Pub Date : 2025-06-26DOI: 10.1038/s41579-025-01208-4
Andrea Du Toit
This study shows that regional mismatches between transplanted microbiota and the host gut environment alter the metabolic and immune states of host tissues as well as the composition of regional microbiomes.
{"title":"A misplaced microbiome","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01208-4","DOIUrl":"10.1038/s41579-025-01208-4","url":null,"abstract":"This study shows that regional mismatches between transplanted microbiota and the host gut environment alter the metabolic and immune states of host tissues as well as the composition of regional microbiomes.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 8","pages":"472-472"},"PeriodicalIF":103.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144488730","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}
Pub Date : 2025-06-25DOI: 10.1038/s41579-025-01209-3
Andrea Du Toit
This study discovers that two distinct cryptic Pseudogymnoascus destructans species cause white-nose disease.
本研究发现两种不同的隐生破坏假裸子霉引起白鼻病。
{"title":"A long-lost species","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01209-3","DOIUrl":"10.1038/s41579-025-01209-3","url":null,"abstract":"This study discovers that two distinct cryptic Pseudogymnoascus destructans species cause white-nose disease.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 8","pages":"472-472"},"PeriodicalIF":103.3,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478954","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}
Pub Date : 2025-06-11DOI: 10.1038/s41579-025-01203-9
Agustina Taglialegna
In a recent study, Sidhu et al. show that depletion of the pla virulence gene in Yersinia pestis ancient and modern pandemic strains reduced their virulence, thereby promoting the pathogen’s persistence and transmission.
{"title":"Persistence over virulence in Yersinia pestis","authors":"Agustina Taglialegna","doi":"10.1038/s41579-025-01203-9","DOIUrl":"10.1038/s41579-025-01203-9","url":null,"abstract":"In a recent study, Sidhu et al. show that depletion of the pla virulence gene in Yersinia pestis ancient and modern pandemic strains reduced their virulence, thereby promoting the pathogen’s persistence and transmission.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 8","pages":"471-471"},"PeriodicalIF":103.3,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144260201","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}
Pub Date : 2025-06-11DOI: 10.1038/s41579-025-01204-8
Agustina Taglialegna
In a recent study, Li et al. report microbial mechanisms that enhance plant adaptation to drought conditions.
在最近的一项研究中，Li等人报道了增强植物对干旱条件适应的微生物机制。
{"title":"Microbial allies in plant defence against drought","authors":"Agustina Taglialegna","doi":"10.1038/s41579-025-01204-8","DOIUrl":"10.1038/s41579-025-01204-8","url":null,"abstract":"In a recent study, Li et al. report microbial mechanisms that enhance plant adaptation to drought conditions.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 8","pages":"471-471"},"PeriodicalIF":103.3,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144260218","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}
Pub Date : 2025-05-30DOI: 10.1038/s41579-025-01198-3
Amy K. Winter, Spencer J. Fox
Measles vaccination rates fell during the COVID-19 pandemic and have yet to recover, fuelling large and disruptive outbreaks globally. Now, a substantial outbreak in the Americas threatens elimination status in the region. The US response, marked by mixed messaging and a retreat from global health leadership and partnerships, further jeopardizes progress that took decades to achieve.
