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Spatial engineering for improved microbial cell factories. 改进微生物细胞工厂的空间工程。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-06-09 DOI: 10.1016/j.tim.2026.05.010
Binbing Xu, Zhuoya Zhang, Jing Wu, Liming Liu, Guipeng Hu
{"title":"Spatial engineering for improved microbial cell factories.","authors":"Binbing Xu, Zhuoya Zhang, Jing Wu, Liming Liu, Guipeng Hu","doi":"10.1016/j.tim.2026.05.010","DOIUrl":"10.1016/j.tim.2026.05.010","url":null,"abstract":"<p><p>Microbial cell factories enable the sustainable production of fuels, chemicals, and pharmaceuticals, yet their performance is often constrained by inefficient metabolic flux distribution, cofactor imbalance, and pathway-associated toxicity. Spatial engineering has emerged as an effective approach to address these limitations. It does so by controlling the organization of metabolic processes. This review summarizes recent advances in spatial engineering at three levels: natural organelle engineering, artificial compartmentalization, and intercellular coordination. We discuss how these strategies enhance pathway efficiency through enzyme colocalization, metabolic insulation, and division of labor. We also underscore current challenges regarding targeting efficiency and system integration. Future directions for advancing spatial design and metabolic coordination in microbial systems are outlined.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"973-988"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148212608","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
Acidification-driven mineral weathering ability of bacteria: genetics, conservation, and regulations. 酸化驱动的细菌矿物风化能力：遗传、保护和调控。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-06-02 DOI: 10.1016/j.tim.2026.05.004
Stéphane Uroz, Cintia Blanco Nouche, Ségolène Bouche, Marie-Pierre Turpault
{"title":"Acidification-driven mineral weathering ability of bacteria: genetics, conservation, and regulations.","authors":"Stéphane Uroz, Cintia Blanco Nouche, Ségolène Bouche, Marie-Pierre Turpault","doi":"10.1016/j.tim.2026.05.004","DOIUrl":"10.1016/j.tim.2026.05.004","url":null,"abstract":"<p><p>Mineral weathering (MWe) is a fundamental driver of nutrient release in nutrient-poor ecosystems, sustaining both nutrient cycling and plant growth. Among the strategies employed by MWe bacteria-acidification, chelation, and oxidoreduction reactions-acidification stands out as the most widespread but least understood at the ecological and genetic levels. This review synthesizes current knowledge on acidification-driven MWe bacteria, the factors determining their effectiveness, genetic determinants, and regulatory mechanisms revealed through interdisciplinary approaches (transcriptomics/proteomics, mineralogy, and geochemistry). We also highlight newly discovered genes and critically assess the limitations of current approaches, offering new perspectives on the mechanisms and evolution underlying bacterial contributions to MWe.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"956-972"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148151204","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
Ancient pathogen genomics in Africa: Current evidence and future directions. 非洲古代病原体基因组学：当前证据和未来方向。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-07-14 DOI: 10.1016/j.tim.2026.06.004
Maja Vukovikj, Carla Mavian, Helen Wang, Robert J Gifford, Tulio de Oliveira, Carina Schlebusch
{"title":"Ancient pathogen genomics in Africa: Current evidence and future directions.","authors":"Maja Vukovikj, Carla Mavian, Helen Wang, Robert J Gifford, Tulio de Oliveira, Carina Schlebusch","doi":"10.1016/j.tim.2026.06.004","DOIUrl":"10.1016/j.tim.2026.06.004","url":null,"abstract":"<p><p>Ancient pathogen genomics has redefined how infectious disease histories are reconstructed, revealing unexpected origins, transmission routes, and lineage turnovers that are invisible from modern genomes alone. Yet, this perspective remains heavily biased toward Eurasia, leaving Africa-central to human evolution and home to diverse ecological settings relevant to zoonotic and vector-borne disease emergence-largely unexplored. In this review, we assess the current state of ancient pathogen research in Africa and synthesize insights from bacterial, parasitic, and viral perspectives. We identify Africa as a pivotal frontier for the field and outline strategic priorities for moving from isolated detections toward continent-scale reconstructions of past disease landscapes, with potential relevance for understanding long-term patterns of endemicity, emergence, and epidemic risk.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1003-1016"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148438031","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
Disarming a pathogen with programmable phage-derived particles. 用可编程的噬菌体衍生粒子解除病原体的武装。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-08-18 DOI: 10.1016/j.tim.2026.07.013
Siqi Yang, Brady F Cress
{"title":"Disarming a pathogen with programmable phage-derived particles.","authors":"Siqi Yang, Brady F Cress","doi":"10.1016/j.tim.2026.07.013","DOIUrl":"10.1016/j.tim.2026.07.013","url":null,"abstract":"<p><p>Shiga toxin-producing Escherichia coli (STEC) presents a therapeutic dilemma because antibiotic treatment induces prophage-encoded Shiga toxin expression. Galtier et al. engineer phage-derived particles with programmable cell specificity, genetic cargo, and CRISPR guide RNAs that destroy stx while killing STEC in animal models.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"909-911"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798253","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
Ochrobactrum intermedium.
