Sofie Peeters, Chloé Stévenne, H Julia van Duijnhoven, Marcellina Rola, Manuela Quiroga-Pérez, Aschwin H Engelen, Gerard Muyzer, Pedro R Frade, Olivier De Clerck
{"title":"From holobionts to habitats: opportunities and limitations of microbiome-assisted restoration strategies of marine ecosystem engineers.","authors":"Sofie Peeters, Chloé Stévenne, H Julia van Duijnhoven, Marcellina Rola, Manuela Quiroga-Pérez, Aschwin H Engelen, Gerard Muyzer, Pedro R Frade, Olivier De Clerck","doi":"10.1093/femsre/fuag044","DOIUrl":"10.1093/femsre/fuag044","url":null,"abstract":"<p><p>Marine ecosystem engineers such as corals, seaweeds, and seagrasses are foundational to coastal ecosystems, yet are declining at unprecedented rates due to accelerating climate and anthropogenic pressures. Microbiome-based approaches have attracted attention as a promising avenue to enhance the resilience and recovery of these organisms. Over the past decade, diverse marine probiotic microbes have been isolated and shown to positively influence key host life functions, including growth, development, reproduction, responses to environmental stressors, and pathogen defence. However, current research remains confined to laboratory settings, with few practical field applications tested or utilised, likely driven by practical and technological challenges and lacking communication between science and policy. To help close this gap, we propose a set of risk and success assessment criteria for microbiome-assisted restoration. This framework is built around four pillars: (1) ensuring environmental compatibility of candidate probiotics, (2) establishing scientific validation for their mechanisms of action, (3) securing legal clarity before application, and (4) implementing mandatory in situ monitoring to evaluate ecological outcomes. By integrating these pillars into a cycle of risk assessment, monitoring, and adaptive management, microbiome-assisted restoration could progress from an experimental concept to a practical application complementing existing conservation tools, strengthening the resilience of these ecosystems.</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":"148817932","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}
Jack Orebaugh, Alyssa A Carrell, Larry M York, Melissa A Cregger, Ilenne Del Valle Kessra
{"title":"Synthetic soils for ecological and synthetic biology applications.","authors":"Jack Orebaugh, Alyssa A Carrell, Larry M York, Melissa A Cregger, Ilenne Del Valle Kessra","doi":"10.1093/femsre/fuag012","DOIUrl":"10.1093/femsre/fuag012","url":null,"abstract":"<p><p>Soils are heterogeneous and dynamic systems characterized by complex physical, chemical, and biological interactions. Understanding these interactions is critical, as they influence plant productivity, global biogeochemical cycles, and ecosystem resilience. While ecologists have long studied soils in field, greenhouse, and laboratory settings, their complexity and heterogeneity make it challenging to pinpoint key properties driving biological processes and derive mechanistic insights. Advancements in synthetic biology, which seeks to engineer and control biological processes in soils, have increased the demand for standardized and controllable experimental platforms. These platforms, referred to here as 'synthetic soils', are systems designed to reproduce selected physicochemical characteristics of natural soils in a simplified and defined format, allowing scientists to systematically change soil physicochemical properties (i.e. texture, mineralogy, pH) to study how biological components (i.e. microbes, plants, soil fauna, etc.) respond to, modify, or interact within these controlled environments. This review explores existing synthetic soils, their advantages, limitations, and applications in ecology and synthetic biology, and discusses potential directions for their future development.</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/PMC13044576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147485292","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}
Lucie Suchánková, Libor Kvítek, Milan Kolář, Aleš Panáček
{"title":"Emerging strategies of bacterial adaptation mechanisms to silver and metal oxide nanomaterials.","authors":"Lucie Suchánková, Libor Kvítek, Milan Kolář, Aleš Panáček","doi":"10.1093/femsre/fuaf060","DOIUrl":"10.1093/femsre/fuaf060","url":null,"abstract":"<p><p>This review addresses the crucial and emerging field of bacterial adaptation to antimicrobial nanomaterials, challenging prior assumptions that their multi-level action prevents the development of reduced bacterial sensitivity. It provides a comprehensive overview of experimentally induced adaptation mechanisms across various nanomaterials (e.g. AgNPs, ZnO) and bacterial species. Bacterial adaptations encompass genetic adaptations (e.g. efflux systems, mutagenesis), biomolecule production (e.g. flagellin, exopolysaccharides forming biofilms, protein coronas), and structural changes (e.g. altered shape, cell wall thickening, enhanced motility, membrane permeability changes). The described adaptation mechanisms to nanomaterials are compared with antibiotic resistance mechanisms, emphasizing common strategies such as efflux and envelope changes, but also unique adaptations specific to nanoparticles, such as aggregation and different roles of biomolecules. The review offers insights and emerging strategies for designing safer, more effective nano-antimicrobials, including membrane potential disruption, biofilm inhibition, and size modulation. It emphasizes the need for standardized evaluation methods and future research on cross-resistance.