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Starvation as a weapon in fungal–plant warfare 饥饿是真菌与植物战争的武器
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-01-23 DOI: 10.1016/j.mib.2026.102708
Sara Vujakovic , Matthias Kretschmer , James W Kronstad
Fungal pathogens cause devastating diseases in staple crops and pose a tremendous threat to food security. Therefore, it is critical to understand the mechanisms of fungal attack and plant defense. Recent studies provide new insights into the role of nutrient manipulation for both plant and pathogen combatants. On the plant side, a defense signaling system has been discovered that provokes starvation during disease to limit access to carbohydrate by the head smut fungus Sporisorium reilianum. For pathogenic fungi, a novel class of effector proteins in the rice blast fungus Magnaporthe oryzae and other fungi has Nudix hydrolase activity to provoke phosphate limitation in host plants. This novel effector strategy impairs plant immunity, thus favoring pathogen proliferation and disease. Intriguing new work also demonstrates that the phytohormones strigolactone and methyl jasmonate influence phosphate and carbon metabolism in fungi. As discussed in this review, these examples illustrate the importance of nutrients in determining disease outcomes and also provide insights to potentially support crop protection.
真菌致病菌对主要作物造成毁灭性疾病,对粮食安全构成巨大威胁。因此,了解真菌攻击和植物防御的机制至关重要。最近的研究为植物和病原体的战斗提供了营养操纵的新见解。在植物方面,已经发现了一种防御信号系统,该系统在疾病期间引发饥饿,以限制头部黑穗病真菌孢子菌对碳水化合物的获取。在致病性真菌方面,稻瘟病菌Magnaporthe oryzae和其他真菌中的一类新型效应蛋白具有Nudix水解酶活性,可在寄主植物中引起磷酸盐限制。这种新的效应策略削弱了植物的免疫力,从而有利于病原体的增殖和疾病。有趣的新研究还表明,植物激素独角麦内酯和茉莉酸甲酯影响真菌的磷酸盐和碳代谢。正如本综述所讨论的,这些例子说明了营养物质在决定疾病结果方面的重要性,也为潜在的支持作物保护提供了见解。
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引用次数: 0
Cave microorganisms: hidden players in global greenhouse gas cycling and climate regulation 洞穴微生物:全球温室气体循环和气候调节的隐藏参与者
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-04-01 Epub Date: 2026-01-27 DOI: 10.1016/j.mib.2026.102707
Tamara Martin-Pozas , Soledad Cuezva , Angel Fernandez-Cortes , Janez Mulec , Marcela Hernández
Caves are unique among ecosystem types because of their physical structures and biological functions. Embedded in rocks, the geological setting defines the boundaries of caves and dictates how energy and matter move through them. General features of caves, compared to surface ecosystems, include absence of light, relatively stable temperature and humidity, and oligotrophic conditions. Despite these conditions, caves are highly diverse ecosystems whose environmental properties are shaped by geological, hydrological, and climatic factors. Cave microbiomes metabolize atmospheric trace gases, such as methane, nitrous oxide, and carbon dioxide, contributing to greenhouse gas (GHG) cycling dynamics. In some cases, these microbes also form biominerals, such as calcium carbonate, highlighting critical gaps in our understanding of subterranean biogeochemical processes. Some of these gaps include the limited genomic data and geographic bias in the literature. Herein, we review the current state of knowledge surrounding the potential of cave microorganisms, including those capable of biomineralizing calcium carbonate, as agents for sustainable GHG sequestration and climate change mitigation, with emerging strategies for developing novel sustainable biotechnological solutions. By revealing the hidden microbial activity beneath the Earth’s surface, this review proposes integrating subterranean ecosystems into global climate models, reframing caves as metabolically and functionally active contributors to the planet’s climate system rather than isolated geological features.
