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Gene transfer drives community cooperation in geothermal habitats. 基因转移推动地热栖息地的社区合作。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-20 DOI: 10.1016/j.tim.2025.06.004
Debashish Bhattacharya, Julia Van Etten, Gabriella Panayotakis, Timothy McDermott, Timothy G Stephens
{"title":"Gene transfer drives community cooperation in geothermal habitats.","authors":"Debashish Bhattacharya, Julia Van Etten, Gabriella Panayotakis, Timothy McDermott, Timothy G Stephens","doi":"10.1016/j.tim.2025.06.004","DOIUrl":"10.1016/j.tim.2025.06.004","url":null,"abstract":"<p><p>Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340429","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
Is genetic manipulation of arbuscular mycorrhizal fungi possible? 丛枝菌根真菌的基因操纵可能吗？
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-19 DOI: 10.1016/j.tim.2025.06.002
Mary-Jane Woodward, Alexandra Dallaire, Uta Paszkowski, Vasilis Kokkoris
{"title":"Is genetic manipulation of arbuscular mycorrhizal fungi possible?","authors":"Mary-Jane Woodward, Alexandra Dallaire, Uta Paszkowski, Vasilis Kokkoris","doi":"10.1016/j.tim.2025.06.002","DOIUrl":"10.1016/j.tim.2025.06.002","url":null,"abstract":"<p><p>Unlike many fungi, arbuscular mycorrhizal (AM) fungi have proven recalcitrant to genetic manipulation due to their obligate biotrophic lifestyle and multinucleate, coenocytic cellular structure. In this review, we examine past attempts at AM fungal transformation, we identify key biological and technical barriers and explore recent advances to overcome them. We focus on techniques never before applied in AM fungi, including CRISPR/Cas9, microinjection, and protoplast-based transformation, and we explore how they provide viable strategies for achieving this elusive goal. We conclude by outlining guidelines for future research, distinguishing between established approaches that are readily applicable to AM fungi and others that first require addressing key outstanding questions in AM fungal cell biology and genetics to ensure success.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337042","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
Maximizing bacterial survival: integrating sense-and-respond and bet-hedging mechanisms. 最大化细菌生存：整合感知-反应和下注对冲机制。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-18 DOI: 10.1016/j.tim.2025.05.010
Lillian C Lowrey, Nicole C Gadda, Rita Tamayo
{"title":"Maximizing bacterial survival: integrating sense-and-respond and bet-hedging mechanisms.","authors":"Lillian C Lowrey, Nicole C Gadda, Rita Tamayo","doi":"10.1016/j.tim.2025.05.010","DOIUrl":"10.1016/j.tim.2025.05.010","url":null,"abstract":"<p><p>Two-component systems allow bacteria to respond to specific environmental signals with defined adaptive phenotypic changes, a process that requires time and may be inadequate for contending with rapidly changing environments. In contrast, phase variation generates baseline levels of phenotypic heterogeneity that helps to ensure survival of the population as a whole. This strategy may be better suited to confront abrupt environmental changes but may produce transiently less-fit subpopulations. Many bacteria have integrated phase variation and two-component signaling - how combining these stochastic and deterministic mechanisms affects bacterial fitness is unclear. Here, we identify three distinct schemes for integration of phase variation and two-component signaling. Using well-characterized examples, we speculate the circumstances in which each integration scheme confers a fitness advantage.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144333887","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
Large-scale microbiome data initiatives call for diversity. 大规模微生物组数据倡议要求多样性。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-17 DOI: 10.1016/j.tim.2025.06.001
Quin Yuhui Xie, Jayne S Danska
{"title":"Large-scale microbiome data initiatives call for diversity.","authors":"Quin Yuhui Xie, Jayne S Danska","doi":"10.1016/j.tim.2025.06.001","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.001","url":null,"abstract":"<p><p>High variability in human gut microbiota is a challenge in the identification of consistent microbe-disease associations. Two Cell papers by Nishijima et al. and Abdill, Graham, et al. addressed this by curating large public microbiome datasets. They highlight long overlooked drivers of gut microbiome variance, such as fecal microbial biomass and geographical locations of study participants, necessitating diverse population representation in microbiome research.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326970","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
Phage tRNAs: decoding the enigma. 噬菌体trna：破解谜题。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-17 DOI: 10.1016/j.tim.2025.05.009
Daan F van den Berg, Stan J J Brouns
