielding the Pez-Ham system. Investigation of a <em>S. thermophilus</em> Pez-Ham system revealed that only the Hachiman system is required for mediating antiphage defence. Biochemical characterization of encoded proteins, i.e., HamA or HamB individually or in protein complex revealed that the HamA nuclease is inactive alone, but upon the formation of heterologous dimer with HamB, the resulting protein complex effectively cleaves DNAs of various forms with a broad specificity (5′-CNNNG-3′), and the nuclease activity is greatly facilitated by ATP-binding in HamB and to a less degree by ATP hydrolysis. Genetic investigations further showed, while the Pez system did not function in antiphage immunity in <em>Escherichia coli</em>, the system repressed the expression of Hachiman, and thereby balancing the trade-off between the fitness cost and the effectiveness of antiphage defence.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100254"},"PeriodicalIF":0.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928177","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

Characterization of Bacillus subtilis phages PJNB030, PJNB031, and PJNB032 reveals wall teichoic acid as a key receptor determinant 枯草芽孢杆菌噬菌体PJNB030、PJNB031和PJNB032的鉴定表明壁磷壁酸是一个关键的受体决定因素

Engineering Microbiology

Pub Date : 2025-12-19 DOI: 10.1016/j.engmic.2025.100253

Jiaoyang Song , Ming Hu , Min Zhao , Shengqing Luo , Yibao Chen , Yuqing Liu , Yingjun Li

Bacillus subtilis is widely used in industrial fermentation and probiotic applications; however, phage contamination poses a substantial economic threat. To address this, we isolated three phages (PJNB030, PJNB031, and PJNB032) from a contaminated B. subtilis fermentation broth and characterized their biological properties. Phenotypic analyses indicated broad pH stability (pH 4–10), variable thermal tolerance, and differential UV sensitivity. Replication kinetics revealed latent periods of 10–20 min and burst sizes ranging from 50 to 73 PFU/cell. Genomic sequencing identified linear dsDNA genomes (64–165 kb) with GC content ranging from 33.5 to 47.4%. Phylogenomic and comparative genomic analyses revealed that these phages were located on distinct branches. Deletion of pgcA (which encodes α-phosphoglucomutase) rendered cells completely resistant to PJNB031 and PJNB032, whereas it reduced PJNB030 infectivity (plaque formation efficiency) by approximately six orders of magnitude. Adsorption assays confirmed that the binding of PJNB031 and PJNB032 to ΔpgcA mutants was abolished, whereas PJNB030 retained partial adsorption capacity. In conclusion, this study identified wall teichoic acid as the primary receptor for these phages and established pgcA deletion as an effective strategy for engineering phage-resistant B. subtilis strains. Our findings provide critical insights into the mitigation of phage contamination in industrial bioprocesses.

枯草芽孢杆菌广泛应用于工业发酵和益生菌领域；然而，噬菌体污染构成了巨大的经济威胁。为了解决这一问题，我们从被污染的枯草芽孢杆菌发酵液中分离出三种噬菌体（PJNB030、PJNB031和PJNB032），并对它们的生物学特性进行了表征。表型分析表明其pH稳定（pH 4-10），耐热性不同，紫外线敏感性不同。复制动力学显示潜伏期为10-20分钟，爆发大小为50至73 PFU/细胞。基因组测序鉴定出线性dsDNA基因组（64-165 kb）， GC含量在33.5 ~ 47.4%之间。系统基因组学和比较基因组学分析显示，这些噬菌体位于不同的分支上。pgcA（编码α-磷酸葡萄糖糖化酶）的缺失使细胞对PJNB031和PJNB032完全耐药，而PJNB030的感染性（斑块形成效率）降低了大约6个数量级。吸附实验证实PJNB031和PJNB032与ΔpgcA突变体的结合被消除，而PJNB030保留了部分吸附能力。综上所述，本研究确定壁苔酸是这些噬菌体的主要受体，并确定pgcA缺失是一种有效的工程策略，可用于抗噬菌体枯草芽孢杆菌菌株。我们的研究结果为减轻工业生物过程中噬菌体污染提供了重要的见解。

