Pub Date : 2024-07-16DOI: 10.1038/s41579-024-01073-7
Shilong Duan, Gu Feng, Erik Limpens, Paola Bonfante, Xianan Xie, Lin Zhang
The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF–plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant–AMF–bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF–bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture. Most plants form symbioses with arbuscular mycorrhizal fungi, which themselves harbour endobacteria and hyphospheric bacteria. In this Review, Duan et al. explore how nutrients are transferred between the partners in this plant–fungus–bacterium continuum.
{"title":"Cross-kingdom nutrient exchange in the plant–arbuscular mycorrhizal fungus–bacterium continuum","authors":"Shilong Duan, Gu Feng, Erik Limpens, Paola Bonfante, Xianan Xie, Lin Zhang","doi":"10.1038/s41579-024-01073-7","DOIUrl":"10.1038/s41579-024-01073-7","url":null,"abstract":"The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF–plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant–AMF–bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF–bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture. Most plants form symbioses with arbuscular mycorrhizal fungi, which themselves harbour endobacteria and hyphospheric bacteria. In this Review, Duan et al. explore how nutrients are transferred between the partners in this plant–fungus–bacterium continuum.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 12","pages":"773-790"},"PeriodicalIF":69.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625073","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 : 2024-07-16DOI: 10.1038/s41579-024-01085-3
Andrea Du Toit
This study shows that accounting for spillover effects increased the cost-effectiveness of combined malaria-elimination interventions.
这项研究表明，考虑到溢出效应会提高综合疟疾消除干预措施的成本效益。
{"title":"Indirect intervention","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01085-3","DOIUrl":"10.1038/s41579-024-01085-3","url":null,"abstract":"This study shows that accounting for spillover effects increased the cost-effectiveness of combined malaria-elimination interventions.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 9","pages":"523-523"},"PeriodicalIF":69.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141625092","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 : 2024-07-15DOI: 10.1038/s41579-024-01068-4
Fiona C. Ross, Dhrati Patangia, Ghjuvan Grimaud, Aonghus Lavelle, Eugene M. Dempsey, R. Paul Ross, Catherine Stanton
Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies. In this Review, Stanton and colleagues examine the effect of different whole diets on the composition and function of the gut microbiome and explore how the diet–microbiome relationship influences human health and the progression of different chronic diseases.
{"title":"The interplay between diet and the gut microbiome: implications for health and disease","authors":"Fiona C. Ross, Dhrati Patangia, Ghjuvan Grimaud, Aonghus Lavelle, Eugene M. Dempsey, R. Paul Ross, Catherine Stanton","doi":"10.1038/s41579-024-01068-4","DOIUrl":"10.1038/s41579-024-01068-4","url":null,"abstract":"Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies. In this Review, Stanton and colleagues examine the effect of different whole diets on the composition and function of the gut microbiome and explore how the diet–microbiome relationship influences human health and the progression of different chronic diseases.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"671-686"},"PeriodicalIF":69.2,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141620408","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 : 2024-07-08DOI: 10.1038/s41579-024-01082-6
Agustina Taglialegna
In this study, White et al. report that Alcaligenes faecalis mediates wound repair in diabetic foot ulcers.
在这项研究中，White 等人报告说，粪钙铝菌能促进糖尿病足溃疡的伤口修复。
{"title":"Getting wound closure with Alcaligenes","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01082-6","DOIUrl":"10.1038/s41579-024-01082-6","url":null,"abstract":"In this study, White et al. report that Alcaligenes faecalis mediates wound repair in diabetic foot ulcers.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 9","pages":"523-523"},"PeriodicalIF":69.2,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556976","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":"Busting Cryptococcus with brilacidin","authors":"Agustina Taglialegna","doi":"10.1038/s41579-024-01081-7","DOIUrl":"10.1038/s41579-024-01081-7","url":null,"abstract":"In this study, Diehl et al. report that brilacidin could be a promising antifungal drug against Cryptococcus neoformans.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 9","pages":"524-524"},"PeriodicalIF":69.2,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556975","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 : 2024-07-03DOI: 10.1038/s41579-024-01067-5
Nancy H. L. Leung, Donald K. Milton
A WHO report suggests the terms ‘airborne transmission/inhalation’, ‘direct deposition’ and ‘infectious respiratory particles’ for describing transmission modes, highlighting the continuum of particle size with greatest exposure near the source. The report did not update infection control guidelines.
