Pub Date : 2024-08-31DOI: 10.1016/j.tim.2024.08.005
Qing-Lin Chen, Kai Yang, Qian Xiang, Li Cui, Yong-Guan Zhu
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.
{"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":"https://doi.org/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":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-31","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}
Pub Date : 2024-08-29DOI: 10.1016/j.tim.2024.08.001
Guillaume Balleux, Monica Höfte, Anthony Arguelles-Arias, Magali Deleu, Marc Ongena
Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.
{"title":"Bacillus lipopeptides as key players in rhizosphere chemical ecology.","authors":"Guillaume Balleux, Monica Höfte, Anthony Arguelles-Arias, Magali Deleu, Marc Ongena","doi":"10.1016/j.tim.2024.08.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.08.001","url":null,"abstract":"<p><p>Microbial natural products are widely explored for their therapeutic potential. Understanding the underlying evolutionary and adaptive forces driving their production remains a fundamental question in biology. Amphiphilic cyclic lipopeptides (CLPs), a prominent category of bacterial specialized metabolites, show strong antimicrobial activity, particularly against phytopathogens. It is thus assumed that these compounds are deployed by soil- or rhizosphere-dwelling bacteria as microbial weapons in competitive natural environments. Here, we challenge this reductionist perspective and present evidence that Bacillus CLPs are prominent chemical mediators of ecological interactions. They help Bacillus to communicate, compete, defend against predators, or cooperate and establish mutualistic relationships with other (micro)organisms. Additional parallel examples are highlighted in other genera, such as Pseudomonas. This broader perspective underscores the need for further investigation into the role of CLPs in shaping the adaptive strategies of key rhizobacterial species.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142112338","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}
Pub Date : 2024-08-22DOI: 10.1016/j.tim.2024.07.001
Elina Gerber-Tichet, Fabien P Blanchet, Karim Majzoub, Eric J Kremer
Since the initial description of Toll receptors in Drosophila and their mammalian counterparts Toll-like receptors (TLRs), numerous fundamental and applied studies have explored their crucial role as sensors of pathogen-associated molecular patterns (PAMPs). Among the ten human TLRs, TLR4 is particularly well known for its ability to detect lipopolysaccharides (LPS), a component of the Gram-negative bacterial cell wall. In addition to its archetypal functions, TLR4 is also a versatile virus sensor. This review provides a background on the discovery of TLR4 and how this knowledge laid a foundation for characterization of its diverse roles in antiviral responses, examined through genetic, biochemical, structural, and immunological approaches. These advances have led to a deeper understanding of the molecular functions that enable TLR4 to orchestrate multi-nodal control by professional antigen-presenting cells (APCs) to initiate appropriate and regulated antiviral immune responses.
{"title":"Toll-like receptor 4 - a multifunctional virus recognition receptor.","authors":"Elina Gerber-Tichet, Fabien P Blanchet, Karim Majzoub, Eric J Kremer","doi":"10.1016/j.tim.2024.07.001","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.001","url":null,"abstract":"<p><p>Since the initial description of Toll receptors in Drosophila and their mammalian counterparts Toll-like receptors (TLRs), numerous fundamental and applied studies have explored their crucial role as sensors of pathogen-associated molecular patterns (PAMPs). Among the ten human TLRs, TLR4 is particularly well known for its ability to detect lipopolysaccharides (LPS), a component of the Gram-negative bacterial cell wall. In addition to its archetypal functions, TLR4 is also a versatile virus sensor. This review provides a background on the discovery of TLR4 and how this knowledge laid a foundation for characterization of its diverse roles in antiviral responses, examined through genetic, biochemical, structural, and immunological approaches. These advances have led to a deeper understanding of the molecular functions that enable TLR4 to orchestrate multi-nodal control by professional antigen-presenting cells (APCs) to initiate appropriate and regulated antiviral immune responses.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047252","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}