{"title":"Phage tRNAs: decoding the enigma.","authors":"Daan F van den Berg, Stan J J Brouns","doi":"10.1016/j.tim.2025.05.009","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.009","url":null,"abstract":"<p><p>The presence of tRNAs in bacteriophage genomes has intrigued scientists since their discovery in the early 1960s, as phages were believed to rely on the host tRNAs for their translation. Over the years, a multitude of hypotheses have been explored, providing evidence that phages with different lifestyles utilize tRNAs in distinct ways. In recent years, several studies have provided evidence that phage tRNAs play a crucial role in evading phage defense systems. In this review we summarize the current state of the field of phage tRNAs, highlighting their diverse roles in phage infection. We also discuss the host response to phage tRNAs and the application of this knowledge to improve phage-based therapeutics to combat bacterial infections.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326971","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 inoculants and invasions: a call to action. 微生物接种剂和入侵：行动呼吁。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-12 DOI: 10.1016/j.tim.2025.04.018
Joshua Ladau, Ashkaan K Fahimipour, Michelle E Newcomer, James B Brown, Gary J Vora, Melissa K Melby, Julia A Maresca
{"title":"Microbial inoculants and invasions: a call to action.","authors":"Joshua Ladau, Ashkaan K Fahimipour, Michelle E Newcomer, James B Brown, Gary J Vora, Melissa K Melby, Julia A Maresca","doi":"10.1016/j.tim.2025.04.018","DOIUrl":"https://doi.org/10.1016/j.tim.2025.04.018","url":null,"abstract":"<p><p>Microbial inoculants are increasingly used for beneficial purposes in agriculture, bioremediation, and medicine, but they can carry risks of generating invasive microbes. Here, we present a roadmap for guarding against these invasions, proposing developing (i) coherent mechanistic understandings of how microbial inoculants can effect invasions, (ii) predictive models forecasting microbial invasion risks, and (iii) effective management strategies. To guide mechanistic understandings, we distill 17 guiding hypotheses. For predictive modeling, we highlight data collection needs and qualitative approaches. For management strategies, we stress the importance of accurately weighing the risks against benefits. The unified approach presented here provides a route toward an effective research and management infrastructure for microbial inoculants in order to avoid potentially catastrophic microbial invasions.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286584","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
Using the microbiota to study connectivity at human-animal interfaces. 利用微生物群研究人与动物界面的连通性。
IF 14 1区 生物学
Trends in Microbiology Pub Date : 2025-06-09 DOI: 10.1016/j.tim.2025.05.006
Dishon M Muloi, Alexandre Caron, James A Berkley, James M Hassell, Ilana L Brito, Kayla King, Arshnee Moodley, Eric M Fèvre
{"title":"Using the microbiota to study connectivity at human-animal interfaces.","authors":"Dishon M Muloi, Alexandre Caron, James A Berkley, James M Hassell, Ilana L Brito, Kayla King, Arshnee Moodley, Eric M Fèvre","doi":"10.1016/j.tim.2025.05.006","DOIUrl":"https://doi.org/10.1016/j.tim.2025.05.006","url":null,"abstract":"<p><p>Interfaces between humans, livestock, and wildlife, mediated by the environment, are critical points for the transmission and emergence of infectious pathogens and call for leveraging the One Health approach to understanding disease transmission. Current research on pathogen transmission often focuses on single-pathogen systems, providing a limited understanding of the broader microbial interactions occurring at these interfaces. In this review, we make a case for the study of host-associated microbiota for understanding connectivity between host populations at human-animal interfaces. First, we emphasize the need to understand changes in microbiota composition dynamics from interspecies contact. Then, we explore the potential for microbiota monitoring at such interfaces as a predictive tool for infectious disease transmission and as an early-warning system to inform public health interventions. We discuss the methodological challenges and gaps in knowledge in analyzing microbiota composition dynamics, the functional meaning of these changes, and how to establish causality between microbiota changes and health outcomes. We posit that integrating microbiota science with social-ecological systems modeling is essential for advancing our ability to manage health risks and harness opportunities arising from interspecies interactions.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267295","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
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
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