FEMS microbiology reviews最新文献

Translation quality control in Pseudomonas aeruginosa: current knowledge and perspectives. 铜绿假单胞菌翻译质量控制：目前的知识和观点。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-04-15 DOI: 10.1093/femsre/fuag018

Bastien L'Hermitte, Reynald Gillet, Christine Baysse

引用次数: 0

Epigenetic Regulation and Antimicrobial Resistance: Functional Roles of DNA Methylation. 表观遗传调控和抗菌素耐药性：DNA甲基化的功能作用。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-04-11 DOI: 10.1093/femsre/fuag017

Rafca Daaboul, Elie El Hayek, Fares Sarraf, Charbel Yazbek, Christ Yazbek, Charbel Al Khoury, Sima Tokajian

{"title":"Epigenetic Regulation and Antimicrobial Resistance: Functional Roles of DNA Methylation.","authors":"Rafca Daaboul, Elie El Hayek, Fares Sarraf, Charbel Yazbek, Christ Yazbek, Charbel Al Khoury, Sima Tokajian","doi":"10.1093/femsre/fuag017","DOIUrl":"https://doi.org/10.1093/femsre/fuag017","url":null,"abstract":"The global rise of antimicrobial resistance (AMR) demands urgent attention. While genetic drivers are well studied, epigenetic mechanisms, particularly DNA methylation, are emerging as key contributors to bacterial adaptation under antibiotic pressure. This review examines the roles of N6-methyladenine (m6A), N4-methylcytosine (m4C), and 5-methylcytosine (m5C), each catalyzed by distinct DNA methyltransferases (MTases), in regulating resistance-related processes such as efflux pump expression, β-lactamase activity, and stress responses. Advances in long-read sequencing technologies, including SMRT and ONT, now enable single-base resolution detection of methylation and support strain-specific methylome mapping. These efforts reveal methylation patterns that are dynamic, strain-dependent, and environmentally responsive, complicating resistance profiling. Emerging applications for tackling methylation-linked AMR include methylation-aware diagnostics and CRISPR-based epigenetic editing. Tools like CRISPR-dCas9 fused to DNA methyltransferases enable targeted, reversible suppression of resistance genes regulated by methylation. Current findings position DNA methylation as both a regulator of AMR and a promising target for next-generation diagnostics and therapeutics. However, challenges remain, including the lack of validated biomarkers, inconsistent protocols, and difficulty interpreting mixed-species data. Integrating methylation profiles with transcriptomic and phenotypic data will be essential to fully understand and target resistance mechanisms.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147671713","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

Small intestinal microbiome, the underrated maestro of SIMO disease. 小肠微生物群，被低估的SIMO疾病大师。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-04-10 DOI: 10.1093/femsre/fuag016

Charlotte Deschamps, Alexandre Tronel, Elodie Bailly, Maurice Raoul Sohnagou Tanfede, Sophie Gilibert, Sylvain Denis, Thomas Soranzo, Tom Van De Wiele, Ludovica Marinelli, Stéphanie Blanquet-Diot

{"title":"Small intestinal microbiome, the underrated maestro of SIMO disease.","authors":"Charlotte Deschamps, Alexandre Tronel, Elodie Bailly, Maurice Raoul Sohnagou Tanfede, Sophie Gilibert, Sylvain Denis, Thomas Soranzo, Tom Van De Wiele, Ludovica Marinelli, Stéphanie Blanquet-Diot","doi":"10.1093/femsre/fuag016","DOIUrl":"https://doi.org/10.1093/femsre/fuag016","url":null,"abstract":"Small intestinal microbial overgrowth (SIMO) results from a breakdown in the delicate equilibrium between luminal environment, gut motility, and microbial ecology. Despite extensive research, these factors have largely been investigated as separate entities, with limited integrative insights into their interplay. This review is the first comprehensive synthesis of physicochemical, mechanical, and microbial parameters shaping SIMO pathogenesis. By reviewing both clinical and experimental data, we reveal how alterations in pH, transit time, digestive secretion dynamics, bile acid composition and impaired intestinal absorption collectively reshape microbial load, diversity, and metabolic output, establishing a self-perpetuating loop of dysfunction. We further discuss the limitations of current diagnostic tools and the transformative potential of emerging approaches, from sampling capsules enabling molecular analyses, to in vitro models simulating human small intestinal ecosystem. This integrative perspective shifts the paradigm from a microbe-centered to an ecosystem-based understanding of SIMO, outlining key challenges and opportunities for personalized diagnostics, mechanistic research, and microbiota-targeted next-generation therapeutics including pre-, pro-, postbiotics and faecal transplantation.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147671672","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

