Trends in MicrobiologyPub Date : 2026-10-01Epub Date: 2026-08-07DOI: 10.1016/j.tim.2026.07.004
Alejandro Tejada-Arranz, Varun Sunder, Marek Basler
{"title":"Intracellular Pseudomonas aeruginosa: internalization and survival.","authors":"Alejandro Tejada-Arranz, Varun Sunder, Marek Basler","doi":"10.1016/j.tim.2026.07.004","DOIUrl":"10.1016/j.tim.2026.07.004","url":null,"abstract":"<p><p>Pseudomonas aeruginosa is an opportunistic human pathogen that can colonize multiple tissues and establish chronic infections with a high rate of relapse. P. aeruginosa survives intracellularly in multiple cell types, including in biopsies from human patients. Intracellular bacteria are partially protected from the immune system, from antibiotics with poor penetration across eukaryotic membranes, and, in some cases, also from antibiotics that penetrate eukaryotic membranes, such as fluoroquinolones. This suggests that P. aeruginosa can establish an intracellular reservoir that may contribute to chronic infection and relapse. However, the intracellular life cycle of P. aeruginosa is poorly understood. In this review, we summarize the ways in which P. aeruginosa interacts with eukaryotic cells and the role of its protein secretion machineries in establishing an intracellular niche.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":"1052-1065"},"PeriodicalIF":18.7,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148689895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vanessa E Thomas, Tomislav Cernava, Corné M J Pieterse, Luiz F W Roesch, Karen A Garrett, Samuel J Martins
{"title":"Dysbiotic microbiomes and the collapse of plant health.","authors":"Vanessa E Thomas, Tomislav Cernava, Corné M J Pieterse, Luiz F W Roesch, Karen A Garrett, Samuel J Martins","doi":"10.1016/j.tim.2026.09.003","DOIUrl":"https://doi.org/10.1016/j.tim.2026.09.003","url":null,"abstract":"<p><p>Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut microbiome, where imbalances similarly contribute to host dysfunction and disease. Here, we discuss the current understanding of plant dysbiosis by integrating host-microbiome interactions and emerging analytical methods. Dysbiosis can extend beyond local compartments, affecting systemic processes such as immunity and nutrient acquisition. Advances in sequencing and quantitative metrics now enable its measurement at the population level, while experimental evidence shows that restoring microbial balance can recover plant function. We highlight translational strategies, including microbiome-informed breeding (Microbiome genes or M genes), synthetic microbial communities (SynComs), and soil microbial priming, to enhance plant resilience. We propose a three-tiered framework for studying and interpreting plant microbiome dysbiosis that integrates compositional profiling, functional omics, and host-performance assessment, and we introduce the concept of functional dysbiosis. We also outline how host-genome-informed M-gene selection, metabolite monitoring, and rationally defined microbial community (SynCom) design can translate this framework into practical crop management strategies.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149115344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gijs Teunis, Louise Roer, Anita C Schürch, Lapo Mughini-Gras, Antoni P A Hendrickx
{"title":"Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance.","authors":"Gijs Teunis, Louise Roer, Anita C Schürch, Lapo Mughini-Gras, Antoni P A Hendrickx","doi":"10.1016/j.tim.2026.09.002","DOIUrl":"https://doi.org/10.1016/j.tim.2026.09.002","url":null,"abstract":"<p><p>Plasmids are central drivers of antimicrobial resistance (AMR) dissemination, yet their modular, recombinogenic genomes defy concepts of relatedness derived from bacterial chromosomes. Long-read sequencing now routinely yields complete plasmid sequences, exposing a key gap: we can reconstruct plasmids but lack agreed principles for comparing them. In response, diverse clustering tools have emerged that emphasise different signals, such as marker genes, whole-sequence similarity, gene content, backbone structure, or explicit rearrangement events. Each encodes a distinct notion of plasmid distance. This review organises these tools into conceptual families, highlights how their assumptions shape surveillance outputs, and proposes hierarchical, multitool strategies and clearer models of plasmid evolution as the basis for scalable and interpretable plasmid-based AMR surveillance.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149040786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Miranda Y Bate, Kelvin Mokaya Abuga, Jethro S Johnson, Sarah H Atkinson
{"title":"Micronutrients, the gut microbiota, and infection susceptibility in infants.","authors":"Miranda Y Bate, Kelvin Mokaya Abuga, Jethro S Johnson, Sarah H Atkinson","doi":"10.1016/j.tim.2026.08.017","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.017","url":null,"abstract":"<p><p>Micronutrient deficiencies are common during infancy, particularly in settings with a high burden of infectious diseases. At the same time, the developing infant gut microbiota is a key determinant of susceptibility to infection from both resident pathobionts and incoming enteric pathogens. Recent human and experimental studies suggest that micronutrients regulate this developing microbial ecosystem in a highly context-dependent manner, with effects varying according to developmental stage, nutritional status, intestinal location, and environmental exposure. In this review, we synthesise current evidence linking micronutrient-microbiota interactions to microbial competition and metabolism, epithelial barrier integrity, and mucosal immunity, and discuss how these interactions may shape susceptibility to enteric and invasive bacterial infections during infancy.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Frank M Aarestrup, Saria Otani, Anne S Meyer, Thomas Bjarnsholt
