Current opinion in microbiology最新文献

英文中文

Protein families secreted by nematodes to modulate host immunity 线虫分泌调节宿主免疫的蛋白家族

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-04-01 Epub Date: 2025-02-15 DOI: 10.1016/j.mib.2025.102582

Florent Colomb, Henry J McSorley

Parasitic nematodes release a wide variety of immunomodulatory proteins, which allow them to escape the host’s immune-mediated killing or ejection mechanisms. This immunomodulation is mediated by nematode excretory/secretory (E/S) products, which contain multiple families of immunomodulatory proteins. Many of these families are conserved across different parasitic nematodes, while others are apparently unique to specific species. While some E/S products interact with host proteins, others have evolved to target host lipids, glycans, and metabolites. In this review, we will focus on three families of immunomodulatory proteins, which are particularly expanded in intestinal nematodes: the venom allergen-like proteins, the apyrases, and the complement control protein domain-containing proteins. These families of proteins suppress host immune responses, and evidence is gathering that these could be effective vaccine antigens against these intractable parasites.

寄生线虫释放各种各样的免疫调节蛋白，使它们能够逃脱宿主免疫介导的杀伤或排斥机制。这种免疫调节是由线虫排泄/分泌（E/S）产物介导的，其中包含多个免疫调节蛋白家族。其中许多科在不同的寄生线虫中都是保守的，而其他科显然是特定物种所特有的。虽然一些E/S产物与宿主蛋白相互作用，但其他E/S产物已经进化到针对宿主脂质，聚糖和代谢物。在这篇综述中，我们将重点介绍在肠道线虫中扩展的三个免疫调节蛋白家族：毒液过敏原样蛋白，apyrases和补体控制蛋白结构域蛋白。这些蛋白家族抑制宿主免疫反应，越来越多的证据表明，这些可能是对抗这些难治性寄生虫的有效疫苗抗原。

引用次数: 0

A CRISPR view on genetic screens in Toxoplasma gondii 刚地弓形虫基因筛选的CRISPR观点。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-01-08 DOI: 10.1016/j.mib.2024.102577

Franziska Hildebrandt , Ana N. Matias , Moritz Treeck

Genome editing technologies, such as CRISPR-Cas9, have revolutionised the study of genes in a variety of organisms, including unicellular parasites. Today, the CRISPR-Cas9 technology is vastly applied in high-throughput screens to investigate interactions between the Apicomplexan parasite Toxoplasma gondii and its hosts. In vitro and in vivo T. gondii screens performed in naive and restrictive conditions have led to the discovery of essential and fitness-conferring T. gondii genes, as well as factors important for virulence and dissemination. Recent studies have adapted the CRISPR-Cas9 screening technology to study T. gondii genes based on phenotypes unrelated to parasite survival. These advances were achieved by using conditional systems coupled with imaging, as well as single-cell RNA sequencing and phenotypic selection. Here, we review the state-of-the-art of CRISPR-Cas9 screening technologies with a focus on T. gondii, highlighting strengths, current limitations and future avenues for its development, including its application to other Apicomplexan species.

CRISPR-Cas9等基因组编辑技术已经彻底改变了对多种生物（包括单细胞寄生虫）基因的研究。今天，CRISPR-Cas9技术被广泛应用于高通量筛选，以研究顶复合体寄生虫弓形虫与其宿主之间的相互作用。在初始条件和限制性条件下进行的体外和体内弓形虫筛查已经发现了必不可少的和具有适应性的弓形虫基因，以及对毒力和传播至关重要的因素。最近的研究采用CRISPR-Cas9筛选技术，基于与寄生虫生存无关的表型研究弓形虫基因。这些进步是通过使用条件系统结合成像，以及单细胞RNA测序和表型选择来实现的。在这里，我们回顾了最新的CRISPR-Cas9筛选技术，重点是弓形虫，突出了其优势，当前的局限性和未来的发展途径，包括其在其他顶复合体物种中的应用。

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引用次数: 0

Gram-positive pathogens, inflammation, and the host lipid environment 革兰氏阳性病原体，炎症和宿主脂质环境

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-02-07 DOI: 10.1016/j.mib.2025.102581

