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Closely related and yet special - how SPβ family phages control lysis-lysogeny decisions. SPβ家族噬菌体如何控制裂解-溶原性决定？
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-06 DOI: 10.1016/j.tim.2024.11.007
Katharina Kohm, Annabel V Clanner, Robert Hertel, Fabian M Commichau
{"title":"Closely related and yet special - how SPβ family phages control lysis-lysogeny decisions.","authors":"Katharina Kohm, Annabel V Clanner, Robert Hertel, Fabian M Commichau","doi":"10.1016/j.tim.2024.11.007","DOIUrl":"https://doi.org/10.1016/j.tim.2024.11.007","url":null,"abstract":"<p><p>Soon after the discovery of genetic competence in the Gram-positive bacterium Bacillus subtilis, lytic and temperate phages that infect this organism were isolated. For instance, the lytic phage ϕ29 became a model for studying processes such as viral DNA packaging, replication, and transcription. By contrast, only a handful of temperate B. subtilis phages have been comprehensively characterized. However, the discovery of a peptide-based quorum sensing (QS) system in 2017 has brought temperate B. subtilis phages, particularly those of the SPβ family, back into the focus of research. The QS system is used by these phages to modulate lysis-lysogeny decisions. Meanwhile, many key components of the lysis-lysogeny management system have been identified. It turned out that a complex co-adaptation between the B. subtilis host cell and SPβ-like phages occurred during evolution and that a host-encoded toxin-antitoxin system plays a key role in controlling lysis-lysogeny decisions. There are many similarities and many important differences between the two well-studied model phages. Thus, a further comparative analysis of the lysis-lysogeny systems is essential to uncover the fundamental differences between ϕ3T and SPβ. Moreover, we believe that it would be exciting to revive research on temperate B. subtilis phages that are not related to SPβ-family phages.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792583","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
Current advancements in fungal engineering technologies for Sustainable Development Goals. 可持续发展目标中真菌工程技术的最新进展。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-06 DOI: 10.1016/j.tim.2024.11.001
Shilpa Garg, Minji Kim, David Romero-Suarez
{"title":"Current advancements in fungal engineering technologies for Sustainable Development Goals.","authors":"Shilpa Garg, Minji Kim, David Romero-Suarez","doi":"10.1016/j.tim.2024.11.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.11.001","url":null,"abstract":"<p><p>Fungi are emerging as key organisms in tackling global challenges related to agricultural and food productivity, environmental sustainability, and climate change. This review delves into the transformative potential of fungal genomics and metabolic engineering, two forefront fields in modern biotechnology. Fungal genomics entails the thorough analysis and manipulation of fungal genetic material to enhance desirable traits, such as pest resistance, nutrient absorption, and stress tolerance. Metabolic engineering focuses on altering the biochemical pathways within fungi to optimize the production of valuable compounds, including biofuels, pharmaceuticals, and industrial enzymes. By artificial intelligence (AI)-driven integration of genetic and metabolic engineering techniques, we can harness the unique capabilities of both filamentous and mycorrhizal fungi to develop sustainable agricultural practices, enhance soil health, and promote ecosystem restoration. This review explores the current state of research, technological advancements, and practical applications, offering insights into scalability challenges on how integrative fungal genomics and metabolic engineering can deliver innovative solutions for a sustainable future.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792584","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
Gene transfer agents: structural and functional properties of domesticated viruses. 基因转移剂：驯化病毒的结构和功能特性。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-05-27 DOI: 10.1016/j.tim.2024.05.002
Matthew W Craske, Jason S Wilson, Paul C M Fogg
{"title":"Gene transfer agents: structural and functional properties of domesticated viruses.","authors":"Matthew W Craske, Jason S Wilson, Paul C M Fogg","doi":"10.1016/j.tim.2024.05.002","DOIUrl":"10.1016/j.tim.2024.05.002","url":null,"abstract":"<p><p>Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1200-1211"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162259","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
Loading and unloading plasmid cargoes. 装载和卸载质粒货物。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-10-10 DOI: 10.1016/j.tim.2024.09.012
James P J Hall
{"title":"Loading and unloading plasmid cargoes.","authors":"James P J Hall","doi":"10.1016/j.tim.2024.09.012","DOIUrl":"10.1016/j.tim.2024.09.012","url":null,"abstract":"<p><p>Plasmids are vehicles for horizontal gene transfer between cells, but they also exchange genes with associated chromosomes in a process termed 'intracellular mobility'. I discuss a recent article by Kadibalban et al. mapping such plasmid-chromosomal sequence similarities across diverse bacteria.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1150-1152"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406918","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 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
