FEMS microbiology reviews最新文献

Stepping out of the dark: How metabolomics shed light on fungal biology. 走出黑暗：代谢组学如何揭示真菌生物学。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-06-25 DOI: 10.1093/femsre/fuaf028

John Adejor, Elisabeth Tumukunde, Guoqi Li, Shehu Tanimu, Lihan Wu, Zhi Wei Jiang, Shihua Wang

{"title":"Stepping out of the dark: How metabolomics shed light on fungal biology.","authors":"John Adejor, Elisabeth Tumukunde, Guoqi Li, Shehu Tanimu, Lihan Wu, Zhi Wei Jiang, Shihua Wang","doi":"10.1093/femsre/fuaf028","DOIUrl":"https://doi.org/10.1093/femsre/fuaf028","url":null,"abstract":"Metabolomics, a critical tool for analyzing small-molecule metabolites, integrates with genomics, transcriptomics, and proteomics to provide a systems-level understanding of fungal biology. By mapping metabolic networks, it elucidates regulatory mechanisms driving physiological and ecological adaptations. In fungal pathogenesis, metabolomics reveals host-pathogen dynamics, identifying virulence factors like gliotoxin in Aspergillus fumigatus and metabolic shifts, such as glyoxylate cycle upregulation in Candida albicans. Ecologically, it highlights fungal responses to abiotic stressors, including osmolyte production like trehalose, enhancing survival in extreme environments. These insights highlight metabolomics' role in decoding fungal persistence and niche colonization. In drug discovery, it aids target identification by profiling biosynthetic pathways, supporting novel antifungal and nanostructured therapy development. Combined with multi-omics, metabolomics advances insights into fungal pathogenesis, ecological interactions, and therapeutic innovation, offering translational potential for addressing antifungal resistance and improving treatment outcomes for fungal infections. Its progress shed light on complex fungal molecular profiles, advancing discovery and innovation in fungal biology.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144483743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 ecology and plasticity of fish skin and gill microbiomes: Seeking what matters in health and disease. 鱼类皮肤和鳃微生物群的生态学和可塑性：寻找健康和疾病的重要因素。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-06-19 DOI: 10.1093/femsre/fuaf027

Jamie McMurtrie, Ashley G Bell, Joanne Cable, Ben Temperton, Charles R Tyler

{"title":"The ecology and plasticity of fish skin and gill microbiomes: Seeking what matters in health and disease.","authors":"Jamie McMurtrie, Ashley G Bell, Joanne Cable, Ben Temperton, Charles R Tyler","doi":"10.1093/femsre/fuaf027","DOIUrl":"https://doi.org/10.1093/femsre/fuaf027","url":null,"abstract":"The microbiomes of skin and gill mucosal surfaces are critical components in fish health and homeostasis by competitively excluding pathogens, secreting beneficial compounds, and priming the immune system. Disruption of these microbiomes can compromise their capacity for disease resilience and maintaining host homeostasis. However, the extent and nature of microbiome disruption required to impact fish health negatively remains poorly understood. This review examines how various stressors influence the community composition and functionality of fish skin and gill microbiomes, and the subsequent effects on fish health. Our findings highlight that the impact of stressors on skin and gill microbiomes may differ for different body sites and are highly context-dependent, influenced by a complex interplay of host-specific factors, stressor characteristics, and environmental conditions. By evaluating current knowledge on the genesis and homeostasis of these microbiomes, we highlight a strong influence of environmental factors especially on skin and gill microbiomes compared with fish gut microbiomes, which appear to be more closely regulated by the host's homeostatic and immunological systems. This review emphasises the importance of understanding the ecology and plasticity of fish skin and gill microbiomes to identify critical thresholds for microbiome shifts that impact fish health and disease resilience.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Editorial. 社论。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-06-18 DOI: 10.1093/femsre/fuaf026

Tomasz Jagielski, Grzegorz Węgrzyn

引用次数: 0

Multidisciplinary methodologies used in the study of cable bacteria. 电缆细菌研究中使用的多学科方法。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuae030

Michaela M H Wawryk, Philip Ley, Diana Vasquez-Cardenas, Rico F Tabor, Perran L M Cook

引用次数: 0

Electrical signaling in fungi: past and present challenges. 真菌中的电信号：过去和现在的挑战。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf009

Matteo Buffi, Julia M Kelliher, Aaron J Robinson, Diego Gonzalez, Guillaume Cailleau, Justine A Macalindong, Eleonora Frau, Silvia Schintke, Patrick S G Chain, Claire E Stanley, Markus Künzler, Saskia Bindschedler, Pilar Junier

