Pub Date : 2025-08-05DOI: 10.1038/s41579-025-01227-1
Andrea Du Toit
This study reports the development of optogenetically engineered microorganisms and optoelectronic capsules that form a bidirectional signal processing system that can be controlled via a wireless smartphone.
{"title":"Switching bacteria on via a smartphone","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01227-1","DOIUrl":"10.1038/s41579-025-01227-1","url":null,"abstract":"This study reports the development of optogenetically engineered microorganisms and optoelectronic capsules that form a bidirectional signal processing system that can be controlled via a wireless smartphone.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 10","pages":"618-618"},"PeriodicalIF":103.3,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778596","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 : 2025-08-04DOI: 10.1038/s41579-025-01211-9
Julia Oh, Anita Y. Voigt
The skin microbiome is composed of a diverse community of microorganisms, including bacteria, fungi, viruses and mites. These microorganisms have a crucial role in maintaining skin health, protecting against pathogens and modulating immune responses. In recent years, our understanding of the skin microbiome has expanded substantially with the deployment of metagenomic sequencing. This technology, by reconstructing microbial species, strains and gene pathways in the microbiomes of different cohorts, has led to identification of numerous therapeutic targets and thus propelled the development of therapeutic approaches that are aimed at leveraging these microorganisms to treat skin conditions and to improve skin health. In this Review, we discuss the composition, ecology, functions and therapeutic horizons of the human skin microbiome, presenting examples of studies that highlight potential therapeutic targets in the skin microbiome, ongoing progress in the development of skin microbiome-based therapeutics and challenges. In this Review, Oh and Voigt explore the major characteristics and functions of the skin microbiome, and they highlight potential therapeutic targets in the skin microbiome and ongoing progress in the development of skin microbiome-based therapeutics.
{"title":"The human skin microbiome: from metagenomes to therapeutics","authors":"Julia Oh, Anita Y. Voigt","doi":"10.1038/s41579-025-01211-9","DOIUrl":"10.1038/s41579-025-01211-9","url":null,"abstract":"The skin microbiome is composed of a diverse community of microorganisms, including bacteria, fungi, viruses and mites. These microorganisms have a crucial role in maintaining skin health, protecting against pathogens and modulating immune responses. In recent years, our understanding of the skin microbiome has expanded substantially with the deployment of metagenomic sequencing. This technology, by reconstructing microbial species, strains and gene pathways in the microbiomes of different cohorts, has led to identification of numerous therapeutic targets and thus propelled the development of therapeutic approaches that are aimed at leveraging these microorganisms to treat skin conditions and to improve skin health. In this Review, we discuss the composition, ecology, functions and therapeutic horizons of the human skin microbiome, presenting examples of studies that highlight potential therapeutic targets in the skin microbiome, ongoing progress in the development of skin microbiome-based therapeutics and challenges. In this Review, Oh and Voigt explore the major characteristics and functions of the skin microbiome, and they highlight potential therapeutic targets in the skin microbiome and ongoing progress in the development of skin microbiome-based therapeutics.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 12","pages":"771-787"},"PeriodicalIF":103.3,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144777768","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 : 2025-07-28DOI: 10.1038/s41579-025-01221-7
Tessa E. F. Quax
In this Journal Club, Tessa Quax discusses a study that was the first to identify the diversity of archaeal viruses in environmental samples from Icelandic hot springs.
