Pub Date : 2024-07-22DOI: 10.1038/s41579-024-01075-5
Benoit J. Kunath, Charlotte De Rudder, Cedric C. Laczny, Elisabeth Letellier, Paul Wilmes
The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease. In this Review, Kunath et al. explore the interaction between the oral and the intestinal microbiota and how they influence each other and the development of different diseases.
{"title":"The oral–gut microbiome axis in health and disease","authors":"Benoit J. Kunath, Charlotte De Rudder, Cedric C. Laczny, Elisabeth Letellier, Paul Wilmes","doi":"10.1038/s41579-024-01075-5","DOIUrl":"10.1038/s41579-024-01075-5","url":null,"abstract":"The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease. In this Review, Kunath et al. explore the interaction between the oral and the intestinal microbiota and how they influence each other and the development of different diseases.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 12","pages":"791-805"},"PeriodicalIF":69.2,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141736890","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 : 2024-07-19DOI: 10.1038/s41579-024-01077-3
Jack A. Gilbert, Erica M. Hartmann
Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments — places where humans spend most of their lives — and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes. In this Review, Gilbert and Hartmann examine the microbial ecology of indoor spaces, the factors that influence the microbiome of the built environment, and their influence on human health.
{"title":"The indoors microbiome and human health","authors":"Jack A. Gilbert, Erica M. Hartmann","doi":"10.1038/s41579-024-01077-3","DOIUrl":"10.1038/s41579-024-01077-3","url":null,"abstract":"Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments — places where humans spend most of their lives — and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes. In this Review, Gilbert and Hartmann examine the microbial ecology of indoor spaces, the factors that influence the microbiome of the built environment, and their influence on human health.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 12","pages":"742-755"},"PeriodicalIF":69.2,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727535","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 : 2024-07-18DOI: 10.1038/s41579-024-01065-7
Patrick E. Duffy, J. Patrick Gorres, Sara A. Healy, Michal Fried
Malaria killed over 600,000 people in 2022, a death toll that has not improved since 2015. Additionally, parasites and mosquitoes resistant to existing interventions are spreading across Africa and other regions. Vaccines offer hope to reduce the mortality burden: the first licensed malaria vaccines, RTS,S and R21, will be widely deployed in 2024 and should substantially reduce childhood deaths. In this Review, we provide an overview of the malaria problem and the Plasmodium parasite, then describe the RTS,S and R21 vaccines (the first vaccines for any human parasitic disease), summarizing their benefits and limitations. We explore next-generation vaccines designed using new knowledge of malaria pathogenesis and protective immunity, which incorporate antigens and platforms to elicit effective immune responses against different parasite stages in human or mosquito hosts. We describe a decision-making process that prioritizes malaria vaccine candidates for development in a resource-constrained environment. Future vaccines might improve upon the protective efficacy of RTS,S or R21 for children, or address the wider malaria scourge by preventing pregnancy malaria, reducing the burden of Plasmodium vivax or accelerating malaria elimination. In this Review, Duffy et al. examine the malaria vaccine landscape, showcasing both achievements and setbacks over the past decades. They discuss approaches and assays for different parasite stages, summarize recent advancements, propose a decision-making process for the field and identify future priorities to address unmet needs.
{"title":"Malaria vaccines: a new era of prevention and control","authors":"Patrick E. Duffy, J. Patrick Gorres, Sara A. Healy, Michal Fried","doi":"10.1038/s41579-024-01065-7","DOIUrl":"10.1038/s41579-024-01065-7","url":null,"abstract":"Malaria killed over 600,000 people in 2022, a death toll that has not improved since 2015. Additionally, parasites and mosquitoes resistant to existing interventions are spreading across Africa and other regions. Vaccines offer hope to reduce the mortality burden: the first licensed malaria vaccines, RTS,S and R21, will be widely deployed in 2024 and should substantially reduce childhood deaths. In this Review, we provide an overview of the malaria problem and the Plasmodium parasite, then describe the RTS,S and R21 vaccines (the first vaccines for any human parasitic disease), summarizing their benefits and limitations. We explore next-generation vaccines designed using new knowledge of malaria pathogenesis and protective immunity, which incorporate antigens and platforms to elicit effective immune responses against different parasite stages in human or mosquito hosts. We describe a decision-making process that prioritizes malaria vaccine candidates for development in a resource-constrained environment. Future vaccines might improve upon the protective efficacy of RTS,S or R21 for children, or address the wider malaria scourge by preventing pregnancy malaria, reducing the burden of Plasmodium vivax or accelerating malaria elimination. In this Review, Duffy et al. examine the malaria vaccine landscape, showcasing both achievements and setbacks over the past decades. They discuss approaches and assays for different parasite stages, summarize recent advancements, propose a decision-making process for the field and identify future priorities to address unmet needs.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 12","pages":"756-772"},"PeriodicalIF":69.2,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723985","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":"Tearing CRISPR apart","authors":"Andrea Du Toit","doi":"10.1038/s41579-024-01084-4","DOIUrl":"10.1038/s41579-024-01084-4","url":null,"abstract":"This study shows that the anti-CRISPR protein AcrIF25 inhibits the type I-F CRISPR–Cas system by pulling apart the fully assembled Csy complex.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"22 9","pages":"524-524"},"PeriodicalIF":69.2,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141631350","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/s41579-024-01073-7
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}
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