Engineering Microbiology最新文献

英文中文

Complexity of antibiotic resistance and its impact on gut microbiota dynamics 抗生素耐药性的复杂性及其对肠道菌群动力学的影响

Engineering Microbiology

Pub Date : 2024-12-30 DOI: 10.1016/j.engmic.2024.100187

H. Shayista , M.N. Nagendra Prasad , S. Niranjan Raj , Ashwini Prasad , S. Lakshmi , H.K. Ranjini , K. Manju , Ravikumara , Raghuraj Singh Chouhan , Olga Y. Khohlova , Olga V. Perianova , Syed Baker

The present review explores the influence of the gut microbiota on antibiotic resistance dynamics, particularly those associated with dysbiosis. The improper use of antibiotics can induce resistance in pathogens through various pathways, which is a topic of increasing interest within the scientific community. This review highlights the importance of microbial diversity, gut metabolism, and inflammatory responses against the dysbiosis due to the action of antibiotics. Additionally, it examines how secondary metabolites secreted by pathogens can serve as biomarkers for the early detection of antibiotic resistance. Although significant progress has been made in this field, key research gaps persist, including the need for a deeper understanding of the long-term effects of antibiotic-induced dysbiosis and the specific mechanisms driving the evolution of resistance in gut bacteria. Based on these considerations, this review systematically analyzed studies from PubMed, Web of Science, Embase, Cochrane Library, and Scopus up to July 2024. This study aimed to explore the dynamics of the interactions between gut microbiota and antibiotic resistance, specifically examining how microbial composition influences the development of resistance mechanisms. By elucidating these relationships, this review provides insights into management strategies for drug resistance and improves our understanding of microbial contributions to host health.

本综述探讨了肠道微生物群对抗生素耐药性动态的影响，特别是与生态失调有关的影响。抗生素的不当使用可通过多种途径诱导病原体产生耐药性，这是科学界日益关注的一个话题。这篇综述强调了微生物多样性、肠道代谢和炎症反应对抗生素作用引起的生态失调的重要性。此外，它还研究了病原体分泌的次生代谢物如何作为抗生素耐药性早期检测的生物标志物。尽管在这一领域取得了重大进展，但关键的研究差距仍然存在，包括需要更深入地了解抗生素诱导的生态失调的长期影响以及驱动肠道细菌耐药性进化的具体机制。基于这些考虑，本综述系统分析了PubMed、Web of Science、Embase、Cochrane Library和Scopus截至2024年7月的研究。本研究旨在探讨肠道微生物群与抗生素耐药性之间相互作用的动力学，特别是研究微生物组成如何影响耐药性机制的发展。通过阐明这些关系，本综述为耐药管理策略提供了见解，并提高了我们对微生物对宿主健康贡献的理解。

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引用次数: 0

Characterization of a small non-coding RNA S612 in Bacillus subtilis 枯草芽孢杆菌非编码小RNA S612的鉴定

Engineering Microbiology

Pub Date : 2024-12-09 DOI: 10.1016/j.engmic.2024.100186

Anqi Peng , Weijiao Zhang , Haibo Xiong , Luyao Zhang , Jian Cheng , Yang Wang , Zhen Kang

Small regulatory RNAs (sRNAs) are non-coding RNA molecules that fine-tune various cellular processes and respond to various environmental stimuli. In Bacillus subtilis, the regulatory mechanisms and specific targets of several sRNAs remain largely unknown. In this study, we identified and characterized S612 as a self-terminating sRNA in B. subtilis. The expression of S612 is regulated by external signals, including nutrient availability and salt concentration. Overexpression of S612 induced filamentous cells with extensive cellular elongation and complete inhibition of sporulation, indicating its potential to control cell morphology and spore formation. S612 directly targets and downregulates genes through post-transcriptional base pairing with mRNAs, including ylmD, trpE, ycxC, yycS, rapH, and amyE, some of which are involved in cell membrane integrity, cell wall synthesis, and sporulation initiation. Therefore, we propose that S612 is an important post-transcriptional regulator of cell morphology and sporulation.

