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":"<p><p>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.</p>","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}
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":"<p><p>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.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"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}
{"title":"Microbial chitinases in the plant holobiont: ecological roles and structural determinants.","authors":"Ruben Eichfeld, Alga Zuccaro","doi":"10.1093/femsre/fuag022","DOIUrl":"10.1093/femsre/fuag022","url":null,"abstract":"<p><p>Complex intra- and inter-kingdom interactions shape microbiota stability and influence the success of microbial invasion into the plant holobiont. Microbial chitinases, enzymes central to fungal physiology and nutrient acquisition, can also function as secreted effector-like proteins that modulate community dynamics by restricting access to occupied ecological niches, such as plant roots, or by contributing to the destabilization of resident consortia. Beyond these antimicrobial functions, microbial chitinases can facilitate plant colonization by interfering with chitin-triggered immunity, suggesting that chitinase diversification has accompanied microbial adaptation to distinct host-associated niches. In this review, we examine microbial chitinase functions in ecological contexts and discuss how structural variation can tune chitinolytic activity, substrate engagement, and biological function. We argue that the ecological roles of microbial chitinases cannot be inferred from catalytic activity alone, but emerge from the interplay between enzyme architecture, substrate accessibility, synergistic enzyme activities, regulated spatiotemporal expression, and the microbial or host context in which chitin is encountered.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147948224","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}
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":"10.1093/femsre/fuag016","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13192418/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Bacterial sulfoquinovose cycling across aquatic ecosystems.","authors":"Reagan Lee, Wonjae Kim, Jihye Bae, Woojun Park","doi":"10.1093/femsre/fuag034","DOIUrl":"10.1093/femsre/fuag034","url":null,"abstract":"<p><p>Sulfoquinovosyldiacylglycerol (SQDG) is a ubiquitous sulfolipid of phototroph membranes, including those of oxygenic phototrophs and some anoxygenic phototrophic bacteria, and its headgroup sulfoquinovose (SQ) represents one of the most abundant organosulfur compounds in the biosphere. Global SQ production is estimated at ∼10 Pg yr-1, with marine systems alone contributing ∼1.5 Pg C yr-1 in SQ-containing compounds. In marine systems, heterotrophic processing of SQ is increasingly well characterized, whereas the pathways governing SQ transformation in freshwater environments remain poorly resolved. SQ enters both marine and freshwater systems primarily through turnover of phototrophic biomass, with freshwater systems also receiving terrestrial plant-derived sulfolipids. Although phototrophs synthesize SQDG for membrane function, cyanobacteria appear to have limited capacity for SQ catabolism, and SQ turnover is largely mediated by heterotrophic microorganisms. This functional partitioning establishes a metabolic relay in which distinct microbial guilds mediate successive steps of SQ processing, from extracellular sulfolipid hydrolysis to intracellular sulfoglycolysis and terminal sulfur mineralization. Here, we integrate current knowledge of the enzymatic pathways and microbial interactions underpinning SQ transformation within their ecological context. We propose that SQ metabolism constitutes an important, yet underappreciated, axis of aquatic sulfur biogeochemistry, particularly in freshwater systems where cyanobacterial production of dimethylsulfoniopropionate is minimal.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13436972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148520367","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}
Angela Boahen, Adrian Issa Abdo, Neil McMillan, Guilherme Pena, Katharina Richter