{"title":"New WHO proposed terminology for respiratory pathogen transmission","authors":"Nancy H. L. Leung, Donald K. Milton","doi":"10.1038/s41579-024-01067-5","DOIUrl":"10.1038/s41579-024-01067-5","url":null,"abstract":"A WHO report suggests the terms ‘airborne transmission/inhalation’, ‘direct deposition’ and ‘infectious respiratory particles’ for describing transmission modes, highlighting the continuum of particle size with greatest exposure near the source. The report did not update infection control guidelines.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 8","pages":"453-454"},"PeriodicalIF":69.2,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141498455","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 : 2024-06-26DOI: 10.1038/s41579-024-01069-3
Hualan Liu
This month’s Genome Watch highlights the use of genetic barcoding towards a better understanding of plant–microorganism interactions and colonization dynamics.
本期 "基因组观察 "重点介绍利用基因条形码更好地了解植物与微生物之间的相互作用和定殖动态。
{"title":"Bacterial barcoding facilitates plant microbiome studies","authors":"Hualan Liu","doi":"10.1038/s41579-024-01069-3","DOIUrl":"10.1038/s41579-024-01069-3","url":null,"abstract":"This month’s Genome Watch highlights the use of genetic barcoding towards a better understanding of plant–microorganism interactions and colonization dynamics.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 8","pages":"459-459"},"PeriodicalIF":69.2,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141458189","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 : 2024-06-25DOI: 10.1038/s41579-024-01062-w
Gordon D. Brown, Elizabeth R. Ballou, Steven Bates, Elaine M. Bignell, Andrew M. Borman, Alexandra C. Brand, Alistair J. P. Brown, Carolina Coelho, Peter C. Cook, Rhys A. Farrer, Nelesh P. Govender, Neil A. R. Gow, William Hope, J. Claire Hoving, Rachael Dangarembizi, Thomas S. Harrison, Elizabeth M. Johnson, Liliane Mukaremera, Mark Ramsdale, Christopher R. Thornton, Jane Usher, Adilia Warris, Duncan Wilson
Human fungal infections are a historically neglected area of disease research, yet they cause more than 1.5 million deaths every year. Our understanding of the pathophysiology of these infections has increased considerably over the past decade, through major insights into both the host and pathogen factors that contribute to the phenotype and severity of these diseases. Recent studies are revealing multiple mechanisms by which fungi modify and manipulate the host, escape immune surveillance and generate complex comorbidities. Although the emergence of fungal strains that are less susceptible to antifungal drugs or that rapidly evolve drug resistance is posing new threats, greater understanding of immune mechanisms and host susceptibility factors is beginning to offer novel immunotherapeutic options for the future. In this Review, we provide a broad and comprehensive overview of the pathobiology of human fungal infections, focusing specifically on pathogens that can cause invasive life-threatening infections, highlighting recent discoveries from the pathogen, host and clinical perspectives. We conclude by discussing key future challenges including antifungal drug resistance, the emergence of new pathogens and new developments in modern medicine that are promoting susceptibility to infection. In this Review, Brown et al. provide an overview of fungal pathobiology from the pathogen, host and clinical perspectives, focusing specifically on pathogens that can cause invasive life-threatening infections.
