Pub Date : 2024-09-09DOI: 10.1038/s41579-024-01102-5
Daniel Cazares, Wendy Figueroa, Adrian Cazares
This Genome Watch highlights how the revived interest in phages that target plasmid-carrying bacteria is expanding our knowledge of viral diversity, ecology and evolution, which is fundamental for developing safe biotherapeutics.
{"title":"Rediscovering plasmid-dependent phages","authors":"Daniel Cazares, Wendy Figueroa, Adrian Cazares","doi":"10.1038/s41579-024-01102-5","DOIUrl":"10.1038/s41579-024-01102-5","url":null,"abstract":"This Genome Watch highlights how the revived interest in phages that target plasmid-carrying bacteria is expanding our knowledge of viral diversity, ecology and evolution, which is fundamental for developing safe biotherapeutics.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"670-670"},"PeriodicalIF":69.2,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142158971","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 : 2024-09-09DOI: 10.1038/s41579-024-01092-4
Morgan R. Timm, Seongmi K. Russell, Scott J. Hultgren
Urinary tract infections (UTIs), which include any infection of the urethra, bladder or kidneys, account for an estimated 400 million infections and billions of dollars in health-care spending per year. The most common bacterium implicated in UTI is uropathogenic Escherichia coli, but diverse pathogens including Klebsiella, Enterococcus, Pseudomonas, Staphylococcus and even yeast such as Candida species can also cause UTIs. UTIs occur in both women and men and in both healthy and immunocompromised patients. However, certain patient factors predispose to disease: for example, female sex, history of prior UTI, or the presence of a urinary catheter or other urinary tract abnormality. The current clinical paradigm for the treatment of UTIs involves the use of antibiotics. Unfortunately, the efficacy of this approach is dwindling as the prevalence of antimicrobial resistance rises among UTI isolates, and the immense quantity of antibiotics prescribed annually for these infections contributes to the emergence of resistant pathogens. Therefore, there is an urgent need for new antibiotics and non-antibiotic treatment and prevention strategies. In this Review, we discuss how recent studies of bacterial pathogenesis, recurrence, persistence, host–pathogen interactions and host susceptibility factors have elucidated new and promising targets for the treatment and prevention of UTIs.
尿路感染（UTI）包括尿道、膀胱或肾脏的任何感染，估计每年有 4 亿例感染和数十亿美元的医疗支出。尿道炎最常见的细菌是尿路致病性大肠杆菌，但包括克雷伯氏菌、肠球菌、假单胞菌、葡萄球菌甚至念珠菌等酵母菌在内的多种病原体也可导致尿道炎。女性和男性、健康和免疫力低下的患者都会发生尿毒症。然而，某些患者因素会导致疾病的发生：例如，女性性别、既往 UTI 病史或存在导尿管或其他泌尿道异常。目前治疗尿道炎的临床模式包括使用抗生素。遗憾的是，随着 UTI 分离物中抗菌素耐药性的增加，这种方法的疗效正在下降，而且每年用于治疗这些感染的抗生素处方量巨大，导致了耐药病原体的出现。因此，迫切需要新的抗生素和非抗生素治疗与预防策略。在本综述中，我们将讨论近期对细菌致病机理、复发、持续存在、宿主与病原体相互作用以及宿主易感性因素的研究如何为治疗和预防UTIs阐明了新的、有前景的靶点。
{"title":"Urinary tract infections: pathogenesis, host susceptibility and emerging therapeutics","authors":"Morgan R. Timm, Seongmi K. Russell, Scott J. Hultgren","doi":"10.1038/s41579-024-01092-4","DOIUrl":"https://doi.org/10.1038/s41579-024-01092-4","url":null,"abstract":"<p>Urinary tract infections (UTIs), which include any infection of the urethra, bladder or kidneys, account for an estimated 400 million infections and billions of dollars in health-care spending per year. The most common bacterium implicated in UTI is uropathogenic <i>Escherichia coli</i>, but diverse pathogens including <i>Klebsiella</i>, <i>Enterococcus</i>, <i>Pseudomonas</i>, <i>Staphylococcus</i> and even yeast such as <i>Candida</i> species can also cause UTIs. UTIs occur in both women and men and in both healthy and immunocompromised patients. However, certain patient factors predispose to disease: for example, female sex, history of prior UTI, or the presence of a urinary catheter or other urinary tract abnormality. The current clinical paradigm for the treatment of UTIs involves the use of antibiotics. Unfortunately, the efficacy of this approach is dwindling as the prevalence of antimicrobial resistance rises among UTI isolates, and the immense quantity of antibiotics prescribed annually for these infections contributes to the emergence of resistant pathogens. Therefore, there is an urgent need for new antibiotics and non-antibiotic treatment and prevention strategies. In this Review, we discuss how recent studies of bacterial pathogenesis, recurrence, persistence, host–pathogen interactions and host susceptibility factors have elucidated new and promising targets for the treatment and prevention of UTIs.</p>","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 1","pages":""},"PeriodicalIF":88.1,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142158973","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 : 2024-09-05DOI: 10.1038/s41579-024-01090-6
Isabelle J. Schalk