{"title":"From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance.","authors":"Frank M Aarestrup, Saria Otani, Anne S Meyer, Thomas Bjarnsholt","doi":"10.1016/j.tim.2026.08.016","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.016","url":null,"abstract":"<p><p>Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better viewed as a context-dependent functional state; the same gene can produce different phenotypes depending on the local microenvironment, enzyme kinetics, antibiotic exposure, and bacterial physiology.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148983646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The textile web as a probiotic interface.","authors":"Rachel Armstrong, Kenneth N Timmis","doi":"10.1016/j.tim.2026.08.007","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.007","url":null,"abstract":"<p><p>Microbiome of the Built Environment research exhibits a marked 'hard-surface bias', overlooking the dynamic soft materials that dominate human-microbial exchange. We propose a theoretical reorientation: the home as a textile web of dynamic, porous microbial reactors. Grounded in immunology's Danger Theory and the principle of 'tissue-based class control', these soft interfaces function as an external tissue analog. By treating textiles as designable interfaces (ranging from airway exchange nodes to laundry bioreactors), architecture becomes a site for proactive probiotic rituals. This framework leverages competitive exclusion to support externalized mucosal 'guard duty', transitioning from prophylactic sterility to a choreography of domestic care. Notably, this reframing recognizes that hygiene encompasses more than infection prevention: domestic cleaning rituals also shape the microbial ecology that educates the immune system. Ultimately, we frame the living home as a tolerogenic exoskeleton, biologically calibrated to protect and prime the human holobiont.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148983684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Serratia plymuthica.","authors":"Birgit Piechulla, Tino Krell, Miguel A Matilla","doi":"10.1016/j.tim.2026.08.014","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.014","url":null,"abstract":"","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Trinh Phan-Canh, Adelheid Elbe-Bürger, Karl Kuchler
{"title":"Antifungal drug resistance in Candida auris: molecular mechanisms and emerging therapeutic approaches.","authors":"Trinh Phan-Canh, Adelheid Elbe-Bürger, Karl Kuchler","doi":"10.1016/j.tim.2026.08.011","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.011","url":null,"abstract":"<p><p>The human fungal pathogen Candida auris (Candidozyma auris) has emerged as a major global health threat due to its pronounced skin tropism, efficient healthcare-associated transmission, as well as frequent resistance to antifungal therapy. These features have enabled outbreaks in healthcare settings worldwide and have complicated the management of life-threatening invasive infections. Understanding the molecular basis of antifungal multidrug resistance in C. auris is therefore essential for improving clinical management and developing new therapeutic strategies. In this review, we discuss current knowledge of C. auris and related emerging fungal pathogens, summarize the mechanisms underlying clinical resistance, and highlight recent advances in antifungal drug discovery and therapeutic approaches.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148971452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Atopic dermatitis and beyond: Staphylococcus aureus skin adaptation.","authors":"Elif Uyar, Anne Jamet","doi":"10.1016/j.tim.2026.08.015","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.015","url":null,"abstract":"<p><p>Chronic skin conditions are natural experiments in within-host bacterial evolution. Taking atopic dermatitis as the main example, we discuss how studies starting from collections of clinical skin isolates identify Staphylococcus aureus variants that arise independently in different patients, and how this convergence can prioritize candidates for functional genetics.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148956820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The bacterial immune system: identifying evolved defense adaptations.","authors":"Ellinor O Alseth, Sam P Brown","doi":"10.1016/j.tim.2026.08.006","DOIUrl":"https://doi.org/10.1016/j.tim.2026.08.006","url":null,"abstract":"<p><p>Recent years have witnessed a rapid expansion in bacterial defense mechanisms. Alongside established defenses against molecular parasites, hundreds of novel mechanisms are being described annually, contributing to an ever-expanding 'bacterial immune system'. Terms like 'defense' and 'immune' are often used as shorthand for an observed anti-infection phenotype, but can also imply an evolutionary adaptation with a specific anti-infection function. Despite the field's growth, no agreed-upon framework exists for identifying defense adaptations. When is a defense mechanism an evolved adaptation? Here, we review prior debates in evolutionary biology and propose a four-part framework to evaluate the case for a defense mechanism being an evolved adaptation. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.</p>","PeriodicalId":23275,"journal":{"name":"Trends in Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148930328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}