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Trends in Microbiology最新文献

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The multifaceted role of atomic force microscopy in bacteriology. 原子力显微镜在细菌学中的多方面作用。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-31 DOI: 10.1016/j.tim.2026.08.005
Carolina Borrelli, Edward J A Douglas, Andrew M Edwards, Bart W Hoogenboom
{"title":"The multifaceted role of atomic force microscopy in bacteriology.","authors":"Carolina Borrelli, Edward J A Douglas, Andrew M Edwards, Bart W Hoogenboom","doi":"10.1016/j.tim.2026.08.005","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.005","url":null,"abstract":"<p><p>Atomic force microscopy (AFM) has become a powerful tool to provide nanoscale insights into the spatial organization, biomechanics, and intermolecular interactions of the cell envelopes of living bacteria in real time and under near-native conditions. Focusing on recent literature, we discuss how AFM has advanced our understanding of Gram-positive, Gram-negative, and mycobacterial cell envelope architectures, as well as the mechanisms of action of established and novel antimicrobials. We also summarize how AFM can be used to probe the adhesion, virulence, and immune evasion of pathogens through single-molecule and single-cell force spectroscopy.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148866855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering nitrogen-fixing symbiosis: bridging signaling and intracellular entry. 工程固氮共生：桥接信号和细胞内进入。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-28 DOI: 10.1016/j.tim.2026.08.004
Jiping Tang, Jilin Yao, Lijin Qiao, Pengbo Liang
{"title":"Engineering nitrogen-fixing symbiosis: bridging signaling and intracellular entry.","authors":"Jiping Tang, Jilin Yao, Lijin Qiao, Pengbo Liang","doi":"10.1016/j.tim.2026.08.004","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.004","url":null,"abstract":"<p><p>Nitrogen availability is a major constraint on plant growth and agricultural productivity. Legumes and several other plant lineages circumvent this limitation by establishing symbiotic associations with nitrogen-fixing microorganisms, which convert atmospheric dinitrogen into ammonia that the host assimilates. Since root nodules were first recognized as sites of biological nitrogen fixation in the late 19th century, engineering this capacity in nonlegume crops has remained a long-standing goal. However, two key challenges remain: enabling intracellular rhizobial infection and establishing a molecular framework that supports nitrogen fixation. Recent advances in the molecular, cellular, and evolutionary mechanisms underlying root nodule symbiosis now provide a conceptual framework toward this goal. In this review, we synthesize these advances and outline staged strategies for engineering nitrogen-fixing symbiosis.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Shiny metal catalysts at the origin of metabolism. 闪亮的金属催化剂在新陈代谢的起源。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-26 DOI: 10.1016/j.tim.2026.07.012
William F Martin, Nadja K Hoffmann, Manon L Schlikker
{"title":"Shiny metal catalysts at the origin of metabolism.","authors":"William F Martin, Nadja K Hoffmann, Manon L Schlikker","doi":"10.1016/j.tim.2026.07.012","DOIUrl":"10.1016/j.tim.2026.07.012","url":null,"abstract":"<p><p>Metabolism is the reaction network that converts inanimate matter into living cells. There is no life without it. The network of approximately 400 enzymatic reactions that synthesize amino acids, nucleosides, and cofactors from compounds in the environment is conserved across life. Before enzymes, how did metabolism arise? The subsurface chemical environment of Earth's crust reveals clues. Serpentinizing (H<sub>2</sub> producing) hydrothermal vents contain naturally deposited, shiny metals in their reduced (native) state and phosphite, a reduced form of phosphate. In the laboratory, native metal catalysts fix CO<sub>2</sub>, replacing hydrogenases, the acetyl-CoA pathway to pyruvate, the Krebs cycle, amino acid syntheses, NADH, and ferredoxin. Native metals also phosphorylate organic compounds in water using phosphite, uncovering a new source of energy at the origin of metabolism.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7619600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148832600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tripartite toxin-antitoxin systems: expanding the paradigm of molecular interplay and antiphage defense. 三方毒素-抗毒素系统：扩展分子相互作用和抗噬菌体防御的范例。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-26 DOI: 10.1016/j.tim.2026.08.001