Reginald A Woods , Sarai Guzman Vela , Francis Alonzo III

The host lipid environment is a barrier to bacterial infection that comprises antimicrobial fatty acids and impermeable lipids that keep infectious agents from penetrating tissues. Bacterial and host lipids also signal to the immune system to regulate inflammation. Notably, bacterial lipids activate Toll-like receptors to initiate cytokine production, immune cell recruitment, and oxidative burst to control infection. Bacterial pathogens must adapt to the lipid environment, including bactericidal host fatty acids and inflammatory lipids, in ways that promote persistence in diverse tissues. Here, we discuss current advances in the understanding of Staphylococcus aureus lipid interactions that contribute to inflammation and innate immunity and consider the complex roles of host inflammatory lipids in driving immune defenses and antibacterial activity. In addition, we endeavor to introduce similar processes in other Gram-positive pathogens. These recent studies highlight the growing body of knowledge on the effects of lipid metabolism on host immunity and pathogenesis.

宿主脂质环境是细菌感染的屏障，包括抗微生物脂肪酸和不渗透脂质，可防止感染因子穿透组织。细菌和宿主的脂质也会向免疫系统发出信号来调节炎症。值得注意的是，细菌脂质激活toll样受体，启动细胞因子产生、免疫细胞募集和氧化爆发，以控制感染。细菌病原体必须适应脂质环境，包括杀菌宿主脂肪酸和炎性脂质，以促进在不同组织中的持久性。在这里，我们讨论了目前对金黄色葡萄球菌脂质相互作用的理解进展，这些相互作用有助于炎症和先天免疫，并考虑宿主炎症脂质在驱动免疫防御和抗菌活性中的复杂作用。此外，我们努力在其他革兰氏阳性病原体中引入类似的过程。最近的研究表明，脂质代谢对宿主免疫及其发病机制的影响越来越多。

引用次数: 0

Harnessing gut microbial communities to unravel microbiome functions 利用肠道微生物群落来揭示微生物群的功能。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-01-08 DOI: 10.1016/j.mib.2024.102578

Samir Giri , Handuo Shi , Athanasios Typas , Kerwyn Casey Huang

The gut microbiome impacts human health in direct and indirect ways. While many associations have been discovered between specific microbiome compositions and diseases, establishing causality, understanding the underlying mechanisms, and developing successful microbiome-based therapies require novel experimental approaches. In this opinion, we discuss how in vitro cultivation of diverse communities enables systematic investigation of the individual and collective functions of gut microbes. Up to now, the field has relied mostly on simple, bottom-up assembled synthetic communities or more complex, undefined stool-derived communities. Although powerful for dissecting interactions and mapping causal effects, these communities suffer either from ignoring the complexity, diversity, coevolution, and dynamics of natural communities or from lack of control of community composition. These limitations can be overcome in the future by establishing personalized culture collections from stool samples of different donors and assembling personalized communities to investigate native interactions and ecological relationships in a controlled manner.

肠道微生物群以直接和间接的方式影响人类健康。虽然已经发现了特定微生物组组成与疾病之间的许多关联，但建立因果关系、了解潜在机制和开发成功的基于微生物组的治疗方法需要新的实验方法。在这种观点下，我们讨论了如何在体外培养不同的群落能够系统地研究肠道微生物的个体和集体功能。到目前为止，该领域主要依赖于简单的，自下而上组装的合成群落或更复杂的，未定义的粪便衍生群落。尽管这些群落在剖析相互作用和绘制因果关系方面很强大，但它们要么忽视了自然群落的复杂性、多样性、共同进化和动态，要么缺乏对群落组成的控制。这些限制可以在未来通过从不同捐赠者的粪便样本中建立个性化的培养收集，并以可控的方式组建个性化的社区来调查当地的相互作用和生态关系来克服。

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引用次数: 0

The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes 微生物组设计的理论与数据架构：迈向微生物组的s矩阵。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-01-22 DOI: 10.1016/j.mib.2025.102580

Shreya Arya , Ashish B George , James O'Dwyer

Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models — a middle, third way for using theory to inform design.