{"title":"Electrical signaling in fungi: past and present challenges.","authors":"Matteo Buffi, Julia M Kelliher, Aaron J Robinson, Diego Gonzalez, Guillaume Cailleau, Justine A Macalindong, Eleonora Frau, Silvia Schintke, Patrick S G Chain, Claire E Stanley, Markus Künzler, Saskia Bindschedler, Pilar Junier","doi":"10.1093/femsre/fuaf009","DOIUrl":"10.1093/femsre/fuaf009","url":null,"abstract":"Electrical signaling is a fundamental mechanism for integrating environmental stimuli and coordinating responses in living organisms. While extensively studied in animals and plants, the role of electrical signaling in fungi remains a largely underexplored field. Early studies suggested that filamentous fungi generate action potential-like signals and electrical currents at hyphal tips, yet their function in intracellular communication remained unclear. Renewed interest in fungal electrical activity has fueled developments such as the hypothesis that mycorrhizal networks facilitate electrical communication between plants and the emerging field of fungal-based electronic materials. Given their continuous plasma membrane, specialized septal pores, and insulating cell wall structures, filamentous fungi possess architectural features that could support electrical signaling over long distances. However, studying electrical phenomena in fungal networks presents unique challenges due to the microscopic dimensions of hyphae, the structural complexity of highly modular mycelial networks, and the limitations of traditional electrophysiological methods. This review synthesizes current evidence for electrical signaling in filamentous fungi, evaluates methodological approaches, and highlights experimental challenges. By addressing these challenges and identifying best practices, we aim to advance research in this field and provide a foundation for future studies exploring the role of electrical signaling in fungal biology.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut? 胆汁酸作为艰难梭菌孢子的生发剂，是适应肠道的证据？

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf005

Gianni Vinay, Jurgen Seppen, Peter Setlow, Stanley Brul

{"title":"Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut?","authors":"Gianni Vinay, Jurgen Seppen, Peter Setlow, Stanley Brul","doi":"10.1093/femsre/fuaf005","DOIUrl":"10.1093/femsre/fuaf005","url":null,"abstract":"Bacterial spores formed upon metabolic stress have minimal metabolic activity and can remain dormant for years. Nevertheless, they can sense the environment and germinate quickly upon exposure to various germinants. Germinated spores can then outgrow into vegetative cells. Germination of spores of some anaerobes, especially Clostridioides difficile, is triggered by cholic acid and taurocholic acid. Elevated levels of these bile acids are thought to correlate with a perturbed gut microbiome, which cannot efficiently convert primary bile acids into secondary bile acids. That bile acids are germination-triggers suggests these bacteria have a life cycle taking place partially in the mammalian digestive tract where bile acids are plentiful; notably bile acids can be made by all vertebrates. Thus, spores survive in the environment until taken up by a host where they encounter an environment suitable for germination and then proliferate in the largely anaerobic large intestine; some ultimately sporulate there, regenerating environmentally resistant spores in the C. difficile life cycle. This review summarizes current literature on the effects of bile acids and their metabolites on spore germination in the gut and evidence that adaptation to bile acids as germinants is a consequence of a life cycle both inside and outside the digestive tract.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143382098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Plant exudates-driven microbiome recruitment and assembly facilitates plant health management. 植物分泌物驱动微生物群的招募和组装促进植物健康管理。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf008

Chang-Xin Yang, Shi-Jie Chen, Xiao-Yu Hong, Lv-Zhuang Wang, Hai-Ming Wu, Yang-Yang Tang, Yang-Yang Gao, Ge-Fei Hao

{"title":"Plant exudates-driven microbiome recruitment and assembly facilitates plant health management.","authors":"Chang-Xin Yang, Shi-Jie Chen, Xiao-Yu Hong, Lv-Zhuang Wang, Hai-Ming Wu, Yang-Yang Tang, Yang-Yang Gao, Ge-Fei Hao","doi":"10.1093/femsre/fuaf008","DOIUrl":"10.1093/femsre/fuaf008","url":null,"abstract":"Plant-microbiome symbiotic interactions play a crucial role in regulating plant health and productivity. To establish symbiotic relationships, the plant secretes a variety of substances to facilitate microbial community recruitment and assembly. In recent years, important progress has been made in studying how plant exudates attract beneficial microorganisms and regulate plant health. However, the mechanisms of plant exudates-mediated microbial community recruitment and assembly and their effects on plant health are no comprehensive review. Here, we summarize the interaction mechanisms among plant exudates, microbial community recruitment and assembly, and plant health. First, we systematically evaluate the type and distribution of plant exudates, as well as their role in microbiome recruitment and assembly. Second, we summarize the mechanisms of plant exudates in terms of microbiome recruitment, diversity regulation and chemotaxis. Finally, we list some typical examples for elucidating the importance of plant exudates in promoting plant health and development. This review contributes to utilizing plant exudate or beneficial microbiome resources to manage plant health and productivity.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Seven critical challenges in synthetic one-carbon assimilation and their potential solutions. 合成单碳同化的七个关键挑战及其可能的解决方案。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf011

Òscar Puiggené, Giusi Favoino, Filippo Federici, Michele Partipilo, Enrico Orsi, Maria V G Alván-Vargas, Javier M Hernández-Sancho, Nienke K Dekker, Emil C Ørsted, Eray U Bozkurt, Sara Grassi, Julia Martí-Pagés, Daniel C Volke, Pablo I Nikel