From microbes to animals: a review on prey choice and prey-predator dynamics across organismal scales. 从微生物到动物：跨生物尺度的猎物选择和捕食动力学研究综述。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuag004

Mohor Mitra, Sajan, Shrutarshi Paul, Amit Huppert, Edouard Jurkevitch

{"title":"From microbes to animals: a review on prey choice and prey-predator dynamics across organismal scales.","authors":"Mohor Mitra, Sajan, Shrutarshi Paul, Amit Huppert, Edouard Jurkevitch","doi":"10.1093/femsre/fuag004","DOIUrl":"10.1093/femsre/fuag004","url":null,"abstract":"Predator-prey interactions are intricately linked to ecological systems, from micro-organisms to large animals. Most predator-prey studies use simplified pairwise interactions, constraining our ability to identify general principles. Here, predator-prey choices are examined across scales and levels of environmental complexity. We review current knowledge and emphasize the diversity and complexity of predator-prey systems, point to challenges in integrating them, and propose a framework that could benefit predictive modeling for ecosystem functioning and resilience. To do so, we compare the tools, mechanisms, and strategies deployed by micro- and macro- predators and prey defenses to show that commonalities become identifiable, and suggest structural and functional links between micro- and macro-scales. This provides arguments for both descriptive, and mathematical models. We propose that the use of microbial predators like the Bdellovibrio and like organisms can greatly advance the integration of experimental and mathematical modeling research, as they can provide robust empirical observations of predator-prey interactions tested under multiple conditions and levels of complexity. This facilitates model development, in turn leading to new hypotheses. We conclude by showing examples of current developments, that predator-prey interaction-based knowledge has the potential to provide novel medical tools and to improve environmental and agricultural management.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12927660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164683","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

Phage cocktails: state-of-the-art technologies and strategies for effective design. 噬菌体鸡尾酒：最先进的技术和有效设计策略。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuaf061

Tomoyoshi Kaneko, Kanata Nakatsuka, Satoshi Tsuneda

引用次数: 0

Architecture and regulatory functions of c-di-GMP signaling in classical Bordetella species. 经典博德特菌中c-二- gmp信号的结构和调控功能。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuaf065

Denisa Vondrova, Sabrina Laura Mugni, Jan Blumenstein, Clara Kasiztky, Federico Sisti, Julieta Fernández, Jana Kamanova

{"title":"Architecture and regulatory functions of c-di-GMP signaling in classical Bordetella species.","authors":"Denisa Vondrova, Sabrina Laura Mugni, Jan Blumenstein, Clara Kasiztky, Federico Sisti, Julieta Fernández, Jana Kamanova","doi":"10.1093/femsre/fuaf065","DOIUrl":"10.1093/femsre/fuaf065","url":null,"abstract":"Cyclic di-GMP (c-di-GMP) is a highly conserved bacterial second messenger that regulates important processes such as motility, biofilm formation and virulence. In this review, we investigate the architecture and regulatory functions of c-di-GMP signaling in classical Bordetella species, including B. bronchiseptica, B. parapertussis and B. pertussis. We examine how the c-di-GMP signaling pathway interacts with the BvgAS two-component system and other signaling pathways to coordinate virulence gene expression and surface-associated behaviors in these respiratory pathogens. In particular, we highlight the functions of characterized diguanylate cyclases (DGCs), phosphodiesterases (PDEs) and dual-domain proteins, focusing on regulatory modules such as the BdcA-DdpA scaffold complex, the oxygen-sensing DGC BpeGReg and the LapD-LapG proteolytic switch that controls BrtA adhesin. We also propose a model for the function of BvgR, a PDE-like protein lacking catalytic residues, and discuss how c-di-GMP suppresses the type III secretion system. Importantly, we highlight the diversity of the c-di-GMP network in classical Bordetella species, likely reflecting their evolutionary specialization. To conclude, we outline important open questions and suggest future research directions, including the identification of sensory ligands and c-di-GMP effectors. Overall, our review illustrates the importance of c-di-GMP as a critical, but still incompletely understood, regulatory hub in Bordetella pathogenesis.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12805831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145833328","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

