Trends in MicrobiologyPub Date : 2025-07-01Epub Date: 2025-03-21DOI: 10.1016/j.tim.2025.02.019
Miguel A Matilla, José A Gavira, Elizabet Monteagudo-Cascales, Igor B Zhulin, Tino Krell
{"title":"Structural and functional diversity of sensor domains in bacterial transmembrane receptors.","authors":"Miguel A Matilla, José A Gavira, Elizabet Monteagudo-Cascales, Igor B Zhulin, Tino Krell","doi":"10.1016/j.tim.2025.02.019","DOIUrl":"10.1016/j.tim.2025.02.019","url":null,"abstract":"<p><p>The ability of bacteria to adapt to changing environmental conditions largely depends on transmembrane receptors that sense signal molecules and generate responses such as chemotaxis, changes in gene expression, or alterations in second-messenger levels. Although these receptors differ significantly in function, they share a common mode of activation that involves signal molecule interaction with sensor domains. A major challenge in microbiology lies in the limited knowledge of ligands that stimulate receptors. Here, we review recent advances in this field, including the occurrence of multi-modular sensor domains, the identification of co-component signal transduction systems, evidence for sensor domain evolution from transporters, and the use of binding pocket sequence motifs to identify sensor domain ligands.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"796-809"},"PeriodicalIF":14.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12221819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693399","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}
Trends in MicrobiologyPub Date : 2025-07-01Epub Date: 2025-03-14DOI: 10.1016/j.tim.2025.02.014
Alfredo Chavez-Arroyo, Lauren C Radlinski, Andreas J Bäumler
{"title":"Principles of gut microbiota assembly.","authors":"Alfredo Chavez-Arroyo, Lauren C Radlinski, Andreas J Bäumler","doi":"10.1016/j.tim.2025.02.014","DOIUrl":"10.1016/j.tim.2025.02.014","url":null,"abstract":"<p><p>The gut microbiota plays a critical role in human health, yet its taxonomic complexity, interpersonal variability, and resistance to change in adulthood present challenges for understanding the factors driving shifts in its composition and function. Here, we propose a hierarchy of ecological factors governing gut microbiota assembly, stability, and resilience. At the apex of this hierarchy is habitat filtering by host-derived electron acceptors, which dictates the ecological guilds that dominate distinct gut regions. Host dietary behavior shapes niche availability within these ecological guilds by regulating nutrient availability. Priority effects preserve taxonomic stability whereas microbial antagonism governs competition for open ecological positions. This framework highlights how host control over microbial energy metabolism directs microbiota self-assembly and maintains gut homeostasis.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"718-726"},"PeriodicalIF":14.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634691","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}
Timothy C Cameron, Ronan C Broad, Penelope M C Smith, Dugald Reid
{"title":"Opportunities and challenges to optimise symbiotic nitrogen fixation.","authors":"Timothy C Cameron, Ronan C Broad, Penelope M C Smith, Dugald Reid","doi":"10.1016/j.tim.2025.06.005","DOIUrl":"https://doi.org/10.1016/j.tim.2025.06.005","url":null,"abstract":"<p><p>Legumes are not only major cash crops but also contribute valuable nitrogen to cropping systems due to their ability to form a symbiotic relationship with nitrogen-fixing rhizobia in specialised root organs called nodules. To balance the cost of carbon provision to the rhizobia, nodulation is finely regulated in legumes across various spatiotemporal levels, including host-microbe signalling within the rhizosphere, infection of the legume host, and nodule initiation, function, and senescence. Since symbiotic nitrogen fixation (SNF) evolved in natural ecosystems which lack resemblance to modern agricultural systems, opportunities present themselves to genetically improve SNF. Based on recent findings and the opportunities arising with new breeding technologies, we review here the many opportunities to optimise SNF and highlight the key challenges associated with these approaches.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":14.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144508398","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}
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}
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}
{"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}
{"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}
{"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}
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}
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}