洞穴在生态系统类型中具有独特的物理结构和生物功能。嵌入岩石中的地质环境定义了洞穴的边界,并决定了能量和物质如何在洞穴中移动。与地表生态系统相比,洞穴的一般特征包括缺乏光线、相对稳定的温度和湿度以及少营养条件。尽管有这些条件,洞穴是高度多样化的生态系统,其环境属性受地质、水文和气候因素的影响。洞穴微生物群代谢大气中的微量气体,如甲烷、一氧化二氮和二氧化碳,促进温室气体(GHG)循环动力学。在某些情况下,这些微生物也形成生物矿物,如碳酸钙,突出了我们对地下生物地球化学过程理解的关键空白。其中一些差距包括有限的基因组数据和文献中的地理偏差。在此,我们回顾了洞穴微生物潜力的现状,包括那些能够生物矿化碳酸钙的洞穴微生物,作为可持续温室气体封存和减缓气候变化的代理,以及开发新的可持续生物技术解决方案的新兴战略。通过揭示地表下隐藏的微生物活动,本综述建议将地下生态系统整合到全球气候模型中,将洞穴重新定义为地球气候系统的代谢和功能活跃贡献者,而不是孤立的地质特征。
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引用次数: 0
Model-guided design of regulatable promoters for synthetic biology 合成生物学中可调节启动子的模型引导设计。
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2026-01-03 DOI: 10.1016/j.mib.2025.102701
Robert C Brewster, Vinuselvi Parisutham
Designing regulatable promoters with specified functional output remains difficult because natural promoters are unlikely to match a particular specification, and the sequence design space is large, complex, and challenging to interpret. This review advances a context-minimized, measurement-first approach in Escherichia coli that couples simple assays to a single transcription factor (TF)-based thermodynamic framework. The model is structured around two key concepts related to the TF: occupancy and function. Here, we outline how these concepts can be manipulated and measured at the level of DNA sequence and how those perturbations can impact fold-change and thus features of the promoter, such as dynamic range, leakiness, and sensitivity. LacI serves as a worked example in which sequence–occupancy, copy number, and competition, position-dependent function, and inducer allostery have been measured and can be combined to optimize response features. Overall, simple measurements linked to interpretable models provide a practical route to compiling desired regulatory specifications into sequence-level designs.
设计具有特定功能输出的可调节启动子仍然很困难,因为自然启动子不太可能匹配特定的规格,而且序列设计空间很大,很复杂,很难解释。本综述提出了一种环境最小化、测量优先的大肠杆菌方法,该方法将简单的分析与基于单一转录因子(TF)的热力学框架结合起来。该模型围绕着与TF相关的两个关键概念:占用和功能。在这里,我们概述了如何在DNA序列水平上操纵和测量这些概念,以及这些扰动如何影响折叠变化,从而影响启动子的特征,如动态范围、漏性和灵敏度。LacI是一个有效的例子,其中序列占用、拷贝数、竞争、位置依赖函数和诱导剂变构已经被测量,并且可以结合起来优化响应特征。总体而言,与可解释模型相关联的简单测量提供了将所需的监管规范编译为序列级设计的实用途径。
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引用次数: 0
From edits to insights: precision microbial engineering for systems biology 从编辑到见解:精密微生物工程系统生物学。
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2026-01-19 DOI: 10.1016/j.mib.2025.102705
Vlad S Băţăgui , Antoine Delhaye , Sibylle C Vonesch
Microbes are powerful systems for exploring and engineering biology. Their compact genomes, rapid generation times, and experimental tractability enable quantitative analyses that shed light on both conserved cellular mechanisms and traits of medical or industrial relevance. Building on this foundation, systematic perturbation has become central to microbial systems biology. Genome-scale knockout and CRISPRi/a libraries have mapped gene function and network architecture, yet these approaches largely operate at the level of gene presence or absence, leaving the effects of precise sequence variants unexplored. Recent and emerging precision-perturbation strategies now reveal biological principles inaccessible to gene-level perturbations, from detailed sequence–function maps of proteins to the impact of natural and engineered variation across pathways. In this review, we highlight recent advances that have made systematic interrogation of thousands of variants — within single loci and across entire genomes — increasingly comprehensive and efficient. We will discuss how these technical leaps reveal systems-level principles of genome function and provide outlooks on how they could be complemented by diverse phenotypic readouts and perturbations in combinatorial space. Taken together, empowering precision engineering approaches will further advance our understanding of biological function, while accelerating progress in biotechnology and synthetic biology.
