FEMS microbiology reviews最新文献

Bacterial osmoprotectants - a way to survive in saline conditions and potential crop allies. 细菌渗透保护剂——在盐水条件下生存的一种方法和潜在的作物盟友。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-05-16 DOI: 10.1093/femsre/fuaf020

Aleksandra Goszcz, Karolina Furtak, Robert Stasiuk, Joanna Wójtowicz, Marcin Musiałowski, Michela Schiavon, Klaudia Dębiec-Andrzejewska

{"title":"Bacterial osmoprotectants - a way to survive in saline conditions and potential crop allies.","authors":"Aleksandra Goszcz, Karolina Furtak, Robert Stasiuk, Joanna Wójtowicz, Marcin Musiałowski, Michela Schiavon, Klaudia Dębiec-Andrzejewska","doi":"10.1093/femsre/fuaf020","DOIUrl":"https://doi.org/10.1093/femsre/fuaf020","url":null,"abstract":"Soil salinization, affecting 6.5% of arable land, deteriorates soil properties, reduces microbiota activity, hinders plant growth, and accelerates soil erosion. Excessive salt induces physiological drought and toxicity stress in plants, causing chlorosis, ion imbalances, and enzyme disruptions. This paper discusses microorganisms' resistance mechanisms, plant responses to salt stress and summarizes current knowledge on bacterial osmoprotectants and their functions. It also reviews emerging agrobiotechnological strategies using microbial osmoprotectants to remediate salinized soils and enhance plant growth and productivity under salt stress. Osmoprotectants stabilize proteins, buffer redox potential, and retain water, thus alleviating osmotic stress and promoting bacteria and plants growth. Their application improves soil properties by enhancing aggregate formation, water permeability, moisture content, cation exchange capacity, and ion availability. Despite extensive literature on the function of osmoprotectants, the knowledge about their role in soil environments and agrobiotechnology applications remains limited. This paper indicates proposed research perspectives, including discovering new osmoprotectants, their correlation with soil fertilization, interactions with the soil microbiome, and plant responses. It also identifies significant knowledge gaps in these areas, highlighting the need for further studies to consolidate existing data and assess the potential of this approach to enhance soil health and crop productivity in saline environments.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144076789","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

Exploring heme and iron acquisition strategies of Porphyromonas gingivalis - current facts and hypotheses. 探讨牙龈卟啉单胞菌的血红素和铁获取策略-目前的事实和假设。

IF 10.1 2区生物学

FEMS microbiology reviews Pub Date : 2025-05-09 DOI: 10.1093/femsre/fuaf019

Michał Śmiga, Teresa Olczak

{"title":"Exploring heme and iron acquisition strategies of Porphyromonas gingivalis - current facts and hypotheses.","authors":"Michał Śmiga, Teresa Olczak","doi":"10.1093/femsre/fuaf019","DOIUrl":"https://doi.org/10.1093/femsre/fuaf019","url":null,"abstract":"Iron and heme are crucial for pathogenic bacteria living in the human host but are not available in free form due to their binding by iron- and heme-sequestering proteins. Porphyromonas gingivalis causes dysbiosis in the oral microbiome and is considered a keystone pathogen in the onset and progression of periodontal diseases. Its ability to infect and multiply in host cells and its presence in distant tissues and fluids highlights its pathogenic versatility and explains the relationship between periodontal diseases and systemic or neurodegenerative diseases. P. gingivalis has evolved specialized mechanisms that allow it to thrive in the host under adverse nutrient-limited conditions. This review presents the updated summary of the mechanisms of iron and heme acquisition by P. gingivalis, with a central role played by gingipains and the unique Hmu system. The potential role of other iron and heme acquisition systems, such as Hus and Iht, indicates the importance of the partially conserved heme biosynthesis pathway, involving homologs of the HemN, HemG, and HemH proteins. In light of increasing antibiotic resistance, difficulties with diagnosis, and drug administration, targeting the mechanisms of heme and iron acquisition of P. gingivalis represents a promising target for developing diagnostic tests, preventive or therapeutic strategies.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":10.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993801","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

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

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":"https://doi.org/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

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

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

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