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Trends in Microbiology最新文献

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Analyzing human gut microbiome data from global populations: challenges and resources. 分析全球人群的肠道微生物组数据：挑战和资源。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-06 DOI: 10.1016/j.tim.2025.05.008
Sabrina J Arif, Samantha P Graham, Richard J Abdill, Ran Blekhman
{"title":"Analyzing human gut microbiome data from global populations: challenges and resources.","authors":"Sabrina J Arif, Samantha P Graham, Richard J Abdill, Ran Blekhman","doi":"10.1016/j.tim.2025.05.008","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.008","url":null,"abstract":"<p><p>Research on the human gut microbiome is expanding rapidly; yet, most published studies focus on populations from high-income regions such as North America and Europe. Underrepresentation of populations from low- and middle-income countries in the microbiome literature limits the generalizability of microbiome-health associations. These challenges are compounded by computational barriers, including biases in reference databases, nonrepresentative metadata, and infrastructure limitations in low- and middle-income countries. However, recent efforts in large-scale global sampling have begun to address these problems. This review provides recommendations for future research efforts applying computational analysis to global microbiome data, including guidelines to initiate and maintain equitable partnerships, identify representative datasets, overcome technical limitations, and contextualize results at the global scale.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249771","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 single-cell perspective on host-virus dynamics in the ocean. 海洋中宿主-病毒动力学的单细胞视角。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-05 DOI: 10.1016/j.tim.2025.05.005
Amir Fromm, Talia S Shaler, Frank O Aylward, Assaf Vardi
{"title":"A single-cell perspective on host-virus dynamics in the ocean.","authors":"Amir Fromm, Talia S Shaler, Frank O Aylward, Assaf Vardi","doi":"10.1016/j.tim.2025.05.005","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.005","url":null,"abstract":"<p><p>Viral infections of marine microbes greatly impact ecological and biogeochemical processes. Typically, these host-virus interactions are studied at the population level using bulk transcriptomics, which presents a population-averaged perspective and masks diverse infection states. Recent advancements in single-cell technologies enable a simultaneous view of the virus and its host within a population and expose phenotypic heterogeneity during infection. We present a promising avenue for investigating marine viral ecology from a new single-cell perspective to reveal the viral life cycle and host antiviral strategies employed by rare resistant cells. Consequently, we can detect specific host-virus dynamics in the complex natural population, track the spread of infection across ecosystems, and study the ecological impact of marine viruses at an unprecedented resolution.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249770","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
Genetics of dengue epidemics. 登革热流行的遗传学。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-05 DOI: 10.1016/j.tim.2025.05.007
Allyson N X Choi, Duane J Gubler, Eng Eong Ooi
{"title":"Genetics of dengue epidemics.","authors":"Allyson N X Choi, Duane J Gubler, Eng Eong Ooi","doi":"10.1016/j.tim.2025.05.007","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.007","url":null,"abstract":"<p><p>Dengue is an acute mosquito-borne viral disease widespread throughout tropical regions. Cyclical epidemics on top of high endemic dengue incidence strain many healthcare systems. While low population immunity to the four dengue viruses (DENVs) is often cited as the cause of epidemics, not all new DENV introductions have caused epidemics. Moreover, the role of DENV genetics in epidemic emergence has remained understudied. This review examines how genetic changes affect DENV fitness and links specific epidemics to these changes, focusing especially on those where the biological functions altered by the genetic changes have been experimentally defined. Most of these changes were in the nonstructural genes and untranslated regions of the DENV genome, rather than in the commonly sequenced envelope (E) gene; many genetic traits of DENVs from past epidemics could have been missed through E gene sequencing alone. Our review calls for a systematic approach to understand the genetics of dengue epidemics and to form a foundation for early epidemic warning systems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249772","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
Microbial siderophores for One Health. 同一个健康的微生物铁载体。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-03 DOI: 10.1016/j.tim.2025.05.002