Yunxue Guo, Pierre Genevaux, Xiaoxue Wang
{"title":"Tripartite toxin-antitoxin systems: expanding the paradigm of molecular interplay and antiphage defense.","authors":"Yunxue Guo, Pierre Genevaux, Xiaoxue Wang","doi":"10.1016/j.tim.2026.08.001","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.001","url":null,"abstract":"<p><p>Prokaryotic toxin-antitoxin (TA) systems are genetic modules involved in stress responses, including antiphage defense and the maintenance of mobile genetic elements. Although canonical TA systems consist of two neighboring genes encoding one toxin and one antitoxin, many have evolved into tripartite systems through the incorporation of a third component that serves as a chaperone, a regulator, or an additional antitoxin or toxin to increase functional diversity and regulatory potential. This review compares tripartite TA systems [TA-chaperone (TAC), TA-regulator (TAR), dual-antitoxin, and dual-toxin systems] with bipartite systems, summarizing their neutralizing mechanisms and phage-triggered activation pathways. The regulatory capacity and modularity of tripartite TAs illuminate the evolutionary trajectory of these 'selfish' genetic elements, reflecting complex coevolutionary dynamics among TA systems, host bacteria, and phages.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148832548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The meta-holobiont: rethinking marine species interactions through microbial connectivity. 元全息生物：通过微生物连通性重新思考海洋物种的相互作用。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-25 DOI: 10.1016/j.tim.2026.08.003
Elisabetta Manea, Lorenzo Bramanti, Pierre E Galand
{"title":"The meta-holobiont: rethinking marine species interactions through microbial connectivity.","authors":"Elisabetta Manea, Lorenzo Bramanti, Pierre E Galand","doi":"10.1016/j.tim.2026.08.003","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.003","url":null,"abstract":"<p><p>Positive species interactions underpin ecological resilience, which is critical for counteracting anthropogenic pressures on ecosystems. Current research focuses on intra-holobiont interactions between hosts and their microbiomes, reflecting their recognized importance for host well-being, but overlooks interactions among holobionts. We introduce the meta-holobiont framework for the marine environment, which conceptualizes ecological communities as networks of interacting holobionts connected through microbial transmission and metabolite production. Marine connectivity can facilitate horizontal transmission of microorganisms, potentially enhancing host fitness and stress tolerance across all life stages. Conceptual and empirical findings from sessile benthic species support this view. We argue that investigating meta-holobiont interactions is crucial for advancing knowledge of ecological dynamics and may have important practical implications, particularly for marine restoration strategies.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The narrowing prokaryote-eukaryote divide reveals a complexity spectrum. 原核生物与真核生物之间不断缩小的分界线揭示了一个复杂的谱。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-21 DOI: 10.1016/j.tim.2026.07.008
Julian Vosseberg, Thijs J G Ettema
{"title":"The narrowing prokaryote-eukaryote divide reveals a complexity spectrum.","authors":"Julian Vosseberg, Thijs J G Ettema","doi":"10.1016/j.tim.2026.07.008","DOIUrl":"https://doi.org/10.1016/j.tim.2026.07.008","url":null,"abstract":"<p><p>Cellular organisms can be divided into two basic types of cells: the prokaryotic cells of Bacteria and Archaea and the eukaryotic cells. The rapidly expanding knowledge of the diversity and ultrastructure of prokaryotic cells has revealed cellular intricacies that warrant a critical reappraisal of the profundity of the prokaryote-eukaryote divide.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biological language models uncover hidden bacterial antiviral immunity repertoires. 生物语言模型揭示了隐藏的细菌抗病毒免疫库。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-19 DOI: 10.1016/j.tim.2026.07.009
Gabriel Viégas, Rafael E Marques, Joel H Ellwanger, Leandro N Lemos