微生物是探索和工程生物学的强大系统。它们紧凑的基因组,快速的生成时间和实验可追溯性使定量分析能够阐明保守的细胞机制和医学或工业相关的特征。在此基础上,系统扰动已成为微生物系统生物学的核心。基因组规模的基因敲除和CRISPRi/a文库已经绘制了基因功能和网络结构,但这些方法主要在基因存在或缺失的水平上运行,使得精确序列变异的影响未被探索。最近和新兴的精确扰动策略揭示了基因水平扰动无法达到的生物学原理,从蛋白质的详细序列功能图到自然和工程变异的影响。在这篇综述中,我们重点介绍了最近的进展,即在单个位点和整个基因组中对数千种变异进行系统的询问,越来越全面和有效。我们将讨论这些技术飞跃如何揭示基因组功能的系统级原理,并展望如何通过组合空间中的不同表型读数和扰动来补充它们。总之,授权精密工程方法将进一步推进我们对生物功能的理解,同时加速生物技术和合成生物学的进展。
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引用次数: 0
Emerging governance considerations for the deployment of genetically engineered microbes 对基因工程微生物部署的新兴治理考虑
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2025-12-13 DOI: 10.1016/j.mib.2025.102685
Avery M Brewer , Dalton R George , Emma K Frow
In this review, we identify emerging trends in the governance and policy landscape surrounding the real-world deployment of genetically engineered microbes (GEMs), focusing on the United States and Europe. A recent wave of commercialized GEMs in the US suggests that interest in developing GEMs for open release might be on the rise, after a 40-year period of very low commercial activity. GEMs are receiving renewed attention for their potential roles in agriculture, sustainable manufacturing, biosensing, environmental restoration, energy production, and human health. Advances in genetic modification technologies, combined with the growing number of possible open release applications for GEMs, stand to challenge existing governance frameworks in several ways. First, the feasibility of either strict product- or process-based regulatory frameworks for biotechnology is being increasingly tested. Second, the desirability of long-term persistence and ecological action of GEMs in some application contexts complicates the logic of typical risk assessments for deliberate release of genetically modified organisms. Synergistic, long-term, and indirect impacts of open release are challenging to reliably predict and call for risk assessment methods able to accommodate high levels of uncertainty or ignorance. Third, increasing variety in application types for GEMs is likely to yield new business models and routes to market. Approaches such as direct-to-consumer marketing raise challenging questions around stewardship, consent, transborder movement, and monitoring of GEMs. This constellation of issues will benefit from interdisciplinary research and stakeholder deliberation at local, national, and international levels to promote robust and adaptable GEM governance in the coming decades.
在这篇综述中,我们确定了围绕现实世界中基因工程微生物(GEMs)部署的治理和政策格局的新趋势,重点是美国和欧洲。在经历了40年的低商业活动之后,美国最近一波商业化的GEMs表明,开发公开发布的GEMs的兴趣可能正在上升。GEMs因其在农业、可持续制造、生物传感、环境恢复、能源生产和人类健康方面的潜在作用而重新受到关注。遗传修饰技术的进步,结合gem可能的开放发布应用程序的数量的增长,将在几个方面挑战现有的治理框架。首先,严格的基于产品或基于过程的生物技术管理框架的可行性正在受到越来越多的考验。其次,在某些应用环境中,GEMs的长期持久性和生态作用的可取性使故意释放转基因生物的典型风险评估的逻辑复杂化。开放释放的协同、长期和间接影响是具有挑战性的,难以可靠地预测,并且需要能够适应高度不确定性或无知的风险评估方法。第三,GEMs应用程序类型的增加可能产生新的商业模式和进入市场的途径。直接面向消费者的营销等方法提出了关于gem管理、许可、跨境移动和监控等具有挑战性的问题。这一系列问题将受益于地方、国家和国际层面的跨学科研究和利益相关者审议,以促进未来几十年健全和适应性强的创业板治理。
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引用次数: 0
Insights into the lifecycle of Cryptosporidium and compounds targeting developmental stages 隐孢子虫的生命周期和针对发育阶段的化合物的见解
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2026-01-14 DOI: 10.1016/j.mib.2025.102703
Zoë Reynolds, Sumiti Vinayak
The intestinal protozoan parasite, Cryptosporidium, is a leading cause of diarrhea-associated illness and death in young children, immunocompromised individuals, and neonatal ruminant animals. This apicomplexan parasite completes its entire lifecycle within a single host, involving a timely and coordinated progression through asexual and sexual developmental stages. With no fully effective drugs or vaccines available, a deeper understanding of the parasite’s lifecycle stages is crucial for identifying new molecular targets for disease intervention. In this review, we discuss recent advances in understanding the Cryptosporidium developmental lifecycle, stage-specific gene expression, and the role of parasite proteins in invasion, asexual proliferation, and sexual stages. We also discuss the lifecycle stages targeted by a few highly effective anticryptosporidial compounds.