{"title":"Characterization of Bacillus subtilis phages PJNB030, PJNB031, and PJNB032 reveals wall teichoic acid as a key receptor determinant","authors":"Jiaoyang Song , Ming Hu , Min Zhao , Shengqing Luo , Yibao Chen , Yuqing Liu , Yingjun Li","doi":"10.1016/j.engmic.2025.100253","DOIUrl":"10.1016/j.engmic.2025.100253","url":null,"abstract":"<div><div><em>Bacillus subtilis</em> is widely used in industrial fermentation and probiotic applications; however, phage contamination poses a substantial economic threat. To address this, we isolated three phages (PJNB030, PJNB031, and PJNB032) from a contaminated <em>B. subtilis</em> fermentation broth and characterized their biological properties. Phenotypic analyses indicated broad pH stability (pH 4–10), variable thermal tolerance, and differential UV sensitivity. Replication kinetics revealed latent periods of 10–20 min and burst sizes ranging from 50 to 73 PFU/cell. Genomic sequencing identified linear dsDNA genomes (64–165 kb) with GC content ranging from 33.5 to 47.4%. Phylogenomic and comparative genomic analyses revealed that these phages were located on distinct branches. Deletion of <em>pgcA</em> (which encodes α-phosphoglucomutase) rendered cells completely resistant to PJNB031 and PJNB032, whereas it reduced PJNB030 infectivity (plaque formation efficiency) by approximately six orders of magnitude. Adsorption assays confirmed that the binding of PJNB031 and PJNB032 to Δ<em>pgcA</em> mutants was abolished, whereas PJNB030 retained partial adsorption capacity. In conclusion, this study identified wall teichoic acid as the primary receptor for these phages and established <em>pgcA</em> deletion as an effective strategy for engineering phage-resistant <em>B. subtilis</em> strains. Our findings provide critical insights into the mitigation of phage contamination in industrial bioprocesses.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100253"},"PeriodicalIF":0.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928176","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

Gdx mediates low-affinity Cs⁺/H⁺ antiport and confers cesium resistance in Escherichia coli Gdx介导低亲和力Cs + /H +反端口，并在大肠杆菌中赋予铯抗性

Engineering Microbiology

Pub Date : 2025-12-18 DOI: 10.1016/j.engmic.2025.100251

Daiki Kojima , Masahiro Ito

Following the Fukushima Daiichi nuclear power plant accident, radioactive cesium was released into the environment, prompting intensified efforts to identify cesium-resistant microorganisms. During these studies, we isolated a cesium-resistant Escherichia coli strain, designated ZX-1, which exhibits remarkable tolerance to cesium concentrations exceeding 700 mM. As no prior reports of cesium-resistant E. coli exist, this finding suggests the presence of a previously unrecognized resistance mechanism. This study aims to elucidate the molecular basis of cesium resistance in ZX-1.

RNA-seq analysis comparing ZX-1 with its parental strain, the commercial E. coli Mach1™, revealed constitutive upregulation of the guanidinium exporter gene gdx in ZX-1. Reanalysis of the whole-genome sequence identified a 20-bp deletion upstream of the gdx open reading frame, likely disrupting formation of the guanidinium riboswitch P2 loop and resulting in constitutive gdx expression.

To evaluate gdx function, the gene was cloned into the expression vector pBAD24 and expressed in E. coli. The resulting gdx-expressing strain exhibited even greater cesium resistance than ZX-1. Functional assays demonstrated that this strain mediates not only guanidinium/H⁺ antiport activity but also Cs⁺/H⁺ antiport activity. Cesium resistance was further enhanced in the presence of guanidinium, consistent with riboswitch-mediated induction of gdx.