Metabolic and regulatory adaptations of Staphylococcus epidermidis to host stresses. 表皮葡萄球菌对宿主胁迫的代谢和调节适应。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuag008

Sandra M Carvalho, Lígia M Saraiva

{"title":"Metabolic and regulatory adaptations of Staphylococcus epidermidis to host stresses.","authors":"Sandra M Carvalho, Lígia M Saraiva","doi":"10.1093/femsre/fuag008","DOIUrl":"10.1093/femsre/fuag008","url":null,"abstract":"Staphylococcus epidermidis is a highly adapted commensal of the human skin. However, it can also cause severe infections by exploiting skin fissures to establish antibiotic-resistant biofilms on implanted medical devices, which may subsequently release bacteria into the bloodstream. Emerging studies increasingly highlight the critical role of metabolic status and regulatory mechanisms in governing biofilm formation and, consequently, the pathogenic potential of S. epidermidis. This review examines its metabolic adaptability across different environments, emphasizing how environmental factors such as nutrient availability, oxygen levels, pH, and temperature, shape central metabolic pathways. It covers sugar, amino acid, and fatty acid utilization, regulatory networks controlling respiration, fermentation, and polysaccharide intercellular adhesin (PIA)-mediated biofilm formation, and strategies for surviving host-derived oxidative and nitrosative stresses. Comparisons with S. aureus further reveal species-specific differences in metabolism, nutrient acquisition, and regulation. Altogether, the mechanistic insights provide a comprehensive overview of S. epidermidis physiology in both commensal and infection-associated contexts.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13007877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364492","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 myeloid cells expressing CD169/Siglec-1 in host-pathogen interactions. 表达CD169/ siglec1的骨髓细胞在宿主-病原体相互作用中的作用。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuag013

Ilona Ronco, Branka Horvat

{"title":"Role of myeloid cells expressing CD169/Siglec-1 in host-pathogen interactions.","authors":"Ilona Ronco, Branka Horvat","doi":"10.1093/femsre/fuag013","DOIUrl":"10.1093/femsre/fuag013","url":null,"abstract":"CD169/Siglec-1 is a type-I transmembrane lectin receptor expressed on subcapsular sinus macrophages and activated monocytes, which plays a key role in innate immune surveillance and orchestration of adaptive immunity. As a sialic acid-binding immunoglobulin-like lectin (Siglec), CD169 recognizes sialylated gangliosides and glycoconjugates present on surface of several viral envelopes, including HIV-1, SARS-CoV-2, and Ebola virus as well as sialylated bacterial capsules such as those of Neisseria meningitidis and Campylobacter jejuni. Moreover, different viruses were shown to be captured by CD169+ cells which could play distinctive role during infections: they could enhance efficient immune responses, but also facilitate pathogen dissemination through viral capture and transfer to permissive cells. This last mechanism has been well documented for HIV-1, where CD169 mediates viral trans-infection of CD4⁺ T-cells. CD169 expression is rapidly induced by type-I interferons during acute viral infections and has emerged as a valuable biomarker to distinguish viral from bacterial infection, particularly for COVID-19 and influenza. Detectable by flow cytometry, CD169 represents a solid biomarker in clinical settings and possible target in the development of novel prophylactic and therapeutic strategies. Its dual role, protective in host defence yet exploitable by certain pathogens, highlights the need for careful consideration in future therapeutic approaches.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13070564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147485233","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