小调控RNA （Small regulatory RNA, sRNAs）是一种非编码RNA分子，可以对各种细胞过程进行微调，并对各种环境刺激做出反应。在枯草芽孢杆菌中，几种srna的调控机制和特定靶点在很大程度上仍然未知。在这项研究中，我们鉴定并鉴定了S612是枯草芽孢杆菌中一个自终止的sRNA。S612的表达受外界信号的调控，包括养分有效性和盐浓度。过表达S612诱导的丝状细胞具有广泛的细胞伸长和孢子形成的完全抑制，表明其具有控制细胞形态和孢子形成的潜力。S612通过与mrna的转录后碱基配对直接靶向和下调基因，包括ylmD、trpE、ycxC、yycS、rapH和amyE，其中一些基因参与细胞膜完整性、细胞壁合成和孢子形成起始。因此，我们认为S612是细胞形态和孢子形成的重要转录后调节因子。

引用次数: 0

Terminal deoxynucleotidyl transferase: Properties and applications 末端脱氧核苷酸转移酶：性质与应用

Engineering Microbiology

Pub Date : 2024-11-28 DOI: 10.1016/j.engmic.2024.100179

Chengjie Zhang , Hizar Subthain , Fei Guo , Peng Fang , Shanmin Zheng , Mengzhe Shen , Xianger Jiang , Zhengquan Gao , Chunxiao Meng , Shengying Li , Lei Du

Terminal deoxynucleotidyl transferase (TdT), a unique DNA polymerase, can elongate DNA by adding deoxynucleotides to the 3′ terminal of a DNA chain in a template-independent manner. Owing to their remarkable DNA synthesis activity, TdTs have promoted the development of numerous nucleic acid-based methods, tools, and associated applications, attracting broad interest from both academia and industry. This review summarizes and discusses the recent research on TdTs, including their biochemical characteristics, enzyme engineering, and practical applications. New insights and perspectives on the future development of TdTs are provided.

末端脱氧核苷酸转移酶（TdT）是一种独特的DNA聚合酶，它可以以模板无关的方式将脱氧核苷酸添加到DNA链的3 '端，从而延长DNA。由于其显著的DNA合成活性，tdt促进了许多基于核酸的方法、工具和相关应用的发展，引起了学术界和工业界的广泛兴趣。本文综述了近年来tdt的研究进展，包括tdt的生化特性、酶工程和实际应用。对tdt的未来发展提出了新的见解和观点。

引用次数: 0

Exploring interspecific interaction variability in microbiota: A review 探索微生物群种间相互作用的变异性：综述

Engineering Microbiology

Pub Date : 2024-11-09 DOI: 10.1016/j.engmic.2024.100178

Zhong Yu , Zhihao Gan , Ahmed Tawfik , Fangang Meng

Interspecific interactions are an important component and a strong selective force in microbial communities. Over the past few decades, there has been a growing awareness of the variability in microbial interactions, and various studies are already unraveling the inner working dynamics in microbial communities. This has prompted scientists to develop novel techniques for characterizing the varying interspecific interactions among microbes. Here, we review the precise definitions of pairwise and high-order interactions, summarize the key concepts related to interaction variability, and discuss the strengths and weaknesses of emerging characterization techniques. Specifically, we found that most methods can accurately predict or provide direct information about microbial pairwise interactions. However, some of these methods inevitably mask the underlying high-order interactions in the microbial community. Making reasonable assumptions and choosing a characterization method to explore varying microbial interactions should allow us to better understand and engineer dynamic microbial systems.

种间相互作用是微生物群落的一个重要组成部分，也是一种强大的选择性力量。在过去的几十年里，人们越来越意识到微生物相互作用的可变性，各种研究已经揭示了微生物群落的内部工作动态。这促使科学家们开发新的技术来描述微生物之间不同的种间相互作用。在此，我们回顾了配对相互作用和高阶相互作用的精确定义，总结了与相互作用变异性相关的关键概念，并讨论了新兴表征技术的优缺点。具体来说，我们发现大多数方法都能准确预测或提供微生物成对相互作用的直接信息。然而，其中一些方法不可避免地会掩盖微生物群落中潜在的高阶相互作用。做出合理的假设并选择一种表征方法来探索不同的微生物相互作用，应该能让我们更好地理解和设计动态微生物系统。

引用次数: 0

Proactive monitoring of changes in the microbial community structure in wastewater treatment bioreactors using phospholipid fatty acid analysis 利用磷脂脂肪酸分析主动监测废水处理生物反应器中微生物群落结构的变化

