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Targeting Megasphaera species to promote cervicovaginal health. 针对 Megasphaera 物种促进宫颈阴道健康。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-05-21 DOI: 10.1016/j.tim.2024.04.015
Mariano A Molina, Sneha Biswas, Virginia Núñez-Samudio, Iván Landires

Maintaining a healthy cervicovaginal microbiome (CVM) is vital for women's wellbeing; it is dependent primarily on Lactobacillus dominance. Microbiome imbalances, driven by Megasphaera species, contribute to infections and disease. Comprehensive research into Megasphaera biology and interventions is crucial for personalized women's healthcare, and additional efforts are required to mitigate the risks posed by cervicovaginal dysbiosis.

保持健康的宫颈阴道微生物组(CVM)对女性的健康至关重要;它主要取决于乳酸杆菌的优势。由 Megasphaera 驱动的微生物组失衡会导致感染和疾病。对 Megasphaera 生物学和干预措施的全面研究对于个性化的妇女保健至关重要,需要做出更多努力来减轻宫颈阴道菌群失调带来的风险。
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引用次数: 0
Cable bacteria: widespread filamentous electroactive microorganisms protecting environments. 电缆细菌:保护环境的广泛丝状电活性微生物。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2023-12-26 DOI: 10.1016/j.tim.2023.12.001
Meijun Dong, Lars Peter Nielsen, Shan Yang, Lasse Hyldgaard Klausen, Meiying Xu

Cable bacteria have been identified and detected worldwide since their discovery in marine sediments in Aarhus Bay, Denmark. Their activity can account for the majority of oxygen consumption and sulfide depletion in sediments, and they induce sulfate accumulation, pH excursions, and the generation of electric fields. In addition, they can affect the fluxes of other elements such as calcium, iron, manganese, nitrogen, and phosphorous. Recent developments in our understanding of the impact of cable bacteria on element cycling have revealed their positive contributions to mitigating environmental problems, such as recovering self-purification capacity, enhancing petroleum hydrocarbon degradation, alleviating phosphorus eutrophication, delaying euxinia, and reducing methane emission. We highlight recent research outcomes on their distribution, state-of-the-art findings on their physiological characteristics, and ecological contributions.

自从在丹麦奥胡斯湾的海洋沉积物中发现缆索细菌以来,世界各地都发现并检测到了这种细菌。它们的活动可导致沉积物中大部分氧气消耗和硫化物耗竭,并引起硫酸盐积累、pH 值偏移和电场产生。此外,它们还会影响钙、铁、锰、氮和磷等其他元素的通量。最近,我们对缆索细菌对元素循环的影响的认识有了新的发展,揭示了它们在缓解环境问题方面的积极贡献,如恢复自净能力、提高石油烃降解、减轻磷富营养化、延缓休眠期和减少甲烷排放。我们重点介绍了有关其分布的最新研究成果、有关其生理特征的最新发现以及对生态的贡献。
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引用次数: 0
Diagnosing arthropod-borne flaviviruses: non-structural protein 1 (NS1) as a biomarker. 诊断节肢动物传播的黄病毒:作为生物标志物的非结构蛋白1(NS1)。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2023-12-21 DOI: 10.1016/j.tim.2023.11.016
Martina Ceconi, Kevin K Ariën, Peter Delputte

In recent decades, the presence of flaviviruses of concern for human health in Europe has drastically increased,exacerbated by the effects of climate change - which has allowed the vectors of these viruses to expand into new territories. Co-circulation of West Nile virus (WNV), Usutu virus (USUV), and tick-borne encephalitis virus (TBEV) represents a threat to the European continent, and this is further complicated by the difficulty of obtaining an early and discriminating diagnosis of infection. Moreover, the possibility of introducing non-endemic pathogens, such as Japanese encephalitis virus (JEV), further complicates accurate diagnosis. Current flavivirus diagnosis is based mainly on RT-PCR and detection of virus-specific antibodies. Yet, both techniques suffer from limitations, and the development of new assays that can provide an early, rapid, low-cost, and discriminating diagnosis of viral infection is warranted. In the pursuit of ideal diagnostic assays, flavivirus non-structural protein 1 (NS1) serves as an excellent target for developing diagnostic assays based on both the antigen itself and the antibodies produced against it. This review describes the potential of such NS1-based diagnostic methods, focusing on the application of flaviviruses that co-circulate in Europe.