Iron is an essential nutrient for the growth, survival and virulence of almost all bacteria. To access iron, many bacteria produce siderophores, molecules with a high affinity for iron. Research has highlighted substantial diversity in the chemical structure of siderophores produced by bacteria, as well as remarkable variety in the molecular mechanisms involved in strategies for acquiring iron through these molecules. The metal-chelating properties of siderophores, characterized by their high affinity for iron and ability to chelate numerous other metals (albeit with lower affinity compared with iron), have also generated interest in diverse fields. Siderophores find applications in the environment, such as in bioremediation and agriculture, in which emerging and innovative strategies are being developed to address pollution and enhance nutrient availability for plants. Moreover, in medicine, siderophores could be used as a tool for novel antimicrobial therapies and medical imaging, as well as in haemochromatosis, thalassemia or cancer treatments. This Review offers insights into the diversity of siderophores, highlighting their potential applications in environmental and medical contexts. In this Review, Schalk explores the molecular mechanisms involved in siderophore-mediated iron acquisition in bacteria. In addition, the possible applications for siderophores in the environment, agriculture and medicine are also discussed.
{"title":"Bacterial siderophores: diversity, uptake pathways and applications","authors":"Isabelle J. Schalk","doi":"10.1038/s41579-024-01090-6","DOIUrl":"10.1038/s41579-024-01090-6","url":null,"abstract":"Iron is an essential nutrient for the growth, survival and virulence of almost all bacteria. To access iron, many bacteria produce siderophores, molecules with a high affinity for iron. Research has highlighted substantial diversity in the chemical structure of siderophores produced by bacteria, as well as remarkable variety in the molecular mechanisms involved in strategies for acquiring iron through these molecules. The metal-chelating properties of siderophores, characterized by their high affinity for iron and ability to chelate numerous other metals (albeit with lower affinity compared with iron), have also generated interest in diverse fields. Siderophores find applications in the environment, such as in bioremediation and agriculture, in which emerging and innovative strategies are being developed to address pollution and enhance nutrient availability for plants. Moreover, in medicine, siderophores could be used as a tool for novel antimicrobial therapies and medical imaging, as well as in haemochromatosis, thalassemia or cancer treatments. This Review offers insights into the diversity of siderophores, highlighting their potential applications in environmental and medical contexts. In this Review, Schalk explores the molecular mechanisms involved in siderophore-mediated iron acquisition in bacteria. In addition, the possible applications for siderophores in the environment, agriculture and medicine are also discussed.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 1","pages":"24-40"},"PeriodicalIF":69.2,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160451","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 : 2024-09-02DOI: 10.1038/s41579-024-01100-7
Andrea Du Toit
This study shows that Citrobacter rodentium alters its growth and virulence in response to varying intestinal pH, and, in turn, the host actively induces stomach acidification.
{"title":"Things go sour in C. rodentium infection","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01100-7","DOIUrl":"10.1038/s41579-024-01100-7","url":null,"abstract":"This study shows that Citrobacter rodentium alters its growth and virulence in response to varying intestinal pH, and, in turn, the host actively induces stomach acidification.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"667-667"},"PeriodicalIF":69.2,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118125","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 : 2024-08-28DOI: 10.1038/s41579-024-01093-3
Antonio Pedro Camargo
This Genome Watch highlights recent metagenomic surveys that have revealed the extensive prevalence and diversity of plasmids in the human gut microbiome and discusses the challenges in accurately reporting plasmid genomes identified from metagenomic data.
{"title":"Unveiling plasmid diversity in nature","authors":"Antonio Pedro Camargo","doi":"10.1038/s41579-024-01093-3","DOIUrl":"10.1038/s41579-024-01093-3","url":null,"abstract":"This Genome Watch highlights recent metagenomic surveys that have revealed the extensive prevalence and diversity of plasmids in the human gut microbiome and discusses the challenges in accurately reporting plasmid genomes identified from metagenomic data.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 10","pages":"597-597"},"PeriodicalIF":69.2,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142085508","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}
The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive–Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor. In this Review, Gribaldo and co-workers explore the diversity and evolution of Terrabacteria and highlight their unique cell envelopes that deviate from Gram-positive and Gram-negative classifications, challenging traditional views on the bacterial cell envelope. They also discuss the variations in outer membrane biogenesis and speculate on the evolutionary origin of the outer membrane before the last bacterial common ancestor and how it was repeatedly lost.
