FEMS microbiology reviews最新文献_第2页

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

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

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

Mechanisms conferring multi-layered protection against intestinal Salmonella Typhimurium infection. 肠道鼠伤寒沙门氏菌感染的多层保护机制。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf038

Sanne Kroon, Wolf-Dietrich Hardt

{"title":"Mechanisms conferring multi-layered protection against intestinal Salmonella Typhimurium infection.","authors":"Sanne Kroon, Wolf-Dietrich Hardt","doi":"10.1093/femsre/fuaf038","DOIUrl":"10.1093/femsre/fuaf038","url":null,"abstract":"Enteropathogens cause many gastrointestinal infections every year. However, it is often overlooked that many individuals remain asymptomatic despite exposure to these pathogens. The mechanisms underlying this effective protection against infection may hold important clues for disease prevention or therapy. Here, we focus on Salmonella enterica serovar Typhimurium (S. Tm), a well-studied enteropathogen closely related to commensal Escherichia coli. We discuss the host's multi-layered defence mechanisms that protect against S. Tm infection of the intestine, with an emphasis on the microbiota, epithelial barrier, and immune system. Perturbations in these defences, such as microbiota dysbiosis, variability in epithelial barrier integrity, or immune defects, can impair protection and increase susceptibility to disease. Additionally, we review the virulence mechanisms and metabolic adaptations that S. Tm has evolved to overcome these protective layers. This complex interplay between host defence layers and pathogen traits, shaped by both intrinsic and extrinsic factors, ultimately determines whether exposure results in asymptomatic carriage or symptomatic disease. Understanding these dynamics is critical for developing targeted interventions to prevent S. Tm infections and mitigate their impact on public health.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12405898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834667","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

Correction to: Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes. 更正：波罗的海微生物的生物多样性：鉴定海洋微生物的新方法的力量。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf002

引用次数: 0

Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution. 肺囊虫宿主特异性、遗传多样性和进化的进化谱。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf006

Liang Ma, Christiane Weissenbacher-Lang, Alice Latinne, Spenser Babb-Biernacki, Barbara Blasi, Ousmane H Cissé, Joseph A Kovacs

{"title":"Evolving spectrum of Pneumocystis host specificity, genetic diversity, and evolution.","authors":"Liang Ma, Christiane Weissenbacher-Lang, Alice Latinne, Spenser Babb-Biernacki, Barbara Blasi, Ousmane H Cissé, Joseph A Kovacs","doi":"10.1093/femsre/fuaf006","DOIUrl":"10.1093/femsre/fuaf006","url":null,"abstract":"Following over a century's worth of research, our understanding of Pneumocystis has significantly expanded in various facets, spanning from its fundamental biology to its impacts on animal and human health. Its significance in public health has been underscored by its inclusion in the 2022 WHO fungal priority pathogens list. We present this review to summarize pivotal advancements in Pneumocystis epidemiology, host specificity, genetic diversity and evolution. Following a concise discussion of Pneumocystis species classification and divergence at the species and strain levels, we devoted the main focus to the following aspects: the epidemiological characteristics of Pneumocystis across nearly 260 mammal species, the increasing recognition of coinfection involving multiple Pneumocystis species in the same host species, the diminishing host specificity of Pneumocystis among closely related host species, and the intriguingly discordant evolution of certain Pneumocystis species with their host species. A comprehensive understanding of host specificity, genetic diversity, and evolution of Pneumocystis can provide important insights into pathogenic mechanisms and transmission modes. This, in turn, holds the potential to facilitate the development of innovative strategies for the prevention and control of Pneumocystis infection.","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/PMC11916894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457360","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

Insight into the environmental cues modulating the expression of bacterial toxin-antitoxin systems. 洞察环境线索调节细菌毒素-抗毒素系统的表达。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf007