Zhong Wei, Shaohua Gu, Vera Vollenweider, Yuanmei Zuo, Zhiyuan Li, Rolf Kümmerli
{"title":"Microbial siderophores for One Health.","authors":"Zhong Wei, Shaohua Gu, Vera Vollenweider, Yuanmei Zuo, Zhiyuan Li, Rolf Kümmerli","doi":"10.1016/j.tim.2025.05.002","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.002","url":null,"abstract":"<p><p>One Health is an integrative concept striving for healthy environments, animals, and humans. Microbes play a fundamental role for this concept as they are key drivers of ecosystem stability and host health. A central microbial feature across various environments is the secretion of siderophores, low-molecular-weight metabolites that chelate ferric iron (Fe<sup>3+</sup>) with high affinity. We propose that, by steering iron and metal availability, siderophores can be important for One Health in four key areas via: (i) enhancing crop yield, (ii) mitigating heavy metal pollution, (iii) preventing pathogen colonization, and (iv) serving as potential treatments for established infections. Collectively, siderophores are attractive molecules to complement our efforts in increasing human, animal, and environmental health.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226813","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
Fungal cell walls: the rising importance of carbohydrate-active enzymes. 真菌细胞壁：碳水化合物活性酶的重要性日益提高。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-02 DOI: 10.1016/j.tim.2025.05.001
Roseline Assiah Yao, Jean-Guy Berrin, Lauren S McKee, Bastien Bissaro
{"title":"Fungal cell walls: the rising importance of carbohydrate-active enzymes.","authors":"Roseline Assiah Yao, Jean-Guy Berrin, Lauren S McKee, Bastien Bissaro","doi":"10.1016/j.tim.2025.05.001","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.001","url":null,"abstract":"<p><p>As the interface between the fungal cell and its surroundings, the fungal cell wall (FCW) plays an essential physiological role in a myriad of biological processes. It provides support, protection, and enables material exchange with the environment, playing a key role in microbiome and host-microbe interactions. The fact that FCWs are mainly composed of complex carbohydrates makes carbohydrate-active enzymes (CAZymes) the main players in FCW remodelling and degradation. Despite the biological importance of these processes, our understanding of the underlying enzymology remains limited. In this review, we discuss the role of FCW-active CAZymes in various contexts, including fungal physiology, pathogenesis, human gut microbiomes, and the global carbon cycle, while highlighting knowledge gaps and potential applications in agriculture, biotechnology, and health.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217026","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
ESCRTs - a multi-purpose membrane remodeling device encoded in all life forms. escrt -一种在所有生命形式中编码的多用途膜重塑装置。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-01 Epub Date: 2025-02-19 DOI: 10.1016/j.tim.2025.01.009
Dikla Nachmias, Béla P Frohn, Carsten Sachse, Itzhak Mizrahi, Natalie Elia
{"title":"ESCRTs - a multi-purpose membrane remodeling device encoded in all life forms.","authors":"Dikla Nachmias, Béla P Frohn, Carsten Sachse, Itzhak Mizrahi, Natalie Elia","doi":"10.1016/j.tim.2025.01.009","DOIUrl":"10.1016/j.tim.2025.01.009","url":null,"abstract":"<p><p>The ESCRT (endosomal sorting complexes required for transport) membrane remodeling complex, found across all life forms, exhibits a versatility that transcends evolutionary boundaries. From orchestrating the constriction of micron-wide tubes in cell division to facilitating the budding of 50 nm vesicles in receptor degradation, ESCRTs perform diverse functions in animal cells. However, the basis of this functional diversity remains enigmatic. While extensively studied in eukaryotes, the role of ESCRTs in prokaryotes is only beginning to emerge. This review synthesizes data on ESCRT systems across the tree of life, focusing on microorganisms and drawing parallels to their functions in human cells. This comparative approach highlights the remarkable plasticity of the ESCRT system across functional, structural, and genomic levels in both prokaryotes and eukaryotes. This integrated knowledge supports a model in which the ESCRT system evolved as a multipurpose membrane remodeling tool, adaptable to specific functions within and across organisms. Our review not only underscores the significance of ESCRTs in microorganisms but also paves the way for exciting avenues of research into the intricacies of cellular membrane dynamics, offering valuable insights into the evolution of cellular complexity across diverse organisms and ecosystems.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"665-687"},"PeriodicalIF":14.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469352","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