细菌包膜是最古老、最基本的细胞成分之一，传统上被分为革兰氏阳性（单膜）和革兰氏阴性（双膜）。最近具有里程碑意义的研究挑战了微生物学中的一个重要范式，推断出细菌的最后一个共同祖先具有单膜包膜，而外膜（OM）在进化过程中一再丧失，从而产生了单膜细菌。耐人寻味的是，外膜丧失似乎只发生在两大细菌支系之一的地球细菌中。在这篇综述中，我们介绍了目前关于 Terrabacteria 的知识。我们描述了它们的多样性和系统发育，然后重点介绍了 Terrabacteria 细胞包膜的巨大表型多样性，这些表型与教科书上的双膜和单膜示例有很大偏差，对经典的革兰氏阳性-革兰氏阴性划分提出了挑战。我们强调了地球细菌中涉及 OM 生物发生的系统与经典的双球菌实验模型的显著差异，以及它们如何为细菌细胞包膜的多样性和生物发生提供了新的见解。我们还讨论了可能导致 OM 多次丧失的潜在进化步骤，并推测了最早的 OM 可能是如何在最后一个细菌共同祖先之前出现的。
{"title":"Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution","authors":"Basile Beaud Benyahia, Najwa Taib, Christophe Beloin, Simonetta Gribaldo","doi":"10.1038/s41579-024-01088-0","DOIUrl":"10.1038/s41579-024-01088-0","url":null,"abstract":"The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive–Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor. In this Review, Gribaldo and co-workers explore the diversity and evolution of Terrabacteria and highlight their unique cell envelopes that deviate from Gram-positive and Gram-negative classifications, challenging traditional views on the bacterial cell envelope. They also discuss the variations in outer membrane biogenesis and speculate on the evolutionary origin of the outer membrane before the last bacterial common ancestor and how it was repeatedly lost.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 1","pages":"41-56"},"PeriodicalIF":69.2,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142085754","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 : 2024-08-20DOI: 10.1038/s41579-024-01096-0
Agustina Taglialegna
In this study, Li, Feng et al. identify an antimicrobial compound produced by plant root-associated Pseudomonas fluorescens with potent activity against drug-resistant, Gram-positive bacteria.
{"title":"From soil to battling antimicrobial resistance","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01096-0","DOIUrl":"10.1038/s41579-024-01096-0","url":null,"abstract":"In this study, Li, Feng et al. identify an antimicrobial compound produced by plant root-associated Pseudomonas fluorescens with potent activity against drug-resistant, Gram-positive bacteria.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 10","pages":"596-596"},"PeriodicalIF":69.2,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007383","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":"Testing fast with uRAST","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01097-z","DOIUrl":"10.1038/s41579-024-01097-z","url":null,"abstract":"In this study, Kim, Kang, Jang et al. report a phenotype-based, ultra-rapid and blood culture-free antimicrobial susceptibility testing approach.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 10","pages":"596-596"},"PeriodicalIF":69.2,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007594","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":"Tagging for degradation — bacteria do it too","authors":"Francesca Ester Morreale","doi":"10.1038/s41579-024-01094-2","DOIUrl":"10.1038/s41579-024-01094-2","url":null,"abstract":"In this Journal Club, Francesca Ester Morreale revisits a paper reporting that arginine phosphorylation marks proteins for degradation in bacteria.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"669-669"},"PeriodicalIF":69.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142002818","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}
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production. In this Review, Compant et al. explore the functions, mechanisms, assembly and interactions of plant microbiomes, highlighting current applications and their limitations. They also discuss how recent advances could lead to new or improved applications and identify research gaps crucial for harnessing microbiome functions in sustainable plant production.
{"title":"Harnessing the plant microbiome for sustainable crop production","authors":"Stéphane Compant, Fabricio Cassan, Tanja Kostić, Linda Johnson, Günter Brader, Friederike Trognitz, Angela Sessitsch","doi":"10.1038/s41579-024-01079-1","DOIUrl":"10.1038/s41579-024-01079-1","url":null,"abstract":"Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production. In this Review, Compant et al. explore the functions, mechanisms, assembly and interactions of plant microbiomes, highlighting current applications and their limitations. They also discuss how recent advances could lead to new or improved applications and identify research gaps crucial for harnessing microbiome functions in sustainable plant production.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 1","pages":"9-23"},"PeriodicalIF":69.2,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141986312","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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