Engineering Microbiology

Pub Date : 2024-11-03 DOI: 10.1016/j.engmic.2024.100177

Lawson Mensah , Elise Cartmell , Mandy Fletton , Mark Scrimshaw , Pablo Campo

Diverse microbial community structures (MCS) in wastewater treatment plants (WWTPs) are vital for effectively removing nutrients and chemicals from wastewater. However, the regular monitoring of MCS in WWTP bioreactors remains unattractive owing to the skill and cost required for deploying modern microbial molecular techniques in the routine assessment of engineered systems. In contrast, low-resolution methods for assessing broad changes in the MCS, such as phospholipid fatty acid (PLFA) analysis, have been used effectively in soil studies for decades. Despite using PLFA analysis in soil remediation studies to capture the long-term effects of environmental changes on MCS, its application in WWTPs, where the microbial mass is dynamic and operational conditions are more fluid, remains limited. In this study, microbial communities in a controlled pilot plant and 12 full-scale activated sludge plants (ASPs) were surveyed over a two-year period using PLFA analysis. This study revealed that changes in the MCS in wastewater bioreactors could be detected using PLFA analysis. The MCS comprised 59 % Gram-negative and 9 % Gram-positive bacteria, 31 % fungi, and 1 % actinomycetes. The abundances of Gram-negative bacteria and fungi were strongly inversely correlated, with an R² = 0.93, while the fatty acids cy17:0 and 16:1ω7c positively correlated (R² = 0.869). Variations in temperature, solid retention time, and WWTP configuration significantly influenced the MCS in activated sludge reactors. This study showed that WWTP bioreactors can be routinely monitored using PLFA analysis, and changes in the bioreactor profile that may indicate imminent bioreactor failure can be identified.

污水处理厂（WWTP）中多样化的微生物群落结构（MCS）对于有效去除污水中的营养物质和化学物质至关重要。然而，由于在工程系统的常规评估中部署现代微生物分子技术所需的技能和成本，定期监测污水处理厂生物反应器中的微生物群落结构仍然缺乏吸引力。相比之下，低分辨率方法（如磷脂脂肪酸 (PLFA) 分析）可评估 MCS 的广泛变化，几十年来一直被有效地用于土壤研究。尽管在土壤修复研究中使用磷脂脂肪酸分析来捕捉环境变化对 MCS 的长期影响，但其在污水处理厂中的应用仍然有限，因为污水处理厂中的微生物数量是动态的，运行条件也更加多变。在这项研究中，使用 PLFA 分析法对一个受控试验工厂和 12 个正式活性污泥厂 (ASP) 的微生物群落进行了为期两年的调查。这项研究表明，使用 PLFA 分析法可以检测到废水生物反应器中微生物群落的变化。微生物控制系统包括 59 % 的革兰氏阴性菌和 9 % 的革兰氏阳性菌、31 % 的真菌和 1 % 的放线菌。革兰氏阴性菌和真菌的丰度呈强烈的反相关，R2 = 0.93，而脂肪酸 cy17:0 和 16:1ω7c 呈正相关（R2 = 0.869）。温度、固体停留时间和污水处理厂配置的变化对活性污泥反应器中的 MCS 有显著影响。这项研究表明，可以利用 PLFA 分析对污水处理厂生物反应器进行常规监测，并可识别生物反应器概况中可能预示生物反应器即将发生故障的变化。

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引用次数: 0

Immobilization of Thermomyces lanuginosus lipase on metal-organic frameworks and investigation of their catalytic properties and stability 在金属有机框架上固定热霉菌脂肪酶并研究其催化特性和稳定性

Engineering Microbiology

Pub Date : 2024-10-28 DOI: 10.1016/j.engmic.2024.100176

Zeynab Rangraz , Mostafa M. Amini , Zohreh Habibi

Surface adsorption is a convenient and readily available method for immobilizing enzymes on metal-organic frameworks (MOFs). Metal-organic framework-5 (MOF-5), isoreticular metal-organic frameworks-3 (IRMOF-3), and multivariate analysis of MOF-5/IRMOF-3 (MMI) with a half-amino group (-NH₂) were prepared in this study. Thermomyces lanuginosus lipase (TLL) was chosen as a commercially available enzyme for immobilization on the surfaces of these MOFs. Briefly, 1.5 mg of TLL was added to 10 mg of the MOFs, and after 24 h, 67, 74, and 88% of the TLL was immobilized on MOF-5, IRMOF-3, and MMI, respectively. Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, scanning electron microscopy, energy-dispersive X-ray analysis, and Brunauer–Emmett–Teller analysis were used to characterize the resulting biocomposites. TLL@MOF-5, TLL@IRMOF-3, and TLL@MMI exhibited activities of 55, 75, and 110 U/mg, respectively. Investigation of the activity and stability of the prepared biocatalysts showed that TLL immobilized on MMI was 2.34-fold more active than free TLL. TLL@MMI exhibited high stability and activity even under harsh conditions. After 24 h of incubation in a mixture of 50% (v/v) MeOH, TLL@MMI retained 80% of its activity, whereas TLL@MOF-5 and free TLL lost 50 and 60% of their activities, respectively. TLL@MMI was used to synthesize 2-arylidenehydrazinyl-4-arylthiozole derivatives (91–98%) in a one-pot vessel by adding benzaldehydes, phenacyl bromides, and thiosemicarbazide to water. The efficiency of the 4a derivative with free TLL was 43%, whereas that with TLL@MMI was 98%.