Pub Date : 2024-08-19DOI: 10.1016/j.tim.2024.07.003
Lauren S J Cook, Andrew G Briscoe, Vera G Fonseca, Jens Boenigk, Guy Woodward, David Bass
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
微生物环境 DNA 和 RNA(统称为 "ENA")来源于环境样本中多种多样的微生物。这些 "ENA "信号在很大程度上代表了完整的生物体,是对来自大型生物体片段或残余的信号的有力补充。因此,将微生物数据整合到生态系统评估和生物指数的工具箱中,有可能改变我们使用enera数据了解生物多样性动态和生态系统功能的方式,并为下一代环境监测提供信息。将全生物体和生命之树方法纳入ENA分析,可以进一步全面了解微生物与其他生物之间的生态相互作用,为我们进一步了解并最终操纵与环境管理、保护、野生动物健康和食品生产相关的生态系统特性铺平道路。
{"title":"Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment.","authors":"Lauren S J Cook, Andrew G Briscoe, Vera G Fonseca, Jens Boenigk, Guy Woodward, David Bass","doi":"10.1016/j.tim.2024.07.003","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.003","url":null,"abstract":"<p><p>Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009515","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}
Pub Date : 2024-08-19DOI: 10.1016/j.tim.2024.07.009
Davide Roncarati, Andrea Vannini, Vincenzo Scarlato
Pathogenic bacteria can detect a variety of environmental signals, including temperature changes. While sudden and significant temperature variations act as danger signals that trigger a protective heat-shock response, minor temperature fluctuations typically signal to the pathogen that it has moved from one environment to another, such as entering a specific niche within a host during infection. These latter temperature fluctuations are utilized by pathogens to coordinate the expression of crucial virulence factors. Here, we elucidate the critical role of temperature in governing the expression of virulence factors in bacterial pathogens. Moreover, we outline the molecular mechanisms used by pathogens to detect temperature fluctuations, focusing on systems that employ proteins and nucleic acids as sensory devices. We also discuss the potential implications and the extent of the risk that climate change poses to human pathogenic diseases.
{"title":"Temperature sensing and virulence regulation in pathogenic bacteria.","authors":"Davide Roncarati, Andrea Vannini, Vincenzo Scarlato","doi":"10.1016/j.tim.2024.07.009","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.009","url":null,"abstract":"<p><p>Pathogenic bacteria can detect a variety of environmental signals, including temperature changes. While sudden and significant temperature variations act as danger signals that trigger a protective heat-shock response, minor temperature fluctuations typically signal to the pathogen that it has moved from one environment to another, such as entering a specific niche within a host during infection. These latter temperature fluctuations are utilized by pathogens to coordinate the expression of crucial virulence factors. Here, we elucidate the critical role of temperature in governing the expression of virulence factors in bacterial pathogens. Moreover, we outline the molecular mechanisms used by pathogens to detect temperature fluctuations, focusing on systems that employ proteins and nucleic acids as sensory devices. We also discuss the potential implications and the extent of the risk that climate change poses to human pathogenic diseases.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009516","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}
Pub Date : 2024-08-06DOI: 10.1016/s0966-842x(24)00183-5
No Abstract
无摘要
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/s0966-842x(24)00183-5","DOIUrl":"https://doi.org/10.1016/s0966-842x(24)00183-5","url":null,"abstract":"No Abstract","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":15.9,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141948236","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}
Pub Date : 2024-08-06DOI: 10.1016/s0966-842x(24)00186-0
No Abstract
无摘要
{"title":"Subscription and Copyright Information","authors":"","doi":"10.1016/s0966-842x(24)00186-0","DOIUrl":"https://doi.org/10.1016/s0966-842x(24)00186-0","url":null,"abstract":"No Abstract","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":15.9,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141948235","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}
Pub Date : 2024-08-01Epub Date: 2024-06-19DOI: 10.1016/j.tim.2024.06.001
Kun Jiang, Xiang Gao
Biological control, based on microbial insecticidal proteins, has become an important strategy for sustainable pest management. This forum discusses recent advancements and research strategies of the bacterial insecticidal protein vegetative insecticidal protein 3 (Vip3), aiming to provide valuable insights for future investigations on Vip3 and other insecticidal proteins.