Collectively, these findings provide evidence for a novel cesium efflux mechanism in E. coli and uncover an unexpected role of the guanidinium exporter Gdx in cesium export. These insights may facilitate the discovery of additional cesium-resistant microorganisms and broaden the potential for future applications.

福岛第一核电站事故发生后，放射性铯被释放到环境中，促使人们加强了识别抗铯微生物的努力。在这些研究中，我们分离出一株铯耐药大肠杆菌，命名为ZX-1，它对铯浓度超过700 mM表现出显著的耐受性。由于之前没有关于铯耐药大肠杆菌的报道，这一发现表明存在一种以前未被认识到的耐药机制。本研究旨在阐明ZX-1耐铯的分子基础。将ZX-1与其亲本菌株（商业大肠杆菌Mach1™）进行RNA-seq分析，发现ZX-1中的胍输出基因gdx组成上调。对全基因组序列的重新分析发现，gdx开放阅读框上游有一个20bp的缺失，可能破坏了胍核糖开关P2环的形成，导致了gdx的组成性表达。为了评估gdx的功能，我们将该基因克隆到表达载体pBAD24中，并在大肠杆菌中表达。表达gdx的菌株表现出比ZX-1更强的抗铯能力。功能测试表明，该菌株不仅介导胍+ /H +的反端口活性，还介导Cs + /H +的反端口活性。在胍的存在下，对铯的抗性进一步增强，这与核糖体开关介导的gdx诱导一致。总的来说，这些发现为大肠杆菌中新的铯外排机制提供了证据，并揭示了胍出口基因Gdx在铯出口中的意想不到的作用。这些见解可能有助于发现更多的抗铯微生物，并扩大未来应用的潜力。

{"title":"Gdx mediates low-affinity Cs⁺/H⁺ antiport and confers cesium resistance in Escherichia coli","authors":"Daiki Kojima , Masahiro Ito","doi":"10.1016/j.engmic.2025.100251","DOIUrl":"10.1016/j.engmic.2025.100251","url":null,"abstract":"<div><div>Following the Fukushima Daiichi nuclear power plant accident, radioactive cesium was released into the environment, prompting intensified efforts to identify cesium-resistant microorganisms. During these studies, we isolated a cesium-resistant <em>Escherichia coli</em> strain, designated ZX-1, which exhibits remarkable tolerance to cesium concentrations exceeding 700 mM. As no prior reports of cesium-resistant <em>E. coli</em> exist, this finding suggests the presence of a previously unrecognized resistance mechanism. This study aims to elucidate the molecular basis of cesium resistance in ZX-1.</div><div>RNA-seq analysis comparing ZX-1 with its parental strain, the commercial <em>E. coli</em> Mach1™, revealed constitutive upregulation of the guanidinium exporter gene <em>gdx</em> in ZX-1. Reanalysis of the whole-genome sequence identified a 20-bp deletion upstream of the <em>gdx</em> open reading frame, likely disrupting formation of the guanidinium riboswitch P2 loop and resulting in constitutive <em>gdx</em> expression.</div><div>To evaluate <em>gdx</em> function, the gene was cloned into the expression vector pBAD24 and expressed in <em>E. coli</em>. The resulting <em>gdx</em>-expressing strain exhibited even greater cesium resistance than ZX-1. Functional assays demonstrated that this strain mediates not only guanidinium/H⁺ antiport activity but also Cs⁺/H⁺ antiport activity. Cesium resistance was further enhanced in the presence of guanidinium, consistent with riboswitch-mediated induction of <em>gdx</em>.</div><div>Collectively, these findings provide evidence for a novel cesium efflux mechanism in <em>E. coli</em> and uncover an unexpected role of the guanidinium exporter Gdx in cesium export. These insights may facilitate the discovery of additional cesium-resistant microorganisms and broaden the potential for future applications.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100251"},"PeriodicalIF":0.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928175","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

Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution 脆弱拟杆菌的阶段变异控制着对微病毒的易感性并驱动其进化

Engineering Microbiology

Pub Date : 2025-12-18 DOI: 10.1016/j.engmic.2025.100252

Pan Huang , Meiqi Du , Yanqiu Liu , Zhenhao Han , Qian Wan , Fuming Liang , Wenyuan Han

The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the Microviridae phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting Microviridae phage φHBP1 from human feces. Infection of its host Bacteroides fragilis with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in B. fragilis H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.