表面吸附是将酶固定在金属有机框架（MOFs）上的一种方便易得的方法。本研究制备了金属有机框架-5（MOF-5）、等规金属有机框架-3（IRMOF-3）以及带有半氨基（-NH2）的MOF-5/IRMOF-3（MMI）的多元分析。热酵母脂肪酶（TLL）被选为固定在这些 MOF 表面的市售酶。简单地说，将 1.5 毫克 TLL 加入 10 毫克 MOF，24 小时后，分别有 67%、74% 和 88% 的 TLL 被固定在 MOF-5、IRMOF-3 和 MMI 上。傅立叶变换红外光谱、X 射线衍射、热重分析、扫描电子显微镜、能量色散 X 射线分析和布鲁瑙尔-艾美特-泰勒分析被用来表征所得到的生物复合材料。TLL@MOF-5、TLL@IRMOF-3 和 TLL@MMI 的活性分别为 55、75 和 110 U/mg 。对所制备的生物催化剂的活性和稳定性的研究表明，固定在 MMI 上的 TLL 的活性是游离 TLL 的 2.34 倍。即使在苛刻的条件下，TLL@MMI 也表现出很高的稳定性和活性。在 50%（v/v）MeOH 混合液中培养 24 小时后，TLL@MMI 保持了 80% 的活性，而 TLL@MOF-5 和游离 TLL 则分别丧失了 50% 和 60% 的活性。将 TLL@MMI 加入苯甲醛、苯基溴化物和硫代氨基甲酰肼水溶液中，在一锅容器中合成了 2-芳基肼基-4-芳基硫唑衍生物（91-98%）。使用游离 TLL 的 4a 衍生物的效率为 43%，而使用 TLL@MMI 的效率为 98%。

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引用次数: 0

The way to uncovering and utilizing marine microbial resources 发掘和利用海洋微生物资源之路

Engineering Microbiology

Pub Date : 2024-09-24 DOI: 10.1016/j.engmic.2024.100175

Zhi-Feng Zhang, Meng Li

Recently, Chen et al. published their breakthrough results on a marine microbial genomic catalog and genetic potentials in bioprospecting in Nature, providing unprecedented opportunities for development and utilization of genetic resources of marine microorganisms. To highlight this article, we summarized and highlighted their breakthroughs seriatim

最近，Chen 等人在《自然》杂志上发表了他们在海洋微生物基因组目录和生物勘探中的遗传潜力方面的突破性成果，为海洋微生物遗传资源的开发和利用提供了前所未有的机遇。为了突出这篇文章，我们对他们的突破性成果进行了逐一总结和强调

引用次数: 0

Biofuel production from lignocellulose via thermophile-based consolidated bioprocessing 通过基于嗜热菌的综合生物加工技术利用木质纤维素生产生物燃料

Engineering Microbiology

Pub Date : 2024-09-10 DOI: 10.1016/j.engmic.2024.100174

Yilin Le , Mengqi Zhang , Pengju Wu , Huilei Wang , Jinfeng Ni

The depletion of fossil fuels and their impact on the environment have led to efforts to develop alternative sustainable fuels. While biofuel derived from lignocellulose is considered a sustainable, renewable, and green energy source, enhancing biofuel production and achieving a cost-effective bioconversion of lignocellulose at existing bio-refineries remains a challenge. Consolidated bioprocessing (CBP) using thermophiles can simplify this operation by integrating multiple processes, such as hydrolytic enzyme production, lignocellulose degradation, biofuel fermentation, and product distillation. This paper reviews recent developments in the conversion of lignocellulose to biofuel using thermophile-based CBP. First, advances in thermostable enzyme and thermophilic lignocellulolytic microorganism discovery and development for lignocellulosic biorefinery use are outlined. Then, several thermophilic CBP candidates and thermophilic microbes engineered to drive CBP of lignocellulose are reviewed. CRISPR/Cas-based genome editing tools developed for thermophiles are also highlighted. The potential applications of the Design-Build-Test-Learn (DBTL) synthetic biology strategy for designing and constructing thermophilic CBP hosts are also discussed in detail. Overall, this review illustrates how to develop highly sophisticated thermophilic CBP hosts for use in lignocellulosic biorefinery applications.