设计微生物组在健康、生物工程和可持续性方面的应用与对微生物群落组装规则的基本理论理解有着内在的联系。微生物生态学家已经使用了一系列数学模型来理解、预测和控制微生物群，从以微生物种群及其相互作用为重点的机械模型，到纯粹的统计方法，在经验和实验数据中寻找模式。我们回顾了这些建模方法在设计新型微生物组时的成功和局限性，特别是在（不可避免地）不完整的实验数据指导下。虽然在预测群落组装的一般模式方面取得了成功，但机械和现象学模型往往达不到设计和实现微生物组特定功能所需的精度。我们认为，为了在不同环境中有效地设计具有最佳功能的微生物群落，生态学家应该将数据驱动技术与机制模型结合起来——这是利用理论为设计提供信息的第三种中间方式。

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引用次数: 0

Alginate catabolic systems in marine bacteria 海藻酸盐在海洋细菌中的分解代谢系统。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2024-12-09 DOI: 10.1016/j.mib.2024.102564

Fei Xu , Xiu-Lan Chen , Yu-Zhong Zhang

Brown algae, constituting the second largest group of marine macroalgae, fix significant amounts of inorganic carbon into alginate, the most abundant polysaccharide found in their cell walls. Alginate serves as an important macromolecular carbon source for marine bacteria. The catabolism of alginate by bacteria is an important step in the marine carbon cycle, and this area of research has attracted growing interests over the past decade. Here, we provide an overview of the recent advances in our understanding of marine bacterial alginate catabolic systems, both in individual organisms and within bacterial consortia, discuss the possibility of additional alginate metabolic pathways in light of the present findings, and highlight the future research foci.

褐藻是海洋大型藻类的第二大群体，它们将大量的无机碳固定在藻酸盐中，而藻酸盐是它们细胞壁中含量最多的多糖。藻酸盐是海洋细菌重要的大分子碳源。海藻酸盐的细菌分解代谢是海洋碳循环的一个重要步骤，这一研究领域在过去十年中引起了越来越多的兴趣。在这里，我们概述了我们对海洋细菌藻酸盐分解代谢系统的最新进展，无论是在个体生物还是在细菌群体中，根据目前的发现讨论了其他藻酸盐代谢途径的可能性，并强调了未来的研究重点。

引用次数: 0

Revisiting the potential of natural products in antimycobacterial therapy: advances in drug discovery and semisynthetic solutions 重新审视天然产物在抗细菌治疗中的潜力：药物发现和半合成解决方案的进展。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2024-12-31 DOI: 10.1016/j.mib.2024.102576

Maya George, Gerard D Wright

Natural products have been pivotal in treating mycobacterial infections with early antibiotics such as streptomycin, forming the foundation of tuberculosis therapy. However, the emergence of multidrug-resistant and extensively drug-resistant Mycobacterium species has intensified the need for novel antimycobacterial agents. In this review, we revisit the historical contributions of natural products to antimycobacterial drug discovery and highlight recent advances in the field. We assess the application of molecular networking and the exploration of unculturable bacteria in identifying new antimycobacterial compounds such as amycobactin and levesquamides. We also highlight the role of semisynthesis in optimizing natural products, exemplified by sequanamycins and spectinomycin analogs that evade M. tuberculosis’ intrinsic resistance. Finally, we discuss emerging technologies that are promising to accelerate the discovery and development of next-generation antimycobacterial therapies. Despite ongoing challenges, these innovative approaches offer renewed hope in addressing the growing crisis of drug-resistant mycobacterial infections.

天然产物在用链霉素等早期抗生素治疗分枝杆菌感染方面起着关键作用，形成了结核病治疗的基础。然而，多药耐药和广泛耐药分枝杆菌物种的出现加剧了对新型抗细菌药物的需求。在这篇综述中，我们回顾了天然产物对抗真菌药物发现的历史贡献，并重点介绍了该领域的最新进展。我们评估了分子网络和探索不可培养细菌在鉴定新的抗真菌化合物（如amycoactin和levesquamides）中的应用。我们还强调了半合成在优化天然产物中的作用，例如红霉素和大观霉素类似物可以逃避结核分枝杆菌的内在耐药性。最后，我们讨论了有望加速下一代抗细菌疗法的发现和开发的新兴技术。尽管面临着持续的挑战，但这些创新方法为解决日益严重的耐药分枝杆菌感染危机带来了新的希望。