近几十年来,欧洲出现的危害人类健康的黄病毒急剧增加,气候变化的影响更是雪上加霜--气候变化使得这些病毒的传播媒介扩展到了新的地区。西尼罗河病毒(WNV)、乌苏图病毒(USUV)和蜱传脑炎病毒(TBEV)的共同传播对欧洲大陆构成了威胁,而难以获得早期和有鉴别力的感染诊断使情况变得更加复杂。此外,日本脑炎病毒(JEV)等非流行性病原体的传入也使准确诊断变得更加复杂。目前黄病毒诊断主要基于 RT-PCR 和病毒特异性抗体检测。然而,这两种技术都存在局限性,因此有必要开发新的检测方法,以提供早期、快速、低成本和有鉴别力的病毒感染诊断。在追求理想诊断方法的过程中,黄病毒非结构蛋白1(NS1)是开发基于抗原本身和针对它产生的抗体的诊断方法的绝佳目标。本综述介绍了这种基于 NS1 的诊断方法的潜力,重点是在欧洲共同流行的黄病毒的应用。
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引用次数: 0
Swimming towards each other: the role of chemotaxis in bacterial interactions. 游向彼此:趋化作用在细菌相互作用中的作用。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2024-01-11 DOI: 10.1016/j.tim.2023.12.008
Justin R Seymour, Douglas R Brumley, Roman Stocker, Jean-Baptiste Raina

Chemotaxis allows microorganisms to direct movement in response to chemical stimuli. Bacteria use this behaviour to develop spatial associations with animals and plants, and even larger microbes. However, current theory suggests that constraints imposed by the limits of chemotactic sensory systems will prevent sensing of chemical gradients emanating from cells smaller than a few micrometres, precluding the utility of chemotaxis in interactions between individual bacteria. Yet, recent evidence has revealed surprising levels of bacterial chemotactic precision, as well as a role for chemotaxis in metabolite exchange between bacterial cells. If indeed widespread, chemotactic sensing between bacteria could represent an important, but largely overlooked, phenotype within interbacterial interactions, and play a significant role in shaping cooperative and competitive relationships.

趋化作用使微生物能够在化学刺激下指挥运动。细菌利用这种行为与动植物甚至更大的微生物建立空间联系。然而,目前的理论认为,受趋化感觉系统的限制,细菌无法感知来自小于几微米的细胞的化学梯度,因此趋化作用无法用于单个细菌之间的相互作用。然而,最近的证据显示,细菌趋化的精确性达到了令人惊讶的水平,而且趋化在细菌细胞之间的代谢物交换中也发挥了作用。如果细菌间的趋化感应确实普遍存在,那么它可能代表了细菌间相互作用中一种重要的、但在很大程度上被忽视的表型,并在形成合作与竞争关系方面发挥重要作用。
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引用次数: 0
Modeling nontuberculous mycobacterial infections in zebrafish. 在斑马鱼中模拟非结核分枝杆菌感染。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 Epub Date: 2023-12-21 DOI: 10.1016/j.tim.2023.11.011
Matt D Johansen, Herman P Spaink, Stefan H Oehlers, Laurent Kremer

The incidence of infections due to nontuberculous mycobacteria (NTM) has increased rapidly in recent years, surpassing tuberculosis in developed countries. Due to inherent antimicrobial resistance, NTM infections are particularly difficult to treat with low cure rates. There is an urgent need to understand NTM pathogenesis and to develop novel therapeutic approaches for the treatment of NTM diseases. Zebrafish have emerged as an excellent animal model due to genetic amenability and optical transparency during embryonic development, allowing spatiotemporal visualization of host-pathogen interactions. Furthermore, adult zebrafish possess fully functional innate and adaptive immunity and recapitulate important pathophysiological hallmarks of mycobacterial infection. Here, we report recent breakthroughs in understanding the hallmarks of NTM infections using the zebrafish model.