</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/PMC12757747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145707926","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":"The honeybee gut microbiome: a novel multidimensional model of antimicrobial resistance transmission and immune homeostasis from environmental interactions to health regulation.","authors":"Qianmin Hai, Dufu Li, Tingyue Huang, Xiaoqun Dang, Jinshan Xu, Zhengang Ma, Zeyang Zhou","doi":"10.1093/femsre/fuag001","DOIUrl":"10.1093/femsre/fuag001","url":null,"abstract":"<p><p>The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an \"Environment-Microbiota-Host Health\" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.</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/PMC12866650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911185","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 photosynthetic electron flow to gene regulation: redox signal transduction in cyanobacteria.","authors":"Zachary Johnson, Bin Yang, Pavlo Bohutskyi","doi":"10.1093/femsre/fuag030","DOIUrl":"10.1093/femsre/fuag030","url":null,"abstract":"<p><p>In cyanobacteria, the free-living ancestors of chloroplasts, photosynthesis simultaneously sustains growth and generates reactive oxygen species (ROS) that damage proteins, lipids, and DNA when light capture outpaces carbon fixation. Maintaining redox balance, therefore, requires cells to read photosynthetic electron flow as a signal that continuously tunes gene expression and protein activity. This review traces how these redox signals are transduced to transcription machinery through three routes: membrane-localized sensors, cytoplasmic redox sensors downstream of photosystem I, and ROS generated when electron sinks are saturated. Membrane-bound histidine kinases (two-component systems) relay the redox state of the plastoquinone pool to control photosystem remodeling, pigment biosynthesis, and circadian timing. Cytoplasmic one-component regulators, by contrast, sense redox directly through thiol-disulfide switches, glutathionylation, iron-sulfur clusters, and metal-catalyzed oxidation to control photosystem-cofactor, electron-carrier, and transition-metal homeostasis. Because many of these regulators persist in algal and plant chloroplasts, cyanobacteria illuminate principles of redox control across photosynthetic eukaryotes. Post-transcriptional and translational control further shapes redox-dependent gene expression programs through transcript stability, ribosome assembly, and translation initiation, extending redox regulation beyond transcription to every step of protein synthesis and even activity modulation. Finally, we connect redox regulation to photosynthetic physiology, stress resilience, and the rational engineering of cyanobacteria for sustainable bioproduction.</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/PMC13421787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148445250","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}
Shi Kang, Yang Bai, Neil Crickmore, Mario Soberón, Xuguo Zhou, Youjun Zhang, Alejandra Bravo, Zhaojiang Guo
{"title":"From gatekeeper to target: MAPK cascades as control circuits at the insect-microbe interface.","authors":"Shi Kang, Yang Bai, Neil Crickmore, Mario Soberón, Xuguo Zhou, Youjun Zhang, Alejandra Bravo, Zhaojiang Guo","doi":"10.1093/femsre/fuag027","DOIUrl":"10.1093/femsre/fuag027","url":null,"abstract":"<p><p>Mitogen-activated protein kinase (MAPK) signaling cascades are conserved modules that orchestrate multiple processes, including immunity, stress adaptation, and tissue homeostasis. In insects, MAPK pathways function as central regulatory circuits, coordinating defense responses and resistance mechanisms against diverse pathogens. MAPK cascades couple damage sensing in the gut epithelium to intestinal regeneration, pathogen/microbiota stability, cellular and humoral immune responses, and immune homeostasis. Consequently, a wide range of pathogens (parasites, viruses, and bacteria) target, suppress, or hijack key regulatory bottlenecks in MAPK networks to promote pathogen invasion, replication, or transmission. Understanding this molecular arms race provides insight into fundamental principles governing insect-microbe coevolution and reveals critical regulatory nodes that could be exploited to develop innovative strategies for controlling insect pests and vector-borne diseases.</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/PMC13308350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148216999","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}