{"title":"Biological language models uncover hidden bacterial antiviral immunity repertoires.","authors":"Gabriel Viégas, Rafael E Marques, Joel H Ellwanger, Leandro N Lemos","doi":"10.1016/j.tim.2026.07.009","DOIUrl":"https://doi.org/10.1016/j.tim.2026.07.009","url":null,"abstract":"<p><p>Biological language models, including protein and genomic language models, are accelerating the discovery of bacterial antiviral defenses by identifying defense-associated proteins that lack detectable homology to known systems. These approaches reveal a vast, previously unexplored repertoire of defense-associated genes and suggest that antiviral defense-associated functions are more diverse and distributed across genomic contexts than previously appreciated.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Applications of machine learning in microbial source tracking. 机器学习在微生物源跟踪中的应用。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-18 DOI: 10.1016/j.tim.2026.07.010
Jiaying Li, Kai Feng, Le Wang, Qiulong Hu, Shaolong Wu, Ye Deng
{"title":"Applications of machine learning in microbial source tracking.","authors":"Jiaying Li, Kai Feng, Le Wang, Qiulong Hu, Shaolong Wu, Ye Deng","doi":"10.1016/j.tim.2026.07.010","DOIUrl":"https://doi.org/10.1016/j.tim.2026.07.010","url":null,"abstract":"<p><p>Microbial source tracking (MST) has become important in environmental ecology, food safety, and forensic investigation. With advances in microbiome technologies, MST has shifted from single-indicator methods to community-level inference, creating demand for stronger analytical frameworks. Machine learning (ML) now plays a central role in handling large-scale microbiome data and capturing complex relationships between microbial communities and their sources. This review summarizes major ML methods used in MST, representative tools, and applications in pollution tracing, geospatial attribution, food safety, and forensics. Current studies show that ML substantially improves the accuracy, resolution, and scalability of MST. We also discuss key challenges, including limited interpretability, ecological dynamics, and a lack of benchmark datasets with explicit ground truth and evaluation criteria, and highlight how next-generation AI, especially deep learning, may further advance robust and intelligent MST.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Forests: methane sinks or methane sources? 森林：甲烷汇还是甲烷源？
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-14 DOI: 10.1016/j.tim.2026.07.007
Xiaoqi Zhou, Wensheng Xiao, Josep Peñuelas
{"title":"Forests: methane sinks or methane sources?","authors":"Xiaoqi Zhou, Wensheng Xiao, Josep Peñuelas","doi":"10.1016/j.tim.2026.07.007","DOIUrl":"https://doi.org/10.1016/j.tim.2026.07.007","url":null,"abstract":"<p><p>Forests are not a uniform methane (CH<sub>4</sub>) sink; soils, stems, and canopies act as sources or sinks depending on local conditions. We synthesize emerging evidence, expose the limitations of component-based approaches, and advocate integrated observational-modeling frameworks to accurately quantify net forest CH<sub>4</sub> exchange and climate feedbacks.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the concept of longevity in fungi. 探索真菌的长寿概念。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-13 DOI: 10.1016/j.tim.2026.07.001
Ayla Mongès, Dimitrios Floudas, Kristin Aleklett
{"title":"Exploring the concept of longevity in fungi.","authors":"Ayla Mongès, Dimitrios Floudas, Kristin Aleklett","doi":"10.1016/j.tim.2026.07.001","DOIUrl":"https://doi.org/10.1016/j.tim.2026.07.001","url":null,"abstract":"<p><p>For most organisms, we rely on the ability to observe them from birth to death in order to fully understand their ecology, life cycles, adaptations, and interactions with other organisms. For fungi, this is a challenge, and little is known about how old they can become and in what form they persist in the environment. In this opinion article, we highlight the complexity of determining the longevity of fungi. We provide an overview of how the age of fungal individuals and the persistence of mycelial structures have been measured in different groups of fungi. Finally, we propose ideas for advancing the study of fungal longevities and discuss how differences in fungal longevity and mycelial persistence can impact the ways we study and manage fungi in ecosystems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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