近年来,非结核分枝杆菌(NTM)感染的发病率迅速上升,在发达国家已超过结核病。由于固有的抗菌药耐药性,NTM 感染尤其难以治疗,治愈率很低。目前迫切需要了解非淋菌性结核病的发病机制,并开发治疗非淋菌性结核病的新型疗法。斑马鱼在胚胎发育过程中具有遗传适应性和光学透明性,可对宿主与病原体之间的相互作用进行时空可视化,因此已成为一种极佳的动物模型。此外,成年斑马鱼具有功能完备的先天性和适应性免疫,并能再现分枝杆菌感染的重要病理生理特征。在此,我们报告了利用斑马鱼模型了解非典型肺炎感染特征的最新突破。
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引用次数: 0
The use of experimentally evolved coral photosymbionts for reef restoration. 利用实验进化的珊瑚光合共生体恢复珊瑚礁。
IF 14 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-12 DOI: 10.1016/j.tim.2024.05.008
Matthew R Nitschke, David Abrego, Corinne E Allen, Carlos Alvarez-Roa, Nadine M Boulotte, Patrick Buerger, Wing Yan Chan, Wladimir A Fae Neto, Elizabeth Ivory, Bede Johnston, Luka Meyers, Catalina Parra V, Lesa Peplow, Tahirih Perez, Hugo J Scharfenstein, Madeleine J H van Oppen

The heat tolerance of corals is largely determined by their microbial photosymbionts (Symbiodiniaceae, colloquially known as zooxanthellae). Therefore, manipulating symbiont communities may enhance the ability of corals to survive summer heatwaves. Although heat-tolerant and -sensitive symbiont species occur in nature, even corals that harbour naturally tolerant symbionts have been observed to bleach during summer heatwaves. Experimental evolution (i.e., laboratory selection) of Symbiodiniaceae cultures under elevated temperatures has been successfully used to enhance their upper thermal tolerance, both in vitro and, in some instances, following their reintroduction into corals. In this review, we present the state of this intervention and its potential role within coral reef restoration, and discuss the next critical steps required to bridge the gap to implementation.

珊瑚的耐热性在很大程度上取决于其微生物光合共生体(Symbiodiniaceae,俗称zooxanthellae)。因此,操纵共生体群落可以提高珊瑚在夏季热浪中的生存能力。虽然自然界中存在耐热和不耐热的共生物种,但即使是天然耐热共生物种的珊瑚也会在夏季热浪中出现白化现象。在高温条件下对共生藻培养物进行实验性进化(即实验室选择)已被成功地用于提高它们在体外以及在某些情况下重新引入珊瑚后的上层耐热性。在这篇综述中,我们介绍了这种干预措施的现状及其在珊瑚礁恢复中的潜在作用,并讨论了弥合实施差距所需的下一个关键步骤。
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引用次数: 0
KAP1/TRIM28 - antiviral and proviral protagonist of herpesvirus biology. KAP1/TRIM28--疱疹病毒生物学中的抗病毒和激病毒主角。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-12 DOI: 10.1016/j.tim.2024.05.007
Sumita Bhaduri-McIntosh, Beth A Rousseau

Dysregulation of the constitutive heterochromatin machinery (HCM) that silences pericentromeric regions and endogenous retroviral elements in the human genome has consequences for aging and cancer. By recruiting epigenetic regulators, Krüppel-associated box (KRAB)-associated protein 1 (KAP1/TRIM28/TIF1β) is integral to the function of the HCM. Epigenetically silencing DNA genomes of incoming herpesviruses to enforce latency, KAP1 and HCM also serve in an antiviral capacity. In addition to gene silencing, newer reports highlight KAP1's ability to directly activate cellular gene transcription. Here, we discuss the many facets of KAP1, including recent findings that unexpectedly connect KAP1 to the inflammasome, reveal KAP1 cleavage as a novel mode of regulation, and argue for a pro-herpesviral KAP1 function that ensures transition from transcription to replication of the herpesvirus genome.

组成型异染色质机制(HCM)沉默了人类基因组中的围中心染色质区域和内源性逆转录病毒元件,这种机制的失调会对衰老和癌症产生影响。通过招募表观遗传调节因子,Krüppel相关盒(KRAB)相关蛋白1(KAP1/TRIM28/TIF1β)对HCM的功能起着不可或缺的作用。KAP1 和 HCM 还能在表观遗传学上沉默传入疱疹病毒的 DNA 基因组,以加强潜伏性。除了基因沉默之外,最新的报告还强调了 KAP1 直接激活细胞基因转录的能力。在此,我们将讨论 KAP1 的方方面面,包括最近的研究结果,这些结果出人意料地将 KAP1 与炎症小体联系在一起,揭示了 KAP1 裂解是一种新的调控模式,并论证了 KAP1 的促疱疹病毒功能,该功能可确保疱疹病毒基因组从转录过渡到复制。
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引用次数: 0
The growing repertoire of phage anti-defence systems. 噬菌体抗防御系统的种类越来越多。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-05 DOI: 10.1016/j.tim.2024.05.005
Khalimat Murtazalieva, Andre Mu, Aleksandra Petrovskaya, Robert D Finn