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引用次数: 0

The promise of CRISPR-associated transposons for bacterial functional genomics crispr相关转座子在细菌功能基因组学中的应用前景。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2024-12-03 DOI: 10.1016/j.mib.2024.102563

Amy B Banta , Rodrigo A Cuellar , Nischala Nadig , Bryce C Davis , Jason M Peters

CRISPR-associated transposons (CASTs) are naturally occurring amalgamations of CRISPR-Cas machinery and Tn7-like transposons that direct site-specific integration of transposon DNA via programmable guide RNAs. Although the mechanisms of CAST-based transposition have been well studied at the molecular and structural level, CASTs have yet to be broadly applied to bacterial genome engineering and systematic gene phenotyping (i.e. functional genomics) — likely due to their relatively recent discovery. Here, we describe the function and applications of CASTs, focusing on well-characterized systems, including the type I-F CAST from Vibrio cholerae (VcCAST) and type V-K CAST from Scytonema hofmanni (ShCAST). Further, we discuss the potentially transformative impact of targeted transposition on bacterial functional genomics by proposing genome-scale extensions of existing CAST tools.

crispr相关转座子（cast）是CRISPR-Cas机制和tn7样转座子的自然合并，通过可编程引导rna指导转座子DNA的位点特异性整合。尽管基于cast的转位机制已经在分子和结构水平上得到了很好的研究，但cast尚未广泛应用于细菌基因组工程和系统基因表型（即功能基因组学）-可能是由于它们相对较新的发现。本文介绍了CAST的功能和应用，重点介绍了具有良好特征的系统，包括来自霍乱弧菌的I-F型CAST （VcCAST）和来自hofmanni Scytonema的V-K型CAST （ShCAST）。此外，我们通过提出现有CAST工具的基因组规模扩展，讨论了靶向转位对细菌功能基因组学的潜在变革性影响。

引用次数: 0

Corrigendum to “Innovative and potential treatments for fungal central nervous system infections” [Curr Opin Microbiol 76 (2023) 102397] “真菌性中枢神经系统感染的创新和潜在治疗方法”的更正[现行微生物学杂志76(2023)102397]。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-01-30 DOI: 10.1016/j.mib.2025.102583

Marta Reguera-Gomez , Michael R. Dores , Luis R. Martinez

引用次数: 0

Dissecting S-itaconation at host–pathogen interactions with chemical proteomics tools 利用化学蛋白质组学工具分析宿主-病原体相互作用中的S-itaconation。

IF 5.9 2区生物学 Q1 MICROBIOLOGY

Current opinion in microbiology

Pub Date : 2025-02-01 Epub Date: 2025-01-21 DOI: 10.1016/j.mib.2025.102579

Zihua Liu , Chu Wang

The molecular essence of the battle between host and pathogens lies in the protein–protein or protein–metabolite interactions. Itaconate is one of the most upregulated immunometabolites, regulating immune responses through either noncovalent binding or covalent modification in the host. We herein briefly review recent progresses in the discoveries of physiological and pathological roles of itaconate and applications of chemical proteomic technologies in exploring itaconate modifications on cysteines (S-itaconation) at the interface of host–pathogen interactions. Key challenges are also proposed as future outlook.

宿主和病原体之间战斗的分子本质在于蛋白质-蛋白质或蛋白质-代谢物的相互作用。衣康酸酯是一种上调最多的免疫代谢物，通过非共价结合或共价修饰在宿主体内调节免疫反应。本文简要介绍衣康酸的生理和病理作用的最新发现，以及化学蛋白质组学技术在探索衣康酸在宿主-病原体相互作用界面上对半胱氨酸的修饰（S-itaconation）方面的应用。并提出了未来展望的主要挑战。

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全部化学•材料生命科学医学物理工程技术环境•农林材料科学地球科学法学管理学化学环境科学与生态学计算机科学教育学经济学农林科学人文科学生物学数学物理与天体物理心理学综合性期刊其他工业工程理学历史学农学文学信息工程

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