{"title":"Plasma-activated water: a dual-action disinfectant and wound-healing therapy for diabetes-related foot infections.","authors":"Angela Boahen, Adrian Issa Abdo, Neil McMillan, Guilherme Pena, Katharina Richter","doi":"10.1093/femsre/fuag051","DOIUrl":"10.1093/femsre/fuag051","url":null,"abstract":"<p><p>Globally, approximately 18.6 million individuals develop diabetes-related foot ulcers each year, with 50%-60% of these cases subsequently becoming infected. Diabetes-related foot infections (DFI) are a serious complication often resulting in gangrene, lower extremity amputation and death-outcomes exacerbated by multidrug-resistant and biofilm-forming pathogens that render standard antibiotics and antiseptics inadequate, driving up healthcare costs and morbidity. Addressing this challenge necessitates the development of novel, dual-action therapeutic strategies capable of eradicating infection while simultaneously promoting tissue regeneration. Plasma-activated water (PAW) is an emerging solution, produced by treating water with cold plasma; an ionized gas that generates a complex mixture of reactive oxygen and nitrogen species. PAW elicits potent broad-spectrum antimicrobial and antibiofilm activity against a wide range of pathogens implicated in chronic wound infections, including DFI. PAW has also been shown to accelerate wound healing by modulating immune cell activity and promoting epithelial cell proliferation and migration. In this review, we summarize DFI prevalence and recurrence, PAW generation and physicochemical properties, antimicrobial and antibiofilm efficacy against relevant pathogens, effects on cellular responses, therapeutic potential and current limitations. This review positions PAW as a dual-action, resistance-refractory therapeutic strategy for DFIs and other chronic wounds and outlines the translational pathway towards clinical implementation.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149024223","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}
Yu Ye, Ying Zhang, Haobing Nie, Xiaoyi Liao, Shuigen Rao, Chunfu Zheng
{"title":"The race between viral immune evasion and the MHC class I antigen processing pathway.","authors":"Yu Ye, Ying Zhang, Haobing Nie, Xiaoyi Liao, Shuigen Rao, Chunfu Zheng","doi":"10.1093/femsre/fuag036","DOIUrl":"10.1093/femsre/fuag036","url":null,"abstract":"<p><p>Viral immune evasion of the major histocompatibility complex class I (MHC-I) antigen processing and presentation (APP) pathway is a centerpiece of the art of deception that enables persistence, reinfection, and severe disease. It does so by blunting peptide-MHC-I (pMHC-I) display, weakening CD8+ cytotoxic T lymphocyte (CTL) surveillance, and balancing the counterpressure imposed by natural killer (NK) cell missing-self responses. Rather than relying on a single trick, viruses deploy coordinated, multinode interference that functionally rewires the APP assembly line. These deceptive strategies include limiting antigen substrate availability, reshaping proteasomal peptide generation, sabotaging transporters associated with antigen processing (TAP)-dependent peptide import, disrupting peptide-loading complex-assisted editing, misdirecting MHC-I trafficking, and accelerating surface pMHC-I degradation. In parallel, many viruses fine-tune immune visibility through allele-selective modulation and nonclassical MHC circuits such as human leukocyte antigen E (HLA-E), thereby optimizing CTL evasion without inducing overwhelming NK activation. This review, therefore, describes the development of pathway-centered mechanistic synthesis across DNA and RNA virus families. We further integrate innate immune antagonism, endoplasmic reticulum stress, antigen-presentation competence, cross-presentation limits, and virus-shaped peptide landscapes into a unified framework for understanding viral control of MHC-I output and its translational implications.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148600812","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}
David C Nwobodo, Melford C Egbujor, Sammy Kiprotich, Michael M Meijler
{"title":"Organosulfur scaffolds as quorum sensing and biofilm modulators in Gram-negative bacteria.","authors":"David C Nwobodo, Melford C Egbujor, Sammy Kiprotich, Michael M Meijler","doi":"10.1093/femsre/fuag032","DOIUrl":"10.1093/femsre/fuag032","url":null,"abstract":"<p><p>Quorum sensing (QS) is a cell-density-dependent communication system that coordinates bacterial virulence, biofilm formation, motility, and stress adaptation, making it a compelling target for antivirulence intervention. Due to the possibility of sulfonyl (-SO₂-) and sulfinyl (-S = O-) functional groups to impart specific electronic and steric properties that can modulate bacterial signaling and receptor interactions, organosulfur compounds are increasingly gaining attention. This review highlights recent advances in the development of sulfonyl- and sulfinyl-containing organosulfur compounds as