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}
Pub Date : 2025-07-22DOI: 10.1038/s41579-025-01219-1
Andrea Du Toit
This study shows that bacterial prey cells are covered in a dense network of curli fibres that confer defence against predatory bacteria.
这项研究表明，细菌的猎物细胞被浓密的卷曲纤维网络所覆盖，这赋予了对掠食性细菌的防御作用。
{"title":"Body armour keeps predators away","authors":"Andrea Du Toit","doi":"10.1038/s41579-025-01219-1","DOIUrl":"10.1038/s41579-025-01219-1","url":null,"abstract":"This study shows that bacterial prey cells are covered in a dense network of curli fibres that confer defence against predatory bacteria.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"546-546"},"PeriodicalIF":103.3,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677318","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 : 2025-07-22DOI: 10.1038/s41579-025-01218-2
Rafael Laso-Pérez
In this Journal Club Rafael Laso Pérez revisits a paper that provided evidence of the syntrophic relation between anaerobic methane-oxidizing archaea and sulfate-reducing bacteria and highlights how scientific collaboration can propel a field forward.
{"title":"Anaerobic oxidation of methane: it takes two to tango","authors":"Rafael Laso-Pérez","doi":"10.1038/s41579-025-01218-2","DOIUrl":"10.1038/s41579-025-01218-2","url":null,"abstract":"In this Journal Club Rafael Laso Pérez revisits a paper that provided evidence of the syntrophic relation between anaerobic methane-oxidizing archaea and sulfate-reducing bacteria and highlights how scientific collaboration can propel a field forward.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 10","pages":"620-620"},"PeriodicalIF":103.3,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677317","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 : 2025-07-21DOI: 10.1038/s41579-025-01217-3
Adrian Cazares, Daniel Cazares, Wendy Figueroa
This Genome Watch discusses recent findings in bacterial mutational hotspots, their impact on pathogenesis and antimicrobial resistance, and how we can harness this knowledge to predict pathogen evolution.
{"title":"Evolutionary hotspots in bacterial genomes","authors":"Adrian Cazares, Daniel Cazares, Wendy Figueroa","doi":"10.1038/s41579-025-01217-3","DOIUrl":"10.1038/s41579-025-01217-3","url":null,"abstract":"This Genome Watch discusses recent findings in bacterial mutational hotspots, their impact on pathogenesis and antimicrobial resistance, and how we can harness this knowledge to predict pathogen evolution.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 10","pages":"621-621"},"PeriodicalIF":103.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677396","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 : 2025-07-21DOI: 10.1038/s41579-025-01214-6
Masaru K. Nobu
In this Journal Club, Masaru Nobu revisits a paper that introduced the concept of syntrophy.
在这个杂志俱乐部，Masaru Nobu重新审视了一篇介绍syntrophy概念的论文。
{"title":"A model ‘organism’ split to uncover microbial symbiosis","authors":"Masaru K. Nobu","doi":"10.1038/s41579-025-01214-6","DOIUrl":"10.1038/s41579-025-01214-6","url":null,"abstract":"In this Journal Club, Masaru Nobu revisits a paper that introduced the concept of syntrophy.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"548-548"},"PeriodicalIF":103.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677320","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 : 2025-07-21DOI: 10.1038/s41579-025-01215-5
Juliana Almario
In this Journal Club, Juliana Almario revisits papers showing nutrient transfers between endophytic insect-parasitic fungi and plants, blurring the lines between mycorrhizal fungi and fungal root endophytes.
{"title":"Blurred lines in the mycorrhiza world","authors":"Juliana Almario","doi":"10.1038/s41579-025-01215-5","DOIUrl":"10.1038/s41579-025-01215-5","url":null,"abstract":"In this Journal Club, Juliana Almario revisits papers showing nutrient transfers between endophytic insect-parasitic fungi and plants, blurring the lines between mycorrhizal fungi and fungal root endophytes.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 10","pages":"619-619"},"PeriodicalIF":103.3,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144677394","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 : 2025-07-11DOI: 10.1038/s41579-025-01200-y
Nelson G. Oliveira Júnior, Camila M. Souza, Danieli F. Buccini, Marlon H. Cardoso, Octávio L. Franco
Novel solutions to combat the rapid evolution of antimicrobial resistance in human and animal pathogens are urgently required. Antimicrobial peptides (AMPs) represent promising therapeutic molecules, as they exhibit structural nuances and distinct molecular targets against pathogenic microorganisms. In this Review, we explore the multifaceted structural nature of AMPs and advanced structural conformations, discuss the distinct mechanisms of action and explore novel targets. Additionally, we discuss resistance mechanisms, cross-resistance and innovative strategies for AMP design and optimization. We argue that gaining insight into novel AMP structural arrangements, targets and design optimization is crucial for the development of innovative therapies that can be translated into clinical as well as broader applications. In this Review, Franco and colleagues explore the structural and functional diversity of antimicrobial peptides (AMPs), their mechanism of action, recent advances in AMP design and optimization, and their potential to address antimicrobial resistance.
{"title":"Antimicrobial peptides: structure, functions and translational applications","authors":"Nelson G. Oliveira Júnior, Camila M. Souza, Danieli F. Buccini, Marlon H. Cardoso, Octávio L. Franco","doi":"10.1038/s41579-025-01200-y","DOIUrl":"10.1038/s41579-025-01200-y","url":null,"abstract":"Novel solutions to combat the rapid evolution of antimicrobial resistance in human and animal pathogens are urgently required. Antimicrobial peptides (AMPs) represent promising therapeutic molecules, as they exhibit structural nuances and distinct molecular targets against pathogenic microorganisms. In this Review, we explore the multifaceted structural nature of AMPs and advanced structural conformations, discuss the distinct mechanisms of action and explore novel targets. Additionally, we discuss resistance mechanisms, cross-resistance and innovative strategies for AMP design and optimization. We argue that gaining insight into novel AMP structural arrangements, targets and design optimization is crucial for the development of innovative therapies that can be translated into clinical as well as broader applications. In this Review, Franco and colleagues explore the structural and functional diversity of antimicrobial peptides (AMPs), their mechanism of action, recent advances in AMP design and optimization, and their potential to address antimicrobial resistance.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 11","pages":"687-700"},"PeriodicalIF":103.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144603099","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 : 2025-07-08DOI: 10.1038/s41579-025-01212-8
Shimona Starling
In a recent study, Jia and colleagues report that the DRT9 system in Escherichia coli synthesizes a long poly(A)-rich cDNA molecule with an antiphage function.
{"title":"A molecular decoy for phage defence","authors":"Shimona Starling","doi":"10.1038/s41579-025-01212-8","DOIUrl":"10.1038/s41579-025-01212-8","url":null,"abstract":"In a recent study, Jia and colleagues report that the DRT9 system in Escherichia coli synthesizes a long poly(A)-rich cDNA molecule with an antiphage function.","PeriodicalId":18838,"journal":{"name":"Nature Reviews Microbiology","volume":"23 9","pages":"545-545"},"PeriodicalIF":103.3,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578398","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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