{"title":"Hunting archaeal viruses","authors":"Tessa E. F. Quax","doi":"10.1038/s41579-025-01221-7","DOIUrl":"10.1038/s41579-025-01221-7","url":null,"abstract":"In this Journal Club, Tessa Quax discusses a study that was the first to identify the diversity of archaeal viruses in environmental samples from Icelandic hot springs.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 11","pages":"684-684"},"PeriodicalIF":103.3,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715360","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 : 2025-07-25DOI: 10.1038/s41579-025-01213-7
John D. Helmann
Life depends on metal ions. The levels of metal ions vary widely across environments; many areas of the open ocean are chronically metal-limited, whereas other natural and human-affected environments have exceptionally high metal concentrations. Within the human host, the fitness of commensal and pathogenic microorganisms can be constrained by both metal limitation and intoxication. Limitation occurs when metals are deficient or in forms not suitable for import. Conversely, metal excess can lead to toxicity; microorganisms then rely on metal export to maintain suitable intracellular levels. Metalloregulatory systems play a central part in enabling microorganisms to acclimate to changes in metal availability. The analysis of metalloregulators and their regulons unveils physiologically relevant transport and trafficking functions, reveals processes affected by metal imbalance and provides insights into intracellular metal pools. In this Review, I explore the key processes of metal transport, trafficking, storage and regulation. I next highlight selected microorganisms that illustrate how to thrive in environments that are chronically or transiently metal-limited, or where high metal levels are toxic. A detailed understanding of microbial metal physiology can be harnessed to improve the health of diverse ecosystems, for bioremediation and biomining, and to restrict the growth of bacterial pathogens. Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review, Helmann discusses the key chemical concepts underlying microbial metal physiology and highlights several exemplary microbial systems.
{"title":"Microbial metal physiology: ions to ecosystems","authors":"John D. Helmann","doi":"10.1038/s41579-025-01213-7","DOIUrl":"10.1038/s41579-025-01213-7","url":null,"abstract":"Life depends on metal ions. The levels of metal ions vary widely across environments; many areas of the open ocean are chronically metal-limited, whereas other natural and human-affected environments have exceptionally high metal concentrations. Within the human host, the fitness of commensal and pathogenic microorganisms can be constrained by both metal limitation and intoxication. Limitation occurs when metals are deficient or in forms not suitable for import. Conversely, metal excess can lead to toxicity; microorganisms then rely on metal export to maintain suitable intracellular levels. Metalloregulatory systems play a central part in enabling microorganisms to acclimate to changes in metal availability. The analysis of metalloregulators and their regulons unveils physiologically relevant transport and trafficking functions, reveals processes affected by metal imbalance and provides insights into intracellular metal pools. In this Review, I explore the key processes of metal transport, trafficking, storage and regulation. I next highlight selected microorganisms that illustrate how to thrive in environments that are chronically or transiently metal-limited, or where high metal levels are toxic. A detailed understanding of microbial metal physiology can be harnessed to improve the health of diverse ecosystems, for bioremediation and biomining, and to restrict the growth of bacterial pathogens. Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review, Helmann discusses the key chemical concepts underlying microbial metal physiology and highlights several exemplary microbial systems.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 12","pages":"805-819"},"PeriodicalIF":103.3,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701414","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 : 2025-07-24DOI: 10.1038/s41579-025-01224-4
Andrea Du Toit
The data in this study suggest that the detection of EBV nuclear antigen-specific antibodies are potentially an early marker predicting the diagnosis of multiple sclerosis.
本研究的数据提示EBV核抗原特异性抗体的检测可能是预测多发性硬化症诊断的早期标志物。
{"title":"Towards a prognostic biomarker for multiple sclerosis","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01224-4","DOIUrl":"10.1038/s41579-025-01224-4","url":null,"abstract":"The data in this study suggest that the detection of EBV nuclear antigen-specific antibodies are potentially an early marker predicting the diagnosis of multiple sclerosis.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"547-547"},"PeriodicalIF":103.3,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693991","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":"Finding the lock to fit the key: Ebola virus entry","authors":"Emily Speranza","doi":"10.1038/s41579-025-01220-8","DOIUrl":"10.1038/s41579-025-01220-8","url":null,"abstract":"In this Journal Club, Emily Speranza revists a paper that identifies NPC1 as a crucial host factor required for Ebola virus entry.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 1","pages":"6-6"},"PeriodicalIF":103.3,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144694059","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 : 2025-07-23DOI: 10.1038/s41579-025-01222-6
Shimona Starling
This study reports the emergence of a novel, highly pathogenic feline–canine recombinant coronavirus responsible for a rapidly spreading outbreak of feline infectious peritonitis, which originated in Cyprus.