{"title":"Measles is resurging in the Americas and the world is watching","authors":"Amy K. Winter, Spencer J. Fox","doi":"10.1038/s41579-025-01198-3","DOIUrl":"10.1038/s41579-025-01198-3","url":null,"abstract":"Measles vaccination rates fell during the COVID-19 pandemic and have yet to recover, fuelling large and disruptive outbreaks globally. Now, a substantial outbreak in the Americas threatens elimination status in the region. The US response, marked by mixed messaging and a retreat from global health leadership and partnerships, further jeopardizes progress that took decades to achieve.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 7","pages":"407-408"},"PeriodicalIF":103.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176806","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}
Pub Date : 2025-05-29DOI: 10.1038/s41579-025-01193-8
Morgana Letizia, Stephen P. Diggle, Marvin Whiteley
Pseudomonas aeruginosa has long served as a model organism in microbiology, particularly for studies on gene expression, quorum sensing, antibiotic resistance, virulence and biofilm formation. Its genetic tractability has advanced the understanding of complex regulatory networks and experimental evolution. The versatility of this bacterium stems from its genomic variability, metabolic flexibility and phenotypic diversity, enabling it to thrive in diverse environments, both as a harmless saprophyte and an opportunistic human pathogen. P. aeruginosa can cause acute and chronic human infections, particularly in patients with underlying immune deficiencies. Its intrinsic antibiotic tolerance and resistance, together with its ability to produce multiple virulence factors while rapidly adapting to infection conditions, pose a major clinical challenge. In this Review, we explore key features contributing to the ecological and pathogenic versatility of P. aeruginosa. We examine the molecular mechanisms and ecological and evolutionary implications of quorum sensing and biofilm formation. We explore the virulence strategies and in vivo fitness determinants, as well as the evolutionary dynamics and global epidemiology of P. aeruginosa, with a focus on antimicrobial resistance. Finally, we discuss emerging strategies to control P. aeruginosa infections and address outstanding questions in the field. Pseudomonas aeruginosa is a functionally versatile bacterium, a leading opportunistic human pathogen and a model organism in microbiology. In this Review, Letizia, Diggle and Whiteley discuss P. aeruginosa’s quorum sensing, biofilm formation, virulence, epidemiology, resistance mechanisms and infection control strategies.
{"title":"Pseudomonas aeruginosa: ecology, evolution, pathogenesis and antimicrobial susceptibility","authors":"Morgana Letizia, Stephen P. Diggle, Marvin Whiteley","doi":"10.1038/s41579-025-01193-8","DOIUrl":"10.1038/s41579-025-01193-8","url":null,"abstract":"Pseudomonas aeruginosa has long served as a model organism in microbiology, particularly for studies on gene expression, quorum sensing, antibiotic resistance, virulence and biofilm formation. Its genetic tractability has advanced the understanding of complex regulatory networks and experimental evolution. The versatility of this bacterium stems from its genomic variability, metabolic flexibility and phenotypic diversity, enabling it to thrive in diverse environments, both as a harmless saprophyte and an opportunistic human pathogen. P. aeruginosa can cause acute and chronic human infections, particularly in patients with underlying immune deficiencies. Its intrinsic antibiotic tolerance and resistance, together with its ability to produce multiple virulence factors while rapidly adapting to infection conditions, pose a major clinical challenge. In this Review, we explore key features contributing to the ecological and pathogenic versatility of P. aeruginosa. We examine the molecular mechanisms and ecological and evolutionary implications of quorum sensing and biofilm formation. We explore the virulence strategies and in vivo fitness determinants, as well as the evolutionary dynamics and global epidemiology of P. aeruginosa, with a focus on antimicrobial resistance. Finally, we discuss emerging strategies to control P. aeruginosa infections and address outstanding questions in the field. Pseudomonas aeruginosa is a functionally versatile bacterium, a leading opportunistic human pathogen and a model organism in microbiology. In this Review, Letizia, Diggle and Whiteley discuss P. aeruginosa’s quorum sensing, biofilm formation, virulence, epidemiology, resistance mechanisms and infection control strategies.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 11","pages":"701-717"},"PeriodicalIF":103.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144164785","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}
Pub Date : 2025-05-29DOI: 10.1038/s41579-025-01199-2
Eric Olo Ndela
This Genome Watch article discusses the dominance of uncultivated microorganisms in natural ecosystems and how the consequent genome-driven insights could guide the rational design of synthetic microbial communities.
{"title":"Microorganisms thriving together as communities","authors":"Eric Olo Ndela","doi":"10.1038/s41579-025-01199-2","DOIUrl":"10.1038/s41579-025-01199-2","url":null,"abstract":"This Genome Watch article discusses the dominance of uncultivated microorganisms in natural ecosystems and how the consequent genome-driven insights could guide the rational design of synthetic microbial communities.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"550-550"},"PeriodicalIF":103.3,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144164781","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}
Pub Date : 2025-05-23DOI: 10.1038/s41579-025-01192-9
Timothy J. Rozday
This Genome Watch highlights the advantages and limitations of k-mer approaches versus standard alignment-based methods for analysing metagenomic data, assisting microbial species identification, microbial abundance estimation and their application in pathogen genomic epidemiology.