{"title":"The pathobiology of human fungal infections","authors":"Gordon D. Brown, Elizabeth R. Ballou, Steven Bates, Elaine M. Bignell, Andrew M. Borman, Alexandra C. Brand, Alistair J. P. Brown, Carolina Coelho, Peter C. Cook, Rhys A. Farrer, Nelesh P. Govender, Neil A. R. Gow, William Hope, J. Claire Hoving, Rachael Dangarembizi, Thomas S. Harrison, Elizabeth M. Johnson, Liliane Mukaremera, Mark Ramsdale, Christopher R. Thornton, Jane Usher, Adilia Warris, Duncan Wilson","doi":"10.1038/s41579-024-01062-w","DOIUrl":"10.1038/s41579-024-01062-w","url":null,"abstract":"Human fungal infections are a historically neglected area of disease research, yet they cause more than 1.5 million deaths every year. Our understanding of the pathophysiology of these infections has increased considerably over the past decade, through major insights into both the host and pathogen factors that contribute to the phenotype and severity of these diseases. Recent studies are revealing multiple mechanisms by which fungi modify and manipulate the host, escape immune surveillance and generate complex comorbidities. Although the emergence of fungal strains that are less susceptible to antifungal drugs or that rapidly evolve drug resistance is posing new threats, greater understanding of immune mechanisms and host susceptibility factors is beginning to offer novel immunotherapeutic options for the future. In this Review, we provide a broad and comprehensive overview of the pathobiology of human fungal infections, focusing specifically on pathogens that can cause invasive life-threatening infections, highlighting recent discoveries from the pathogen, host and clinical perspectives. We conclude by discussing key future challenges including antifungal drug resistance, the emergence of new pathogens and new developments in modern medicine that are promoting susceptibility to infection. In this Review, Brown et al. provide an overview of fungal pathobiology from the pathogen, host and clinical perspectives, focusing specifically on pathogens that can cause invasive life-threatening infections.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"687-704"},"PeriodicalIF":69.2,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141448216","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 : 2024-06-21DOI: 10.1038/s41579-024-01064-8
Matthieu Domenech de Cellès, Pejman Rohani
Pertussis, which is caused by Bordetella pertussis, has plagued humans for at least 800 years, is highly infectious and can be fatal in the unvaccinated, especially very young infants. Although the rollout of whole-cell pertussis (wP) vaccines in the 1940s and 1950s was associated with a drastic drop in incidence, concerns regarding the reactogenicity of wP vaccines led to the development of a new generation of safer, acellular (aP) vaccines that have been adopted mainly in high-income countries. Over the past 20 years, some countries that boast high aP coverage have experienced a resurgence in pertussis, which has led to substantial debate over the basic immunology, epidemiology and evolutionary biology of the bacterium. Controversy surrounds the duration of natural immunity and vaccine-derived immunity, the ability of vaccines to prevent transmission and severe disease, and the impact of evolution on evading vaccine immunity. Resolving these issues is made challenging by incomplete detection of pertussis cases, the absence of a serological marker of immunity, modest sequencing of the bacterial genome and heterogeneity in diagnostic methods of surveillance. In this Review, we lay out the complexities of contemporary pertussis and, where possible, propose a parsimonious explanation for apparently incongruous observations. In this Review, Domenech de Cellès and Rohani explore the contemporary epidemiology of pertussis and discuss the controversies surrounding the mechanisms responsible for the re-emergence of pertussis, including the effectiveness and duration of natural immunity and vaccine-derived immunity, the ability of vaccines to prevent transmission and severe disease, and the impact of evolution on evading vaccine immunity.
{"title":"Pertussis vaccines, epidemiology and evolution","authors":"Matthieu Domenech de Cellès, Pejman Rohani","doi":"10.1038/s41579-024-01064-8","DOIUrl":"10.1038/s41579-024-01064-8","url":null,"abstract":"Pertussis, which is caused by Bordetella pertussis, has plagued humans for at least 800 years, is highly infectious and can be fatal in the unvaccinated, especially very young infants. Although the rollout of whole-cell pertussis (wP) vaccines in the 1940s and 1950s was associated with a drastic drop in incidence, concerns regarding the reactogenicity of wP vaccines led to the development of a new generation of safer, acellular (aP) vaccines that have been adopted mainly in high-income countries. Over the past 20 years, some countries that boast high aP coverage have experienced a resurgence in pertussis, which has led to substantial debate over the basic immunology, epidemiology and evolutionary biology of the bacterium. Controversy surrounds the duration of natural immunity and vaccine-derived immunity, the ability of vaccines to prevent transmission and severe disease, and the impact of evolution on evading vaccine immunity. Resolving these issues is made challenging by incomplete detection of pertussis cases, the absence of a serological marker of immunity, modest sequencing of the bacterial genome and heterogeneity in diagnostic methods of surveillance. In this Review, we lay out the complexities of contemporary pertussis and, where possible, propose a parsimonious explanation for apparently incongruous observations. In this Review, Domenech de Cellès and Rohani explore the contemporary epidemiology of pertussis and discuss the controversies surrounding the mechanisms responsible for the re-emergence of pertussis, including the effectiveness and duration of natural immunity and vaccine-derived immunity, the ability of vaccines to prevent transmission and severe disease, and the impact of evolution on evading vaccine immunity.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 11","pages":"722-735"},"PeriodicalIF":69.2,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141435850","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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