{"title":"Current advances on Vip3 highlight the promising potential of bacterial insecticidal proteins.","authors":"Kun Jiang, Xiang Gao","doi":"10.1016/j.tim.2024.06.001","DOIUrl":"10.1016/j.tim.2024.06.001","url":null,"abstract":"<p><p>Biological control, based on microbial insecticidal proteins, has become an important strategy for sustainable pest management. This forum discusses recent advancements and research strategies of the bacterial insecticidal protein vegetative insecticidal protein 3 (Vip3), aiming to provide valuable insights for future investigations on Vip3 and other insecticidal proteins.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141432898","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}
Pub Date : 2024-08-01DOI: 10.1016/j.tim.2024.07.005
During the past two decades, gut microbiome studies have established the significant impact of the gut microbiota and its metabolites on host health. However, the molecular mechanisms governing the production of microbial metabolites in the gut environment remain insufficiently investigated and thus are poorly understood. Here, we propose that an enhanced understanding of gut microbial gene regulation, which is responsive to dietary components and gut environmental conditions, is needed in the research field and essential for our ability to effectively promote host health and prevent diseases through interventions targeting the gut microbiome.
{"title":"Regulation of microbial gene expression: the key to understanding our gut microbiome","authors":"","doi":"10.1016/j.tim.2024.07.005","DOIUrl":"https://doi.org/10.1016/j.tim.2024.07.005","url":null,"abstract":"<p>During the past two decades, gut microbiome studies have established the significant impact of the gut microbiota and its metabolites on host health. However, the molecular mechanisms governing the production of microbial metabolites in the gut environment remain insufficiently investigated and thus are poorly understood. Here, we propose that an enhanced understanding of gut microbial gene regulation, which is responsive to dietary components and gut environmental conditions, is needed in the research field and essential for our ability to effectively promote host health and prevent diseases through interventions targeting the gut microbiome.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":15.9,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870084","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}
Pub Date : 2024-08-01Epub Date: 2024-01-23DOI: 10.1016/j.tim.2024.01.001
Katarzyna Bialas, Felipe Diaz-Griffero
Cleavage and polyadenylation specificity factor subunit 6 (CPSF6, also known as CFIm68) is a 68 kDa component of the mammalian cleavage factor I (CFIm) complex that modulates mRNA alternative polyadenylation (APA) and determines 3' untranslated region (UTR) length, an important gene expression control mechanism. CPSF6 directly interacts with the HIV-1 core during infection, suggesting involvement in HIV-1 replication. Here, we review the contributions of CPSF6 to every stage of the HIV-1 replication cycle. Recently, several groups described the ability of HIV-1 infection to induce CPSF6 translocation to nuclear speckles, which are biomolecular condensates. We discuss the implications for CPSF6 localization in condensates and the potential role of condensate-localized CPSF6 in the ability of HIV-1 to control the protein expression pattern of the cell.
{"title":"HIV-1-induced translocation of CPSF6 to biomolecular condensates.","authors":"Katarzyna Bialas, Felipe Diaz-Griffero","doi":"10.1016/j.tim.2024.01.001","DOIUrl":"10.1016/j.tim.2024.01.001","url":null,"abstract":"<p><p>Cleavage and polyadenylation specificity factor subunit 6 (CPSF6, also known as CFIm68) is a 68 kDa component of the mammalian cleavage factor I (CFIm) complex that modulates mRNA alternative polyadenylation (APA) and determines 3' untranslated region (UTR) length, an important gene expression control mechanism. CPSF6 directly interacts with the HIV-1 core during infection, suggesting involvement in HIV-1 replication. Here, we review the contributions of CPSF6 to every stage of the HIV-1 replication cycle. Recently, several groups described the ability of HIV-1 infection to induce CPSF6 translocation to nuclear speckles, which are biomolecular condensates. We discuss the implications for CPSF6 localization in condensates and the potential role of condensate-localized CPSF6 in the ability of HIV-1 to control the protein expression pattern of the cell.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":null,"pages":null},"PeriodicalIF":14.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11263504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139545439","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}