化石燃料的枯竭及其对环境的影响促使人们努力开发可持续的替代燃料。虽然从木质纤维素中提取的生物燃料被认为是一种可持续、可再生的绿色能源，但在现有的生物精炼厂中提高生物燃料产量和实现木质纤维素的生物转化的成本效益仍然是一项挑战。使用嗜热菌的综合生物处理（CBP）可将水解酶生产、木质纤维素降解、生物燃料发酵和产品蒸馏等多个过程整合在一起，从而简化操作。本文回顾了利用嗜热菌 CBP 将木质纤维素转化为生物燃料的最新进展。首先，概述了用于木质纤维素生物炼制的恒温酶和嗜热木质纤维素分解微生物的发现和开发进展。然后，综述了几种嗜热 CBP 候选者和经改造可驱动木质纤维素 CBP 的嗜热微生物。此外，还重点介绍了为嗜热微生物开发的基于 CRISPR/Cas 的基因组编辑工具。还详细讨论了设计-构建-测试-学习（DBTL）合成生物学策略在设计和构建嗜热 CBP 宿主方面的潜在应用。总之，本综述说明了如何开发高度复杂的嗜热 CBP 宿主，用于木质纤维素生物精炼应用。

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Genetically engineered bacteria as inflammatory bowel disease therapeutics 作为炎症性肠病疗法的基因工程细菌

Engineering Microbiology

Pub Date : 2024-09-01 DOI: 10.1016/j.engmic.2024.100167

Zhen-Ping Zou , Xiao-Peng Zhang , Qian Zhang, Bin-Cheng Yin, Ying Zhou, Bang-Ce Ye

Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.

炎症性肠病（IBD）是一种慢性复发性疾病，由免疫反应紊乱引起，破坏了肠腔共生生态系统，并导致粘膜免疫功能失调。目前治疗 IBD 的疗法主要集中于症状控制，因此早期诊断和及时干预具有挑战性。利用合成生物学开发基因工程细菌为应对这些挑战提供了一种新策略。在这篇综述中，我们介绍了用于治疗和检测 IBD 的工程细菌领域的最新突破，并描述了如何对细菌进行基因改造，使其产生治疗分子或执行诊断功能。我们特别讨论了将活细菌疗法从细菌设计转化为进一步临床应用的递送策略所面临的挑战。

引用次数: 0

Mechanisms of tigecycline resistance in Gram-negative bacteria: A narrative review 革兰氏阴性细菌对替加环素产生耐药性的机制：叙述性综述

Engineering Microbiology

Pub Date : 2024-08-17 DOI: 10.1016/j.engmic.2024.100165

Wenya Su , Wenjia Wang , Ling Li , Mengge Zhang , Hai Xu , Chengzhang Fu , Xiuhua Pang , Mingyu Wang

Tigecycline serves as a critical “final-resort” antibiotic for treating bacterial infections caused by multidrug-resistant bacteria for which treatment options are severely limited. The increasing prevalence of tigecycline resistance, particularly among Gram-negative bacteria, is a major concern. Various mechanisms have been identified as contributors to tigecycline resistance, including upregulation of nonspecific Resistance Nodulation Division (RND) efflux pumps due to mutations in transcriptional regulators, enzymatic modification of tigecycline by monooxygenase enzymes, and mutations affecting tigecycline binding sites. This review aims to consolidate our understanding of tigecycline resistance mechanisms in Gram-negative bacteria and offer insights and perspectives for further drug development.

替加环素是一种重要的 "最后手段 "抗生素，可用于治疗由多重耐药细菌引起的细菌感染，因为对这些细菌的治疗方法非常有限。替加环素耐药性的日益普遍，尤其是在革兰氏阴性细菌中，是一个令人关注的重大问题。导致替加环素耐药性的机制有多种，包括转录调节因子突变导致的非特异性抗性结节分部（RND）外排泵的上调、单氧酶对替加环素的酶修饰以及影响替加环素结合位点的突变。本综述旨在巩固我们对革兰阴性菌中替加环素耐药机制的认识，并为进一步的药物开发提供见解和展望。

引用次数: 0

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