人类肠道细菌及其噬菌体之间的相互作用和共同进化塑造了动态肠道微生物群，对人类健康产生重大影响。然而，潜在的机制在很大程度上尚未被探索。特别是，缺乏拟杆菌门和微病毒科噬菌体的细菌-噬菌体相互作用模型，限制了我们对它们在人类肠道中的生态作用的理解。在这项研究中，我们从人类粪便中分离出一株感染拟杆菌的微病毒科噬菌体φHBP1。其宿主脆弱拟杆菌（Bacteroides fragilis）感染φHBP1引发多种基因组结构变异，这些变异与宿主对φHBP1的抗性相关。反过来，我们在脆弱芽孢杆菌H1噬菌体进化实验中获得了φHBP1突变体，这些突变体在衣壳和先导蛋白内携带突变，并且可以重新感染耐药菌群。总之，我们的研究结果为肠道噬菌体和细菌之间的拮抗共同进化机制提供了新的见解，并对噬菌体通过进化来靶向噬菌体治疗中的耐药细菌而使噬菌体多样化具有重要意义。

{"title":"Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution","authors":"Pan Huang , Meiqi Du , Yanqiu Liu , Zhenhao Han , Qian Wan , Fuming Liang , Wenyuan Han","doi":"10.1016/j.engmic.2025.100252","DOIUrl":"10.1016/j.engmic.2025.100252","url":null,"abstract":"<div><div>The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the <em>Microviridae</em> phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting <em>Microviridae</em> phage φHBP1 from human feces. Infection of its host <em>Bacteroides fragilis</em> with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in <em>B. fragilis</em> H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100252"},"PeriodicalIF":0.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145886454","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

Effect of resistant starch type 5 on gut health through modulating gut microbiota 抗性淀粉5型通过调节肠道菌群对肠道健康的影响

Engineering Microbiology

Pub Date : 2025-12-18 DOI: 10.1016/j.engmic.2025.100250

Raju Ahmmed , Andrew Paff , Lingyan Kong , Songnan Li , Darrell W. Cockburn , Libo Tan

Resistant starch is a dietary fiber that escapes digestion in the small intestine and undergoes fermentation by gut microbiota in the colon, producing beneficial short-chain fatty acids (SCFAs). Among the various types of resistant starch, resistant starch type 5 (RS5) has gained significant attention due to its unique and stable structural and functional properties. RS5 is a self-assembled V-type inclusion complex formed when amylose helices encapsulate guest molecules. This formation occurs through non-covalent interactions after the native starch structure is disrupted, and a guest compound is introduced. This structure provides enhanced resistance to enzymatic digestion, slows fermentation, and facilitates targeted release of bioactive molecules, making it effective in modulating gut health. RS5 promotes the proliferation of beneficial gut microbiota while suppressing pathogenic species, leading to increased SCFAs production, mostly butyrate, acetate, and propionate, which maintain intestinal integrity, reduces inflammation, and supports metabolic regulation. RS5 also contributes to preventing and managing chronic diseases such as obesity, type 2 diabetes, and colorectal cancer. While prior research has focused on its preparation methods and physicochemical characteristics, the influence of RS5 on gut microbiota and host health remains inadequately explored. This review summarizes the formation, classification, and structural diversity of RS5 complexes and how these factors influence digestibility and fermentation kinetics. Furthermore, it explores how RS5 modulates the composition and metabolic activity of the gut microbiota, enhancing SCFAs production. By comparing RS5 with other RS types, this review highlights its superior prebiotic potential and supports RS5-based functional food development for improving gut and metabolic health, targeting gut microecology.