{"title":"Emergence of pathogenic recombinant coronavirus in cats","authors":"Shimona Starling","doi":"10.1038/s41579-025-01222-6","DOIUrl":"10.1038/s41579-025-01222-6","url":null,"abstract":"This study reports the emergence of a novel, highly pathogenic feline–canine recombinant coronavirus responsible for a rapidly spreading outbreak of feline infectious peritonitis, which originated in Cyprus.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"545-545"},"PeriodicalIF":103.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684446","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 : 2025-07-23DOI: 10.1038/s41579-025-01205-7
Alejandra Mejía-Caballero, Maria L. Marco
Lactobacilli encompass more than 300 species, spanning 25 genera, found in the microbiomes of humans, animals and plants with relevance in agriculture, foods and medicine. Lactobacilli comprise all bacteria previously assigned to the Lactobacillus genus and, similar to other lactic acid bacteria, are characterized by their saccharolytic, fermentation-energy metabolism and diverse enzymatic pathways that support redox balance and maintain intracellular pH. Some lactobacilli are pervasive in dairy, meat and plant foods, where they either contribute to spoilage and food waste or are desired and necessary for the production of fermented foods and animal feed. Strains of lactobacilli are the most applied probiotics tested in clinical studies. The study of host-associated intestinal and vaginal microbiomes has demonstrated that lactobacilli drive epithelial and immune cell responses, resulting in mainly beneficial effects on host health. This Review explores both established and emerging concepts related to this group of microorganisms. It highlights central tenants of their genetic diversity, metabolism, stress tolerance and distribution across host-associated microbiomes, as well as their importance in fermented foods and in health modulation as probiotics. With this accumulated knowledge, there remain substantial opportunities for expanded application of lactobacilli across different domains relevant to food production and health. Lactobacilli are important members of human, animal and insect microbiomes and are prominent in food fermentations. In this Review, Mejía-Caballero and Marco explore the diversity of lactobacilli, focusing on their fundamental traits and their applications in foods and medicine.
{"title":"Lactobacilli biology, applications and host interactions","authors":"Alejandra Mejía-Caballero, Maria L. Marco","doi":"10.1038/s41579-025-01205-7","DOIUrl":"10.1038/s41579-025-01205-7","url":null,"abstract":"Lactobacilli encompass more than 300 species, spanning 25 genera, found in the microbiomes of humans, animals and plants with relevance in agriculture, foods and medicine. Lactobacilli comprise all bacteria previously assigned to the Lactobacillus genus and, similar to other lactic acid bacteria, are characterized by their saccharolytic, fermentation-energy metabolism and diverse enzymatic pathways that support redox balance and maintain intracellular pH. Some lactobacilli are pervasive in dairy, meat and plant foods, where they either contribute to spoilage and food waste or are desired and necessary for the production of fermented foods and animal feed. Strains of lactobacilli are the most applied probiotics tested in clinical studies. The study of host-associated intestinal and vaginal microbiomes has demonstrated that lactobacilli drive epithelial and immune cell responses, resulting in mainly beneficial effects on host health. This Review explores both established and emerging concepts related to this group of microorganisms. It highlights central tenants of their genetic diversity, metabolism, stress tolerance and distribution across host-associated microbiomes, as well as their importance in fermented foods and in health modulation as probiotics. With this accumulated knowledge, there remain substantial opportunities for expanded application of lactobacilli across different domains relevant to food production and health. Lactobacilli are important members of human, animal and insect microbiomes and are prominent in food fermentations. In this Review, Mejía-Caballero and Marco explore the diversity of lactobacilli, focusing on their fundamental traits and their applications in foods and medicine.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"24 2","pages":"111-126"},"PeriodicalIF":103.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684467","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 : 2025-07-23DOI: 10.1038/s41579-025-01216-4
Felix Bongomin, David W. Denning
The WHO fungal priority pathogens list exposes critical diagnostic gaps in low- and middle-income countries (LMICs), where limited access to rapid, affordable tests hinders timely treatment. To reduce mortality, LMICs must urgently invest in laboratory capacity, training and point-of-care diagnostics, especially for fungal diseases associated with HIV (cryptococcosis, Pneumocystis pneumonia and histoplasmosis), tuberculosis (chronic pulmonary aspergillosis), hospital-acquired candidiasis and the fungal neglected tropical diseases.