Emeline Ostyn, Yoann Augagneur, Marie-Laure Pinel-Marie

{"title":"Insight into the environmental cues modulating the expression of bacterial toxin-antitoxin systems.","authors":"Emeline Ostyn, Yoann Augagneur, Marie-Laure Pinel-Marie","doi":"10.1093/femsre/fuaf007","DOIUrl":"10.1093/femsre/fuaf007","url":null,"abstract":"Bacteria require sophisticated sensing mechanisms to adjust their metabolism in response to stressful conditions and survive in hostile environments. Among them, toxin-antitoxin (TA) systems play a crucial role in bacterial adaptation to environmental challenges. TA systems are considered as stress-responsive elements, consisting of both toxin and antitoxin genes, typically organized in operons or encoded on complementary DNA strands. A decrease in the antitoxin-toxin ratio, often triggered by specific stress conditions, leads to toxin excess, disrupting essential cellular processes and inhibiting bacterial growth. These systems are categorized into eight types based on the nature of the antitoxin (RNA or protein) and the mode of action of toxin inhibition. While the well-established biological roles of TA systems include phage inhibition and the maintenance of genetic elements, the environmental cues regulating their expression remain insufficiently documented. In this review, we highlight the diversity and complexity of the environmental cues influencing TA systems expression. A comprehensive understanding of how these genetic modules are regulated could provide deeper insights into their functions and support the development of innovative antimicrobial strategies.","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/PMC11951105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572557","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

Vaginal Candida albicans infections: host-pathogen-microbiome interactions. 阴道白色念珠菌感染：宿主-病原体-微生物组相互作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf013

Marisa Valentine, Duncan Wilson, Mark S Gresnigt, Bernhard Hube

{"title":"Vaginal Candida albicans infections: host-pathogen-microbiome interactions.","authors":"Marisa Valentine, Duncan Wilson, Mark S Gresnigt, Bernhard Hube","doi":"10.1093/femsre/fuaf013","DOIUrl":"10.1093/femsre/fuaf013","url":null,"abstract":"Candida albicans is a fungus that colonizes the gut, oral, and vaginal mucosae of most humans without causing disease. However, under certain predisposing conditions this fungus can cause disease. Candida albicans has several factors and attributes that facilitate its commensal and pathogenic lifestyles including the transition from a yeast to a hyphal morphology, which is accompanied by the expression of virulence factors. These factors are central in candidiasis that can range from invasive to superficial. This review focuses on one example of a superficial disease, i.e. vulvovaginal candidiasis (VVC) that affects ~75% of women at least once with some experiencing four or more symptomatic infections per year (RVVC). During VVC, fungal factors trigger inflammation, which is maintained by a dysregulated innate immune response. This in turn leads to immunopathology and symptoms. Another unique characteristic of the vaginal niche, is its Lactobacillus-dominated microbiota with low species diversity that is believed to antagonize C. albicans pathogenicity. The importance of the interactions between C. albicans, the host, and vaginal microbiota during commensalism and (R)VVC is discussed in this review, which also addresses the application of this knowledge to identify novel treatment strategies and to study vaginal C. albicans 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/PMC12071381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063155","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

Role of the LuxR solo, SdiA, in eavesdropping on foreign bacteria. LuxR独奏，SdiA，在窃听外来细菌中的作用。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf015

Andrew Schwieters, Brian M M Ahmer

引用次数: 0

Thermal shift assay to identify ligands for bacterial sensor proteins. 热移法鉴定细菌传感器蛋白的配体。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2025-01-14 DOI: 10.1093/femsre/fuaf033

Elizabet Monteagudo-Cascales, Mario Cano-Muñoz, Roberta Genova, Juan J Cabrera, Miguel A Matilla, Tino Krell

{"title":"Thermal shift assay to identify ligands for bacterial sensor proteins.","authors":"Elizabet Monteagudo-Cascales, Mario Cano-Muñoz, Roberta Genova, Juan J Cabrera, Miguel A Matilla, Tino Krell","doi":"10.1093/femsre/fuaf033","DOIUrl":"10.1093/femsre/fuaf033","url":null,"abstract":"Bacteria sense and respond to changing environmental conditions using a diverse range of receptors. Currently, the signals recognized by most receptors remain unknown, thereby limiting our understanding of their function. Since its introduction a decade ago, ligand screening by the thermal-shift assay has identified the signal molecules recognized by numerous receptors, solute-binding proteins, and transcriptional regulators. This progress is summarized in this review. Signal identification is facilitated by the fact that ligand-binding domains can be generated as individual soluble proteins that retain the signal-binding capabilities of the full-length proteins. Various issues relevant to the reliability of the thermal shift assay are discussed, including false-positive and false-negative results, the value of a protein pH screen prior to ligand screening, and the need to verify results with methods for the direct study of ligand binding, such as isothermal titration calorimetry. This review was inspired by the XVIII conference on Bacterial Locomotion and Signal Transduction (Cancun, January 2025), where several notable advances were reported based on the application of the thermal shift assay.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12358799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729044","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