Tracing epistemic injustice in global antimicrobial resistance research. 追踪全球抗菌素耐药性研究中的认知不公。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tim.2025.02.005
Phaik Yeong Cheah, Sonia Lewycka, Jantina de Vries
{"title":"Tracing epistemic injustice in global antimicrobial resistance research.","authors":"Phaik Yeong Cheah, Sonia Lewycka, Jantina de Vries","doi":"10.1016/j.tim.2025.02.005","DOIUrl":"10.1016/j.tim.2025.02.005","url":null,"abstract":"<p><p>This commentary explores whether there is epistemic injustice in global antimicrobial resistance (AMR) research - who sets priorities, who produces knowledge, and which types of knowledge are valued. We argue that epistemic injustice may have created blind spots in policy. Addressing this requires a commitment to diversity, equity, and inclusion.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"577-579"},"PeriodicalIF":14.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574135","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
Disentangling microbial interaction networks. 分解微生物相互作用网络。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tim.2025.01.013
Leonardo Oña, Shryli K Shreekar, Christian Kost
{"title":"Disentangling microbial interaction networks.","authors":"Leonardo Oña, Shryli K Shreekar, Christian Kost","doi":"10.1016/j.tim.2025.01.013","DOIUrl":"10.1016/j.tim.2025.01.013","url":null,"abstract":"<p><p>The structure and function of microbial communities is shaped by intricate ecological interactions amongst the constituent microorganisms. Thus, a mechanistic understanding of emergent community-level functions requires knowledge on how the architecture of the underlying interaction networks affects these properties. To address this, researchers employ different sequencing-based and experimental approaches to infer the topology of a given network. However, it remains generally unclear which method is best suited for quantifying critical network parameters. Here we provide a comparative overview of different approaches serving this purpose, with particular emphasis on their strengths and weaknesses. In this way, our work can help to guide the design of studies that aim at unraveling structure-function relationships in microbial communities.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"619-634"},"PeriodicalIF":14.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568310","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
Small proteins and peptides conferring protection against antimicrobial compounds. 对抗菌化合物具有保护作用的小蛋白质和肽。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-01 Epub Date: 2025-03-06 DOI: 10.1016/j.tim.2025.01.011
Rianne C Prins, Sonja Billerbeck
{"title":"Small proteins and peptides conferring protection against antimicrobial compounds.","authors":"Rianne C Prins, Sonja Billerbeck","doi":"10.1016/j.tim.2025.01.011","DOIUrl":"10.1016/j.tim.2025.01.011","url":null,"abstract":"<p><p>The secretion of antimicrobials is widespread among microorganisms, many of which have developed protection mechanisms. While well-characterized protection mechanisms involve relatively large proteins - such as exporters or compound- or target-modifying enzymes - we discuss how small proteins and peptides can also confer protection. Recent technological advances have revealed the functional capacity and importance of the small proteome, as well as its potential for de novo evolution. We consolidate examples of diverse small proteins that play a protective role against antimicrobial agents, highlighting characteristics and exploring their mechanisms of protection where data are available. We advocate for further examination of their mechanisms of protection as they may constitute an intriguing, mechanistically, and evolutionary distinct part of the antimicrobial resistome.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"586-602"},"PeriodicalIF":14.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586966","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
9th International Conference on Clinical Metagenomics (ICCMg9): meeting report. 第九届国际临床宏基因组学会议（ICCMg9）：会议报告。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-01 Epub Date: 2025-04-25 DOI: 10.1016/j.tim.2025.03.012
Etienne Ruppé, Vladimir Lazarevic, Jacques Schrenzel
{"title":"9th International Conference on Clinical Metagenomics (ICCMg9): meeting report.","authors":"Etienne Ruppé, Vladimir Lazarevic, Jacques Schrenzel","doi":"10.1016/j.tim.2025.03.012","DOIUrl":"10.1016/j.tim.2025.03.012","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"573-576"},"PeriodicalIF":14.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055114","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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