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-06-27 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
{"title":"The use of experimentally evolved coral photosymbionts for reef restoration.","authors":"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","doi":"10.1016/j.tim.2024.05.008","DOIUrl":"10.1016/j.tim.2024.05.008","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1241-1252"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141470972","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
Agents of change: a partnership between mobile genetic elements facilitates rapid bacterial adaptation. 变化的媒介：流动遗传因子之间的伙伴关系促进了细菌的快速适应。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-11-19 DOI: 10.1016/j.tim.2024.10.010
Elizabeth S Duan, Olivia Kosterlitz, Benjamin Kerr
{"title":"Agents of change: a partnership between mobile genetic elements facilitates rapid bacterial adaptation.","authors":"Elizabeth S Duan, Olivia Kosterlitz, Benjamin Kerr","doi":"10.1016/j.tim.2024.10.010","DOIUrl":"10.1016/j.tim.2024.10.010","url":null,"abstract":"<p><p>While the evolutionary interests of mobile genetic elements may differ from those of their bacterial hosts, these elements can be beneficial for their hosts by delivering, disrupting, or activating genes. A recent paper by Sastre-Domínguez et al. describes a novel synergistic effect of mobile elements in clinically relevant bacteria, whereby conjugative plasmids that carry transposable elements can be agents of rapid adaptive change through an elevation in transposition-mediated mutation rate.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1156-1158"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142682766","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
Tackling the plastisphere: the single-cell Raman spectroscopy framework. 解决质球问题：单细胞拉曼光谱框架。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-08-31 DOI: 10.1016/j.tim.2024.08.005
Qing-Lin Chen, Kai Yang, Qian Xiang, Li Cui, Yong-Guan Zhu
{"title":"Tackling the plastisphere: the single-cell Raman spectroscopy framework.","authors":"Qing-Lin Chen, Kai Yang, Qian Xiang, Li Cui, Yong-Guan Zhu","doi":"10.1016/j.tim.2024.08.005","DOIUrl":"10.1016/j.tim.2024.08.005","url":null,"abstract":"<p><p>Conventional bulk molecular approaches, often limited by their destructive nature and low spatial resolution, face challenges when probing the intricate dynamics of the plastisphere. Here, we outline a framework employing Raman spectroscopy combined with stable isotope profiling (SIP) to interrogate the physiological function of the plastisphere microbiome and track its evolutionary trajectories.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1159-1162"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112341","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 growing repertoire of phage anti-defence systems. 噬菌体抗防御系统的种类越来越多。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-06-05 DOI: 10.1016/j.tim.2024.05.005
Khalimat Murtazalieva, Andre Mu, Aleksandra Petrovskaya, Robert D Finn
{"title":"The growing repertoire of phage anti-defence systems.","authors":"Khalimat Murtazalieva, Andre Mu, Aleksandra Petrovskaya, Robert D Finn","doi":"10.1016/j.tim.2024.05.005","DOIUrl":"10.1016/j.tim.2024.05.005","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1212-1228"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284858","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
A unique bacterial family strikes again! 一个独特的细菌家族再次出现！
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-10-22 DOI: 10.1016/j.tim.2024.10.002
Gyanesh Shukla, Gaurav Sharma
{"title":"A unique bacterial family strikes again!","authors":"Gyanesh Shukla, Gaurav Sharma","doi":"10.1016/j.tim.2024.10.002","DOIUrl":"10.1016/j.tim.2024.10.002","url":null,"abstract":"<p><p>Garcia et al. recently identified a novel myxobacterial family, Pendulisporaceae, encompassing four strains with novel biosynthetic gene clusters. This study underscores the value of exploring underrepresented microbial taxa for novel natural products, highlighting the potential of the family Pendulisporaceae as a source of new antimicrobial and therapeutic agents.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1153-1155"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142508753","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
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 14 1区 生物学
Trends in Microbiology Pub Date : 2024-12-01 Epub Date: 2024-06-04 DOI: 10.1016/j.tim.2024.05.006
Michael L Pepke, Søren B Hansen, Morten T Limborg
{"title":"Unraveling host regulation of gut microbiota through the epigenome-microbiome axis.","authors":"Michael L Pepke, Søren B Hansen, Morten T Limborg","doi":"10.1016/j.tim.2024.05.006","DOIUrl":"10.1016/j.tim.2024.05.006","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1229-1240"},"PeriodicalIF":14.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262218","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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