Marcel Bäcker, Hilje M Doekes, Daniel R Garza, Jeroen Meijer, Simon van Vliet, Rosalind J Allen, Paulien Hogeweg, Bas E Dutilh, Bram van Dijk
{"title":"Spatial structure: shaping the ecology and evolution of microbial communities.","authors":"Marcel Bäcker, Hilje M Doekes, Daniel R Garza, Jeroen Meijer, Simon van Vliet, Rosalind J Allen, Paulien Hogeweg, Bas E Dutilh, Bram van Dijk","doi":"10.1093/femsre/fuaf067","DOIUrl":"10.1093/femsre/fuaf067","url":null,"abstract":"<p><p>Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.</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/PMC12892361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146141427","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}
Adolfo B Poma, Luis F Cofas-Vargas, Fernando L Barroso da Silva, Sergio Pantano, Marta Bally
{"title":"Computational methods in physical virology: a critical perspective across lengths and timescales.","authors":"Adolfo B Poma, Luis F Cofas-Vargas, Fernando L Barroso da Silva, Sergio Pantano, Marta Bally","doi":"10.1093/femsre/fuag050","DOIUrl":"10.1093/femsre/fuag050","url":null,"abstract":"<p><p>Physical virology investigates viral particles by focusing on their assembly, stability, mechanics, and interactions with host cells, neutralizing antibodies, and surfaces. Within this field, computational virology is becoming an indispensable pillar, serving as a \"computational microscope\" that bridges the spatio-temporal scales of viral processes, from individual protein dynamics to capsid assembly and cellular entry. This perspective article offers a critical overview of the current state, challenges, and future directions of computational approaches in physical virology. Our vision is anchored in the research presented at the 2025 EMBO/FEBS Lecture Course on Physical Virology held in Sant Feliu de Guixols, Spain, and complemented by a targeted survey among attendees. We survey the principal methodological frameworks in use, from all-atom to multiscale molecular simulations, mesoscale simulations, and growing integration of artificial intelligence (AI) tools. We also critically examine the central obstacles impeding the field's progress, including the computational-experimental gap, limited accessibility to simulation data, reproducibility concerns, and systemic gender and geographic inequities. Finally, we outline future perspectives, proposing that integrating physics-aware AI with multiscale simulation frameworks, combined with community-driven data-sharing initiatives, will transform the computational microscope from a descriptive tool into a predictive engine for antiviral therapies, rational vaccine design, and biotechnological innovation.</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/PMC13637490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149016070","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}
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":"10.1093/femsre/fuag017","url":null,"abstract":"<p><p>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 catalysed 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.</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/PMC13201069/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The ancient E-ring in bacterial flagellar motors.","authors":"Siqi Zhu, Xueyin Feng, Yanran Liu, Wei Hu, Beile Gao","doi":"10.1093/femsre/fuag011","DOIUrl":"10.1093/femsre/fuag011","url":null,"abstract":"<p><p>The bacterial flagellum is an elaborate nanomachine that powers motility in a variety of environments. While recent cryo-electron tomography studies have revealed great complexity as well as diversity in flagellar motor structures, less is known about the components that constitute the auxiliary structures observed in the periplasm for several species. One example is the E-ring, which was first observed in 1979 in Caulobacter crescentus but whose composition has only recently been shown to be a single protein, FlgY and its homologs. Multiple FlgY dimers form a conserved ring-spoke structure encircling the MS-ring, although the impact of the E-ring on motility seems to differ across bacterial phyla. Remarkably, the E-ring is widely present in flagellated species in the Bacteria domain except β- and γ-proteobacteria, suggesting an ancient origin that likely traces back to the last bacterial common ancestor. Future investigation is required to determine the exact role of this conserved structure in motor function, which may reveal mechanisms distinct from the current working model based on Escherichia coli and Salmonella enterica, which lack the E-ring, and also shed light on the architecture and function of the ancestral motor.</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/PMC13023049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147443013","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}