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-02-13 DOI: 10.1016/j.tim.2025.12.014
Pooja Bhardwaj, Hari Shanker Joshi, Gaurav Raj Dwivedi
{"title":"Ochrobactrum intermedium.","authors":"Pooja Bhardwaj, Hari Shanker Joshi, Gaurav Raj Dwivedi","doi":"10.1016/j.tim.2025.12.014","DOIUrl":"10.1016/j.tim.2025.12.014","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1017-1018"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146198073","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
From genes to epigenomes: rethinking arbuscular mycorrhizal fungi adaptation. 从基因到表观基因组：重新思考丛枝菌根真菌的适应。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-05-21 DOI: 10.1016/j.tim.2026.04.012
Kevin MacColl, Ken Mugambi, Jordana Oliveira, Robert Ferguson, Nicolas Corradi
{"title":"From genes to epigenomes: rethinking arbuscular mycorrhizal fungi adaptation.","authors":"Kevin MacColl, Ken Mugambi, Jordana Oliveira, Robert Ferguson, Nicolas Corradi","doi":"10.1016/j.tim.2026.04.012","DOIUrl":"10.1016/j.tim.2026.04.012","url":null,"abstract":"<p><p>Arbuscular mycorrhizal fungi (AMF) form ecologically important mutualisms with most plant species, yet their unpredictable phenotypes and mutualistic outcomes represent a fundamental barrier to our understanding of their ecological functions. While early models focused on genetic differences between species and strains, evidence is mounting that AMF deploy conserved eukaryotic processes to control gene expression through structural DNA modifications, without changes to underlying sequences, or epigenomic processes, to facilitate rapid plasticity and adaptation. In this opinion article, we summarize recent evidence of epigenomic regulation in AMF and how these mechanisms govern interactions with plants. Drawing from well-studied model systems, we outline multigenerational experiments to pinpoint the epigenomic basis of AMF trait variation.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"923-931"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147983480","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
Managing microbial interactions in environmental biotechnology: can we scale interaction principles? 环境生物技术中微生物相互作用的管理：我们能扩展相互作用原理吗？
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-04-28 DOI: 10.1016/j.tim.2026.04.003
Wenyu Gu, Xiang-Yi Li Richter, David R Johnson
{"title":"Managing microbial interactions in environmental biotechnology: can we scale interaction principles?","authors":"Wenyu Gu, Xiang-Yi Li Richter, David R Johnson","doi":"10.1016/j.tim.2026.04.003","DOIUrl":"10.1016/j.tim.2026.04.003","url":null,"abstract":"<p><p>Microbial interactions hold vast potential for improving sustainability, including waste upcycling, greenhouse gas mitigation, contaminant bioremediation, and host performance. However, attempts to manage interactions in complex, open microbial communities often fall short of expectations, in part because interactions are highly context-dependent, with net effects arising from multiple component interactions, higher-order interactions, and rapid evolution-features largely revealed from studies with simplified communities. Here, we propose how these insights can be translated to complex communities by prioritizing the scales and disturbances that matter, leveraging the ecological context that constrains interactions, targeting function-critical behaviors and traits, and accounting for eco-evolutionary feedbacks. We further propose coupling top-down, trait-based, and coarse-grained approaches with bottom-up synthetic ecology approaches to diagnose failures and design robust microbial processes.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"943-955"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147782104","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
How do bacteria recognize fungal competitors? 细菌如何识别真菌的竞争对手？
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-07-15 DOI: 10.1016/j.tim.2026.06.005
Lingfang Zhu, Changfu Li, Xihui Shen