抗性淀粉是一种膳食纤维，在小肠中不被消化，在结肠中被肠道菌群发酵，产生有益的短链脂肪酸（SCFAs）。在各种类型的抗性淀粉中，抗性淀粉5型（RS5）因其独特而稳定的结构和功能特性而备受关注。RS5是一种自组装的v型包合物，当直链淀粉螺旋包裹客体分子时形成。这种形成是在原生淀粉结构被破坏后通过非共价相互作用发生的，并引入了客体化合物。这种结构增强了对酶消化的抵抗力，减缓了发酵，促进了生物活性分子的靶向释放，使其有效地调节肠道健康。RS5促进有益肠道菌群的增殖，同时抑制致病菌，导致scfa的产生增加，主要是丁酸盐、醋酸盐和丙酸盐，这些scfa维持肠道完整性，减少炎症，并支持代谢调节。RS5还有助于预防和控制慢性疾病，如肥胖、2型糖尿病和结直肠癌。虽然以往的研究主要集中在RS5的制备方法和理化特性上，但对RS5对肠道菌群和宿主健康的影响的探索还不够充分。本文综述了RS5复合物的形成、分类和结构多样性，以及这些因素对消化率和发酵动力学的影响。此外，它还探讨了RS5如何调节肠道微生物群的组成和代谢活性，从而促进SCFAs的产生。通过与其他RS类型的比较，本文强调了RS5在益生元方面的优势，并支持基于RS5的功能性食品的开发，以改善肠道和代谢健康，针对肠道微生态。

{"title":"Effect of resistant starch type 5 on gut health through modulating gut microbiota","authors":"Raju Ahmmed , Andrew Paff , Lingyan Kong , Songnan Li , Darrell W. Cockburn , Libo Tan","doi":"10.1016/j.engmic.2025.100250","DOIUrl":"10.1016/j.engmic.2025.100250","url":null,"abstract":"<div><div>Resistant starch is a dietary fiber that escapes digestion in the small intestine and undergoes fermentation by gut microbiota in the colon, producing beneficial short-chain fatty acids (SCFAs). Among the various types of resistant starch, resistant starch type 5 (RS5) has gained significant attention due to its unique and stable structural and functional properties. RS5 is a self-assembled V-type inclusion complex formed when amylose helices encapsulate guest molecules. This formation occurs through non-covalent interactions after the native starch structure is disrupted, and a guest compound is introduced. This structure provides enhanced resistance to enzymatic digestion, slows fermentation, and facilitates targeted release of bioactive molecules, making it effective in modulating gut health. RS5 promotes the proliferation of beneficial gut microbiota while suppressing pathogenic species, leading to increased SCFAs production, mostly butyrate, acetate, and propionate, which maintain intestinal integrity, reduces inflammation, and supports metabolic regulation. RS5 also contributes to preventing and managing chronic diseases such as obesity, type 2 diabetes, and colorectal cancer. While prior research has focused on its preparation methods and physicochemical characteristics, the influence of RS5 on gut microbiota and host health remains inadequately explored. This review summarizes the formation, classification, and structural diversity of RS5 complexes and how these factors influence digestibility and fermentation kinetics. Furthermore, it explores how RS5 modulates the composition and metabolic activity of the gut microbiota, enhancing SCFAs production. By comparing RS5 with other RS types, this review highlights its superior prebiotic potential and supports RS5-based functional food development for improving gut and metabolic health, targeting gut microecology.</div></div>","PeriodicalId":100478,"journal":{"name":"Engineering Microbiology","volume":"6 1","pages":"Article 100250"},"PeriodicalIF":0.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146078157","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