{"title":"Seven critical challenges in synthetic one-carbon assimilation and their potential solutions.","authors":"Òscar Puiggené, Giusi Favoino, Filippo Federici, Michele Partipilo, Enrico Orsi, Maria V G Alván-Vargas, Javier M Hernández-Sancho, Nienke K Dekker, Emil C Ørsted, Eray U Bozkurt, Sara Grassi, Julia Martí-Pagés, Daniel C Volke, Pablo I Nikel","doi":"10.1093/femsre/fuaf011","DOIUrl":"10.1093/femsre/fuaf011","url":null,"abstract":"Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementation in microbial hosts remains relatively limited. Despite substantial progress in pathway design and prototyping, most efforts stay at the proof-of-concept stage, with frequent failures observed even under in vitro conditions. This review identifies seven major barriers constraining the deployment of synthetic C1 metabolism in microorganisms and proposes targeted strategies for overcoming these issues. A primary limitation is the low catalytic activity of carbon-fixing enzymes, particularly carboxylases, which restricts the overall pathway performance. In parallel, challenges in expressing multiple heterologous genes-especially those encoding metal-dependent or oxygen-sensitive enzymes-further hinder pathway functionality. At the systems level, synthetic C1 pathways often exhibit poor flux distribution, limited integration with the host metabolism, accumulation of toxic intermediates, and disruptions in redox and energy balance. These factors collectively reduce biomass formation and compromise product yields in biotechnological setups. Overcoming these interconnected challenges is essential for moving synthetic C1 assimilation beyond conceptual stages and enabling its application in scalable, efficient bioprocesses towards a circular bioeconomy.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12010959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools. 结核分枝杆菌的分子分型：当前方法、数据库、软件和分析工具的综述。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf017

David Couvin, Anne-Sophie Allaguy, Ayoub Ez-Zari, Tomasz Jagielski, Nalin Rastogi

{"title":"Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools.","authors":"David Couvin, Anne-Sophie Allaguy, Ayoub Ez-Zari, Tomasz Jagielski, Nalin Rastogi","doi":"10.1093/femsre/fuaf017","DOIUrl":"10.1093/femsre/fuaf017","url":null,"abstract":"Studies on the epidemiology and clinical relevance of Mycobacterium tuberculosis complex (MTBC) have immensely benefited from molecular typing methods, associated software applications, and bioinformatics tools. Over the last two decades, the Pasteur Institute of Guadeloupe has developed a range of bioinformatic resources, including databases and software, to advance understanding of TB epidemiology. Traditional methods, such as IS6110-RFLP, MIRU-VNTR typing, and spoligotyping, have been instrumental but are increasingly supplanted by more precise and high-throughput techniques. These typing methods offer relatively good discrimination and reproducibility, making them popular choices for epidemiological studies. However, the advent of whole-genome sequencing (WGS) has revolutionized Mycobacterium tuberculosis complex (MTBC) typing, providing unparalleled resolution and data analysis depth. WGS enables the identification of single nucleotide polymorphisms and other genetic variations, facilitating robust phylogenetic reconstructions, and detailed outbreak investigations. This review summarizes current molecular typing methods, as well as databases and software tools used for MTBC data analysis. A comprehensive comparison of available tools and databases is provided to guide future research on the epidemiology of TB and pathogen-associated variables (drug resistance or virulence) and public health initiatives.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"49 ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12065434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143981746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis. 利用缺氧：囊性纤维化中的细菌适应和慢性感染。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf018

Ciarán J Carey, Niamh Duggan, Joanna Drabinska, Siobhán McClean

{"title":"Harnessing hypoxia: bacterial adaptation and chronic infection in cystic fibrosis.","authors":"Ciarán J Carey, Niamh Duggan, Joanna Drabinska, Siobhán McClean","doi":"10.1093/femsre/fuaf018","DOIUrl":"10.1093/femsre/fuaf018","url":null,"abstract":"The exquisite ability of bacteria to adapt to their environment is essential for their capacity to colonize hostile niches. In the cystic fibrosis (CF) lung, hypoxia is among several environmental stresses that opportunistic pathogens must overcome to persist and chronically colonize. Although the role of hypoxia in the host has been widely reviewed, the impact of hypoxia on bacterial pathogens has not yet been studied extensively. This review considers the bacterial oxygen-sensing mechanisms in three species that effectively colonize the lungs of people with CF, namely Pseudomonas aeruginosa, Burkholderia cepacia complex, and Mycobacterium abscessus and draws parallels between their three proposed oxygen-sensing two-component systems: BfiSR, FixLJ, and DosRS, respectively. Moreover, each species expresses regulons that respond to hypoxia: Anr, Lxa, and DosR, and encode multiple proteins that share similar homologies and function. Many adaptations that these pathogens undergo during chronic infection, including antibiotic resistance, protease expression, or changes in motility, have parallels in the responses of the respective species to hypoxia. It is likely that exposure to hypoxia in their environmental habitats predispose these pathogens to colonization of hypoxic niches, arming them with mechanisms than enable their evasion of the immune system and establish chronic infections. Overcoming hypoxia presents a new target for therapeutic options against chronic lung infections.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"49 ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12071387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143980893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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