{"title":"How do bacteria recognize fungal competitors?","authors":"Lingfang Zhu, Changfu Li, Xihui Shen","doi":"10.1016/j.tim.2026.06.005","DOIUrl":"10.1016/j.tim.2026.06.005","url":null,"abstract":"<p><p>Bacterial-fungal interactions (BFIs) are central to microbial community dynamics in diverse ecosystems, with profound implications for medicine, agriculture, and environmental microbiology. A critical yet unresolved question in BFIs is how bacteria specifically detect and respond to fungal competitors. This review synthesizes recent advances in this field, focusing on four integrated strategies that bacteria employ to recognize fungi: (i) sensing conserved fungal cell wall-derived microbe-associated molecular patterns; (ii) eavesdropping on fungal chemical signals, including quorum-sensing molecules and volatile organic compounds; (iii) contact-dependent recognition via chemotaxis, biofilm adhesion, and specialized secretion systems; and (iv) indirect recognition through resource competition. These mechanisms highlight the sophistication of interkingdom communication and its translational potential in managing polymicrobial infections and engineering biocontrol systems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"989-1002"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456918","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
Along for the ride: prophage-induced flagellar remodelling. 伴随而来的是：噬菌体诱导的鞭毛重塑。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-09-01 Epub Date: 2026-08-18 DOI: 10.1016/j.tim.2026.07.014
Victor D Pool, Wen Y Wu
{"title":"Along for the ride: prophage-induced flagellar remodelling.","authors":"Victor D Pool, Wen Y Wu","doi":"10.1016/j.tim.2026.07.014","DOIUrl":"10.1016/j.tim.2026.07.014","url":null,"abstract":"<p><p>TldRs (TnpB-like nuclease-dead repressors) are RNA-guided transcriptional repressors. Walker et al. show that a temperate, Flagellin Remodelling prophage uses TldRs to repress host flagellin (fliC<sub>H</sub>) while expressing its own isoform (fliC<sub>P</sub>), altering filament architecture. This enhances motility, reduces TLR5-driven immune activation, and improves gut colonisation.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"912-914"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148798242","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 importance of interbacterial relationships in shaping cyanobacterial ecology. 在塑造蓝藻生态的细菌间关系的重要性。
IF 18.7 1区 生物学
Trends in Microbiology Pub Date : 2026-08-31 DOI: 10.1016/j.tim.2026.08.002
Colin Lock, Amaranta Focardi, Michele A Burford, Simon M Mitrovic, Jean-Baptiste Raina, Justin R Seymour
{"title":"The importance of interbacterial relationships in shaping cyanobacterial ecology.","authors":"Colin Lock, Amaranta Focardi, Michele A Burford, Simon M Mitrovic, Jean-Baptiste Raina, Justin R Seymour","doi":"10.1016/j.tim.2026.08.002","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.002","url":null,"abstract":"<p><p>Cyanobacteria are a globally abundant bacterial phylum that make key contributions to primary production and nutrient cycling in aquatic ecosystems. However, some cyanobacteria also cause substantial adverse environmental impacts through harmful blooms and the production of potent toxins. Given their global significance, understanding the processes governing cyanobacterial ecology is critical for assessing aquatic ecosystem function. While abiotic environmental factors have traditionally been considered most important, a growing body of literature indicates that interactions with other microorganisms, in particular heterotrophic bacteria, shape cyanobacterial growth, population dynamics, and ecological success. In this review, we provide a synthesis of the importance of interbacterial interactions in controlling cyanobacterial populations and their ecological impacts on natural aquatic environments and argue that these relationships should be incorporated into conceptual and predictive frameworks of cyanobacterial ecology.</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":"148866654","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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