{"title":"Metagenomics distilled: new k-mer-based methods","authors":"Timothy J. Rozday","doi":"10.1038/s41579-025-01192-9","DOIUrl":"10.1038/s41579-025-01192-9","url":null,"abstract":"This Genome Watch highlights the advantages and limitations of k-mer approaches versus standard alignment-based methods for analysing metagenomic data, assisting microbial species identification, microbial abundance estimation and their application in pathogen genomic epidemiology.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 8","pages":"473-473"},"PeriodicalIF":103.3,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122558","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}
Pub Date : 2025-05-23DOI: 10.1038/s41579-025-01191-w
Jennifer M. Auchtung, Heather E. Hallen-Adams, Robert Hutkins
Fermented foods and beverages, produced by the intentional growth of microorganisms, have long been among the most widely consumed foods in the human diet. Whether microorganisms are added directly to food substrates, or the growth and activity of autochthonous microorganisms colonizing food substrates is encouraged by selective conditions, the production of organic acids, ethanol and other metabolic end products enhance the safety, shelf-life, sensory and functional properties of foods. Whereas some fermented foods may be produced by communities dominated by only a few taxa of limited phylogenetic diversity, others are produced through the concerted action of diverse microbial communities. In this Review, we describe the ecological interactions shaping microbial community structure and function across various categories of fermented foods by providing specific examples. We also describe how the manufacture, quality and sustainability of even traditional fermented foods can be improved by contemporary technologies. Finally, we briefly discuss current research on the ecological impact of microorganisms found in fermented food on the human gut. In this Review, Auchtung, Hallen-Adams and Hutkins examine the ecological interactions among microorganisms in various fermented foods, how these interactions shape microbial community structure within food ecosystems, and the effects of modern technologies on the microbial and organoleptic properties of fermented foods.
{"title":"Microbial interactions and ecology in fermented food ecosystems","authors":"Jennifer M. Auchtung, Heather E. Hallen-Adams, Robert Hutkins","doi":"10.1038/s41579-025-01191-w","DOIUrl":"10.1038/s41579-025-01191-w","url":null,"abstract":"Fermented foods and beverages, produced by the intentional growth of microorganisms, have long been among the most widely consumed foods in the human diet. Whether microorganisms are added directly to food substrates, or the growth and activity of autochthonous microorganisms colonizing food substrates is encouraged by selective conditions, the production of organic acids, ethanol and other metabolic end products enhance the safety, shelf-life, sensory and functional properties of foods. Whereas some fermented foods may be produced by communities dominated by only a few taxa of limited phylogenetic diversity, others are produced through the concerted action of diverse microbial communities. In this Review, we describe the ecological interactions shaping microbial community structure and function across various categories of fermented foods by providing specific examples. We also describe how the manufacture, quality and sustainability of even traditional fermented foods can be improved by contemporary technologies. Finally, we briefly discuss current research on the ecological impact of microorganisms found in fermented food on the human gut. In this Review, Auchtung, Hallen-Adams and Hutkins examine the ecological interactions among microorganisms in various fermented foods, how these interactions shape microbial community structure within food ecosystems, and the effects of modern technologies on the microbial and organoleptic properties of fermented foods.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 10","pages":"622-634"},"PeriodicalIF":103.3,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122555","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}
Pub Date : 2025-05-23DOI: 10.1038/s41579-025-01197-4
Andrea Du Toit
This study explored the inheritance of bacterial metabolic activity at the single-cell level.
本研究在单细胞水平上探讨了细菌代谢活性的遗传。
{"title":"Inheriting traits","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01197-4","DOIUrl":"10.1038/s41579-025-01197-4","url":null,"abstract":"This study explored the inheritance of bacterial metabolic activity at the single-cell level.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 7","pages":"406-406"},"PeriodicalIF":103.3,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122409","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}
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