肠道原生动物寄生虫隐孢子虫是幼儿、免疫功能低下个体和新生反刍动物腹泻相关疾病和死亡的主要原因。这种顶复合体寄生虫在一个寄主内完成其整个生命周期,包括无性和有性发育阶段的及时和协调的进展。由于没有完全有效的药物或疫苗,更深入地了解寄生虫的生命周期阶段对于确定疾病干预的新分子靶点至关重要。本文综述了隐孢子虫的发育周期、阶段特异性基因表达、寄生虫蛋白在入侵、无性繁殖和有性阶段的作用等方面的最新进展。我们还讨论了一些高效的抗隐孢子虫化合物所针对的生命周期阶段。
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引用次数: 0
Engineering microbes to modulate innate immune signaling: strategies for host–microbe interactions 工程微生物调节先天免疫信号:宿主-微生物相互作用的策略。
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2025-12-22 DOI: 10.1016/j.mib.2025.102695
Shanna Bonanno , Neel S Joshi
The human gastrointestinal tract hosts a dense microbial community that closely interfaces with the mucosal immune system to preserve homeostasis. While dysregulation of this interaction contributes to certain disease states, through targeted microbial engineering, these interactions can be modulated for therapeutic benefit. Although engineered microbial therapeutics have shown encouraging preclinical results, few approaches have progressed into clinical pipelines. This gap highlights the need for engineered microbes with greater precision, reliability, and context-dependent control. The innate immune system is primed to rapidly sense microbial signals through pattern recognition receptors and provides accessible and tractable targets for such interventions. This review highlights four strategies that have used engineered probiotics to modulate innate immunity: (1) direct immune cell engagement through surface-display, (2) production of soluble immune effectors, (3) extracellular vesicles for delivery of immune modulators, and (4) environmentally responsive systems to enable spatial and temporal control over immune modulation. Bridging microbial engineering with mucosal immunology can enable engineered probiotics to function as dynamic, context-aware immunomodulators.
人类胃肠道拥有密集的微生物群落,与粘膜免疫系统紧密结合以保持体内平衡。虽然这种相互作用的失调会导致某些疾病状态,但通过靶向微生物工程,可以调节这些相互作用以获得治疗益处。尽管工程微生物疗法已经显示出令人鼓舞的临床前结果,但很少有方法进入临床管道。这一差距突出了对具有更高精度、可靠性和环境依赖控制的工程微生物的需求。先天免疫系统通过模式识别受体快速感知微生物信号,并为此类干预提供了可接近和可处理的靶标。这篇综述强调了使用工程益生菌调节先天免疫的四种策略:(1)通过表面展示直接参与免疫细胞;(2)产生可溶性免疫效应器;(3)细胞外囊泡递送免疫调节剂;(4)环境响应系统实现对免疫调节的空间和时间控制。桥接微生物工程与粘膜免疫学可以使工程益生菌作为动态的,环境敏感的免疫调节剂的功能。
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引用次数: 0
Single-cell analysis and control of microbial systems using optogenetics 微生物系统单细胞分析与光遗传学控制
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2026-01-09 DOI: 10.1016/j.mib.2025.102702
Hellen Huang , Mary J Dunlop
Single-cell resolution studies have transformed our understanding of microbial systems, revealing substantial cell-to-cell heterogeneity and complex dynamic behaviors. This review describes recent advances in using optogenetics, where light-sensitive proteins control cellular processes, to investigate microbial behavior at the individual cell level. We discuss studies where optogenetic approaches have enabled high-resolution analysis of properties such as relative cell positioning, subcellular localization, morphology, and gene expression dynamics. In addition, we highlight emerging feedback and event-driven control methods that dynamically modulate cellular states using light signals. By leveraging light's unique capabilities for spatial and temporal manipulation, researchers can now probe cellular characteristics with unprecedented precision. We anticipate significant advances as researchers introduce more sophisticated dynamically patterned light signals for single-cell microbial research.