{"title":"Addressing the fungal diagnostic gap in LMICs","authors":"Felix Bongomin, David W. Denning","doi":"10.1038/s41579-025-01216-4","DOIUrl":"10.1038/s41579-025-01216-4","url":null,"abstract":"The WHO fungal priority pathogens list exposes critical diagnostic gaps in low- and middle-income countries (LMICs), where limited access to rapid, affordable tests hinders timely treatment. To reduce mortality, LMICs must urgently invest in laboratory capacity, training and point-of-care diagnostics, especially for fungal diseases associated with HIV (cryptococcosis, Pneumocystis pneumonia and histoplasmosis), tuberculosis (chronic pulmonary aspergillosis), hospital-acquired candidiasis and the fungal neglected tropical diseases.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"543-544"},"PeriodicalIF":103.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684448","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 : 2025-07-23DOI: 10.1038/s41579-025-01206-6
P. J. Klasse, Rogier W. Sanders, Andrew B. Ward, Ian A. Wilson, John P. Moore
To end the AIDS pandemic, an effective vaccine is sought to prevent new infections by inducing broadly active HIV-1 neutralizing antibodies. Monoclonal neutralizing antibodies can be administered therapeutically to people living with HIV-1 and preventively to those who are uninfected and at risk. Neutralizing antibodies block viral entry into susceptible cells by targeting the HIV-1 envelope glycoprotein, which mediates entry by membrane fusion. The envelope glycoprotein evades neutralizing antibody responses by multiple means, including extreme sequence variation and a dense protective glycan shield. Despite these impediments, many broadly active neutralizing human antibodies have been isolated, typically after years of HIV-1 infection. In this Review, we describe how such antibodies target distinct epitope clusters that cumulatively now cover most of the external surface of the envelope glycoprotein. These antibodies vary in potency, in the degree to which they reduce infectivity, in mechanism of action, and in structural basis, affinity and kinetics of binding. Broadly neutralizing antibody responses have, however, so far not been elicited by immunization with envelope glycoproteins. That situation may change though with the rapid advancement of structure-guided immunogen design strategies that engage germline versions of human antibodies and guide their maturation towards greater neutralization potency and breadth. In this Review, Klasse et al. explore the biogenesis and structure of the HIV-1 envelope glycoprotein (Env) and examine its functional role in viral entry. They also discuss how neutralizing antibodies interact with Env, the evolution of broadly neutralizing antibodies (bnAbs) and strategies to elicit bnAbs through germline-targeting immunogen design.
{"title":"The HIV-1 envelope glycoprotein: structure, function and interactions with neutralizing antibodies","authors":"P. J. Klasse, Rogier W. Sanders, Andrew B. Ward, Ian A. Wilson, John P. Moore","doi":"10.1038/s41579-025-01206-6","DOIUrl":"10.1038/s41579-025-01206-6","url":null,"abstract":"To end the AIDS pandemic, an effective vaccine is sought to prevent new infections by inducing broadly active HIV-1 neutralizing antibodies. Monoclonal neutralizing antibodies can be administered therapeutically to people living with HIV-1 and preventively to those who are uninfected and at risk. Neutralizing antibodies block viral entry into susceptible cells by targeting the HIV-1 envelope glycoprotein, which mediates entry by membrane fusion. The envelope glycoprotein evades neutralizing antibody responses by multiple means, including extreme sequence variation and a dense protective glycan shield. Despite these impediments, many broadly active neutralizing human antibodies have been isolated, typically after years of HIV-1 infection. In this Review, we describe how such antibodies target distinct epitope clusters that cumulatively now cover most of the external surface of the envelope glycoprotein. These antibodies vary in potency, in the degree to which they reduce infectivity, in mechanism of action, and in structural basis, affinity and kinetics of binding. Broadly neutralizing antibody responses have, however, so far not been elicited by immunization with envelope glycoproteins. That situation may change though with the rapid advancement of structure-guided immunogen design strategies that engage germline versions of human antibodies and guide their maturation towards greater neutralization potency and breadth. In this Review, Klasse et al. explore the biogenesis and structure of the HIV-1 envelope glycoprotein (Env) and examine its functional role in viral entry. They also discuss how neutralizing antibodies interact with Env, the evolution of broadly neutralizing antibodies (bnAbs) and strategies to elicit bnAbs through germline-targeting immunogen design.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 11","pages":"734-752"},"PeriodicalIF":103.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684531","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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