The biological interplay between phages and bacteria has driven the evolution of phage anti-defence systems (ADSs), which evade bacterial defence mechanisms. These ADSs bind and inhibit host defence proteins, add covalent modifications and deactivate defence proteins, degrade or sequester signalling molecules utilised by host defence systems, synthesise and restore essential molecules depleted by bacterial defences, or add covalent modifications to phage molecules to avoid recognition. Overall, 145 phage ADSs have been characterised to date. These ADSs counteract 27 of the 152 different bacterial defence families, and we hypothesise that many more ADSs are yet to be discovered. We discuss high-throughput approaches (computational and experimental) which are indispensable for discovering new ADSs and the limitations of these approaches. A comprehensive characterisation of phage ADSs is critical for understanding phage-host interplay and developing clinical applications, such as treatment for multidrug-resistant bacterial infections.

噬菌体与细菌之间的生物相互作用推动了噬菌体抗防御系统(ADS)的进化,这种系统可以躲避细菌的防御机制。这些 ADS 可结合并抑制宿主防御蛋白,添加共价修饰并使防御蛋白失活,降解或封存宿主防御系统使用的信号分子,合成并恢复被细菌防御系统耗尽的必需分子,或对噬菌体分子添加共价修饰以避免被识别。迄今为止,已对 145 种噬菌体 ADS 进行了鉴定。这些 ADS 抵消了 152 种不同细菌防御家族中的 27 种,我们假设还有更多的 ADS 尚待发现。我们讨论了发现新 ADS 必不可少的高通量方法(计算和实验)以及这些方法的局限性。全面描述噬菌体 ADS 对于理解噬菌体与宿主的相互作用以及开发临床应用(如治疗耐多药细菌感染)至关重要。
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引用次数: 0
Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. 通过表观基因组-微生物组轴揭示宿主对肠道微生物群的调控。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-04 DOI: 10.1016/j.tim.2024.05.006
Michael L Pepke, Søren B Hansen, Morten T Limborg

Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.

最近对宿主生物的表观遗传修饰与其相关肠道微生物群的组成或活性之间的动态相互作用的研究表明,宿主有机会通过表观遗传改变来塑造其微生物群,从而导致基因表达和非编码 RNA 活性的变化。我们利用从微生物诱导的表观遗传变化中获得的洞察力来审视宿主对其肠道微生物组进行表观遗传调控的潜力,由此产生了一个双向的 "表观遗传组-微生物组轴"。该轴包含环境诱导的变异,可能会影响宿主-微生物相互作用的适应性进化。此外,我们还介绍了如何在整体原子框架内理解和研究表观基因组-微生物组轴,并将其应用于应用健康和食品科学领域。
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引用次数: 0
Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition. 加强农业生态系统氮管理:改善硝化抑制的微生物见解。
IF 15.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-01 Epub Date: 2023-11-15 DOI: 10.1016/j.tim.2023.10.009
Fabian Beeckman, Laure Annetta, Mario Corrochano-Monsalve, Tom Beeckman, Hans Motte

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

硝化作用是氮(N)循环中将氨转化为硝酸盐的关键微生物过程。过度硝化作用通常发生在农业生态系统中,具有负面的环境影响,包括富营养化和温室气体排放。硝化抑制剂通过降低硝化速率和提高氮素利用效率,在农业系统中广泛应用于氮素管理。然而,NIs的有效性可能因土壤条件而异,而土壤条件反过来又影响微生物群落和硝化微生物不同功能群之间的平衡。了解土壤微生物群落或非生物因素对氮肥有效性的影响机制,对促进可持续施肥至关重要。因此,本文综述了不同类型的NIs以及非生物参数如何影响硝化群落,从而影响NIs的功效。通过讨论该领域的最新研究,我们提供了一些见解,可以促进更有针对性、更高效或互补的NIs的发展,从而提高NIs在农业生态系统可持续管理实践中的应用。
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引用次数: 0
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Trends in Microbiology
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