Cross-talk within plant niches: endophytic and arbuscular mycorrhizal fungi for sustainable crop production. 植物生态位内的串扰：可持续作物生产的内生和丛枝菌根真菌。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuaf063

Ma Del Carmen Orozco-Mosqueda, Bernard R Glick, Gustavo Santoyo

{"title":"Cross-talk within plant niches: endophytic and arbuscular mycorrhizal fungi for sustainable crop production.","authors":"Ma Del Carmen Orozco-Mosqueda, Bernard R Glick, Gustavo Santoyo","doi":"10.1093/femsre/fuaf063","DOIUrl":"10.1093/femsre/fuaf063","url":null,"abstract":"World agriculture depends in part on the crop-associated microbiome for improved plant growth, health, and productivity. In particular, endophytic fungi (EF) with plant growth-promoting activities fulfill some of these roles and are central as bioinoculant agents. In the case of arbuscular mycorrhizal fungi (AMF), they form a symbiosis with their host plants, enhancing the uptake of water, phosphorus, nitrogen, and other micronutrients, while the plants provide them with photosynthates. This work reviews the differences in the colonization of internal plant niches between these beneficial fungi, as well as other distinctive ecological traits. It also explores mechanisms of seedborne vertical transmission in AMF and their classification. Genomic and transcriptomic advances in fungal endophytes are highlighted, shedding light on genes and expression profiles that define their lifestyle and plant associations. In addition, recent studies on their abilities to promote plant growth are analyzed, especially focusing on Trichoderma spp., Epichloë spp., Serendipita indica (formerly Piriformospora indica), and entomopathogens like Beauveria spp. and Metarhizium spp. Finally, the multiple interactions among EF, AMF, and other members of the plant microbiome-notably plant growth-promoting bacteria (PGPB)-are discussed, emphasizing how these organisms synergistically benefit the host. A deeper understanding of these fungi and their plant-beneficial effects should facilitate commercialization and help farmers achieve sustainable production, especially under challenges posed by global climate change.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12766460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741786","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 eCISs for precision phytomicrobiome engineering and biocontrol. 利用eCISs进行精密植物微生物组工程和生物防治。

IF 12.3 2区生物学

FEMS microbiology reviews Pub Date : 2026-01-02 DOI: 10.1093/femsre/fuag006

Gunarathna R D S Madushani, Xue Wu, Wikum H Jayasinghe, Qi Wang, Kumar Vinit, Ge-Fei Hao

{"title":"Harnessing eCISs for precision phytomicrobiome engineering and biocontrol.","authors":"Gunarathna R D S Madushani, Xue Wu, Wikum H Jayasinghe, Qi Wang, Kumar Vinit, Ge-Fei Hao","doi":"10.1093/femsre/fuag006","DOIUrl":"10.1093/femsre/fuag006","url":null,"abstract":"Plant microbiome disruption often increases vulnerability to crop diseases, endangering worldwide food production, while chemical pesticides become increasingly less viable and continue to damage ecosystems. To safeguard plant microbiome health, several biological control strategies offer alternatives, yet many operate through broader or weakly defined target mechanisms. In recent years, bacterial contractile injection systems (BCISs) have emerged as a promising class of naturally evolved nanomachines that translocate molecular payloads directly into target cells. Subsets of these systems, extracellular contractile injection systems (eCISs), are distinguished by their specific narrow host range and receptor-dependent specificity. Recent studies have demonstrated that eCISs provide a transformative approach for targeted microbial manipulation, enabling the delivery of specialized molecules into particular microbes with higher precision. However, despite their potential, the integration of these engineered injection systems with microbial modulation for phytomicrobiome remains largely underexplored. Here, we explore the capabilities of eCISs as an advanced approach for the biocontrol, leveraging their tailored mechanisms for targeted payload delivery in plant-associated microbial communities with enhanced host specificity. This study aims to address the potential of engineered injection systems in facilitating sustainable phytomicrobiome engineering strategies that enhance biocontrol, aiming to reduce environmental harm while improving agricultural productivity.","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":12.3,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12961389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147304369","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