单细胞分辨率研究改变了我们对微生物系统的理解,揭示了细胞间的异质性和复杂的动态行为。本文综述了利用光遗传学在单个细胞水平上研究微生物行为的最新进展,其中光敏蛋白控制细胞过程。我们讨论了一些研究,其中光遗传学方法能够对诸如相对细胞定位、亚细胞定位、形态学和基因表达动力学等特性进行高分辨率分析。此外,我们强调了新兴的反馈和事件驱动控制方法,这些方法使用光信号动态调制细胞状态。通过利用光在空间和时间操纵方面的独特能力,研究人员现在可以以前所未有的精度探测细胞特征。随着研究人员为单细胞微生物研究引入更复杂的动态模式光信号,我们预计会取得重大进展。
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引用次数: 0
Corrigendum to “Assembly and maturation of methyl-coenzyme M reductase in methanogenic archaea” [Curr Opin Microbiol, 87 (2025) 102637] “甲基辅酶M还原酶在产甲烷古菌中的组装和成熟”[j] .微生物学报,87(2025):102637。
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2025-12-11 DOI: 10.1016/j.mib.2025.102684
Sophia A Adler , Grayson L Chadwick , Dipti D Nayak
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引用次数: 0
Current perspectives of host-pathogen dynamics in coccidioidomycosis 球孢子菌病宿主-病原体动力学的最新研究进展
IF 7.5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2026-02-01 Epub Date: 2025-11-25 DOI: 10.1016/j.mib.2025.102682
Matthew M Morales , Katrina M Jackson , Bridget M Barker
Coccidioidomycosis (CM), commonly known as Valley fever, is a respiratory infection caused by the inhalation or implantation of infectious arthroconidia produced by the dimorphic human fungal pathogens Coccidioides immitis and Coccidioides posadasii from the environment. The current endemic range includes the southwestern region of the United States and parts of South and Central America. Infected individuals may experience a spectrum of symptoms from asymptomatic to severe respiratory symptoms. Importantly, the fungus can disseminate to other tissues to produce severe symptoms, and in some cases, death. Despite significant effort from Coccidioides researchers to develop effective vaccines against Valley fever, there is currently no human vaccine available. This review highlights the recent advances in understanding host immune response and addressing knowledge gaps in the field.
球孢子菌病(ccidiidomycosis, CM),俗称谷热,是一种呼吸道感染,由吸入或植入由环境中的二态人类真菌病原体球孢子虫(coccidiides immitis)和波萨达球孢子虫(coccidiides posadasii)产生的传染性关节孢子引起。目前的流行范围包括美国西南部地区以及南美洲和中美洲的部分地区。受感染者可能出现从无症状到严重呼吸道症状的一系列症状。重要的是,真菌可以传播到其他组织,产生严重的症状,在某些情况下,死亡。尽管球虫研究人员为开发有效的谷热疫苗做出了巨大努力,但目前还没有可用的人类疫苗。本文综述了在了解宿主免疫反应和解决该领域知识空白方面的最新进展。
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引用次数: 0
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Current opinion in microbiology
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