modulators of QS and biofilm formation in clinically relevant Gram-negative pathogens. Both natural and synthetic quorum-sensing inhibitors are considered, with activity directed toward LuxR-type regulators, diffusible signal factor (DSF)-mediated systems, and the Las/Rhl networks of Gram-negative bacteria, including Pseudomonas aeruginosa, Vibrio spp., Chromobacterium violaceum, and Xylella fastidiosa. Emphasis is placed on emerging structure-activity relationships and mechanistic insights derived from biochemical and computational studies. Key challenges, including resistance potential, pharmacological constraints, and delivery considerations, are also discussed. Together, we provide an integrated microbiological and medicinal chemistry perspective for the rational development of organosulfur-based strategies to attenuate QS-regulated pathogenicity.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13411267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148469907","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}
{"title":"From colonization to immune evasion: a synthesis of the interaction strategies that drive Staphylococcus aureus infection.","authors":"Guangqiang Jia, Kewei Chen, Haijiao Lin, Xin Zhao","doi":"10.1093/femsre/fuag048","DOIUrl":"10.1093/femsre/fuag048","url":null,"abstract":"<p><p>Staphylococcus aureus remains a major human and veterinary pathogen, driven by multiple virulence processes, including toxin activity, biofilm formation, metabolic adaptation, regulatory networks, antimicrobial resistance, and strain-specific traits. Many of these processes involve host-pathogen protein-protein interactions (PPIs). This review focuses on PPIs as a major mechanistic layer that links adhesion, invasion, and immune evasion across infection stages. We synthesize available evidence to explain how selected PPIs support the transition from carriage to invasive disease. We first compare surface adhesins that use distinct binding architectures, including Dock, Lock, and Latch, the Collagen Hug, and the tandem β-zipper, to achieve force-resilient attachment under physiological shear. We then organize immune-evasion PPIs along the chronology of host defence, from early sensing and antimicrobial barriers to phagocyte recruitment, complement and opsonization, intraphagosomal killing, and adaptive immunity. This staged view highlights how mechanoadaptive anchoring, redundancy, and multifunctionality can contribute to robust infection phenotypes and suggests therapeutic opportunities involving allosteric modulation, decoy-based restoration of host pathways, and multi-target biologics.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148988807","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}
Dina A Moustafa, Chandradhish Ghosh, Jakob Jung, Amila Nanayakkara, Madhab Sapkota, Kanna Nagamatsu, Bruce Geller, Jörg Vogel, Joanna B Goldberg, David E Greenberg
{"title":"Developing antisense oligomer biotics \"asobiotics\" as precision antibacterials: designs, strategies, and considerations for future success.","authors":"Dina A Moustafa, Chandradhish Ghosh, Jakob Jung, Amila Nanayakkara, Madhab Sapkota, Kanna Nagamatsu, Bruce Geller, Jörg Vogel, Joanna B Goldberg, David E Greenberg","doi":"10.1093/femsre/fuaf059","DOIUrl":"10.1093/femsre/fuaf059","url":null,"abstract":"<p><p>Antimicrobial resistance poses a pressing global health challenge in the 21st century. The rapid increase and prevalence of multidrug-resistant bacteria will require novel approaches to develop new antibiotics. Major advances in nucleic acid-based therapeutics, particularly antisense technologies, could be one solution for developing precision antibiotics. The selectivity and specificity in the drug design of antibacterial antisense oligomers (ASOs) allows precise gene-specific silencing and ultimately enables targeting of currently undruggable gene products. Our goal here is to comprehensively review the advances in asobiotics (antisense oligomer biotics) leading to therapeutic success, including modifications in the nucleic acid backbone of ASOs, which have improved their properties and progresses in delivery. We will discuss utilization of ASOs against several pathogens, strategies to overcome resistance, and finally future scenarios and prospects for asobiotics as pathogen-specific therapy in the clinic.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":" ","pages":""},"PeriodicalIF":16.9,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12828698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145741766","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}