Nature Microbiology最新文献

{"title":"Advancing equity through community-led, globally connected infectious disease research","authors":"Pontiano Kaleebu, Aliya Naheed, Mahnaz Vahedi, Jackeline Alger, Lyda Osorio, Cristiani Vieira Machado, Francine Ntoumi, Mercedes Rumi, Mohammed AlKhaldi, Pacifique Ndishimye, Evelyn Gitau, Trudie Lang","doi":"10.1038/s41564-026-02489-y","DOIUrl":"10.1038/s41564-026-02489-y","url":null,"abstract":"Platforms for community-led but globally connected knowledge and resource sharing can move us towards more equitable and more effective research and solutions for infectious diseases.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2673-2675"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02489-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data","authors":"Cong-Cong Liu, Shan-Shan Dong, Jing Guo, Zhen Xu, Chen Wang, Yun-Xiao Li, Li-Li Meng, Xi-Cheng Yang, Meng Li, Kun Fu, Yan Guo, Tie-Lin Yang","doi":"10.1038/s41564-026-02472-7","DOIUrl":"10.1038/s41564-026-02472-7","url":null,"abstract":"Recovering high-quality microbial genomes from metagenomic sequencing data is essential for accurate profiling and understanding microbial variation. However, existing clustering methods often suffer from limited accuracy and scalability. Here we present MetaCAT (Metagenome Clustering and Association Tool), a framework that combines recovery of microbial genomes from metagenomic data and analysis of their associations with host traits. MetaCAT incorporates a Sparse Weighted Dirichlet Process Gaussian Mixture Model (SWDPGMM) to accurately and efficiently decompose complex datasets and combines k-mer frequency with read coverage to improve genome reconstruction. It also provides a dedicated workflow for microbial single-nucleotide polymorphism identification and metagenome-wide association studies with the host. MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets. Using metagenomic data from colorectal cancer cohorts, it revealed previously unrecognized marker species and microbial single-nucleotide polymorphisms associated with colorectal cancer. MetaCAT provides a scalable framework for microbial community profiling and advances our understanding of host–microbe interactions. MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with the host physiology using metagenomics data.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2853-2866"},"PeriodicalIF":18.7,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875287","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":"Survival of the driest","authors":"Hemant Joshi, Babak Javid","doi":"10.1038/s41564-026-02461-w","DOIUrl":"10.1038/s41564-026-02461-w","url":null,"abstract":"The journey of Mycobacterium tuberculosis between hosts in aerosol droplets has often been viewed as a passive phase in its life cycle. Recent evidence shows that the inevitable desiccation associated with aerosol transmission triggers a program that imperfectly repairs DNA damage, generating genetic diversity and increased recovery of antibiotic-resistant mutants.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2678-2679"},"PeriodicalIF":18.7,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148865956","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":"Author Correction: Multikingdom and functional gut microbiota markers for autism spectrum disorder.","authors":"Qi Su, Oscar W H Wong, Wenqi Lu, Yating Wan, Lin Zhang, Wenye Xu, Moses K T Li, Chengyu Liu, Chun Pan Cheung, Jessica Y L Ching, Pui Kuan Cheong, Ting Fan Leung, Sandra Chan, Patrick Leung, Francis K L Chan, Siew C Ng","doi":"10.1038/s41564-026-02496-z","DOIUrl":"https://doi.org/10.1038/s41564-026-02496-z","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840948","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":"Autodissemination stations suppress Aedes notoscriptus mosquitoes and reduce Buruli ulcer risk in urban Australia: a randomized controlled field trial","authors":"Véronique Paris, Andrew H. Buultjens, Nicholas Bell, Thomas L. Schmidt, Wendy M. Bamberg, Michael T. Birrell, Finn Romanes, Catarina A. Antao, Maria Globan, Caroline Lavender, Katherine Bond, Sally Dougall, Jake A. Lacey, Yichen Zhai, Peihong Guo, Norelle L. Sherry, Katherine B. Gibney, Jue Tao Lim, Paul D. R. Johnson, Timothy P. Stinear, Ary A. Hoffmann","doi":"10.1038/s41564-026-02439-8","DOIUrl":"10.1038/s41564-026-02439-8","url":null,"abstract":"Aedes notoscriptus are mosquito vectors implicated in transmission of Mycobacterium ulcerans. This bacterium causes a destructive infection of skin and soft tissue called Buruli ulcer. Here we ran a randomized controlled trial in an urban Buruli ulcer endemic area in Melbourne, Australia to test whether autodissemination mosquito control stations, containing pyriproxyfen (larvicide) and Beauveria bassiana (entomopathogenic fungus), suppress Ae. notoscriptus populations. Six geographic areas each received 100 autodissemination stations for 8 weeks, and six control areas received no stations between 25 January 2024 and 21 March 2024. The primary outcome measure was mosquito population numbers. After the trial, there was a 70% average reduction in mosquito egg counts among the six intervention areas compared to control areas (P = 0.0076). In an ad hoc analysis, we then explored human Buruli ulcer notifications in treatment and control areas. After accounting for the 4.8-month mean incubation period, there was an 83% reduction in infection likelihood coinciding with peak intervention effect (intervention zones 1 case, control zones 6 cases, incidence ratio rate 0.167, 95% CI 0.0026–1.054, P = 0.047). The effect was not observed during the same time period in the year previous or following 2024, when no interventions were undertaken. A strong correlation (R2 = 0.85) was observed between decreased disease risk and mosquito suppression. These data show that autodissemination traps can effectively lower urban mosquito populations and reduce the threat of Buruli ulcer in humans. A randomized controlled trial shows that autodissemination stations reduce egg counts for Aedes notoscriptus, the Mycobacterium ulcerans vector, with exploratory analyses suggesting that the intervention could also reduce human Buruli ulcer cases caused by these bacteria, in intervention areas in Melbourne, Australia.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2493-2504"},"PeriodicalIF":18.7,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02439-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Micro-engineering the future","authors":"","doi":"10.1038/s41564-026-02481-6","DOIUrl":"10.1038/s41564-026-02481-6","url":null,"abstract":"Synthetic microbiology has the potential to transform microorganisms into engineered tools for a sustainable future. Nature Microbiology aims to be a platform for sharing innovative breakthroughs and constructive dialogue around the promise and pitfalls of the field.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2387-2388"},"PeriodicalIF":18.7,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02481-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling.","authors":"Sofia Medvedeva, Ulysse Guyet, Eugene V Koonin, Tom O Delmont, Mart Krupovic","doi":"10.1038/s41564-026-02470-9","DOIUrl":"https://doi.org/10.1038/s41564-026-02470-9","url":null,"abstract":"<p><p>The endosomal sorting complexes required for transport (ESCRT) is a membrane-remodelling machinery that mediates membrane constriction and scission. Most enveloped eukaryotic viruses exploit host ESCRT during membrane budding, but none is known to encode ESCRT components. Here, we discovered homologues of two core ESCRT components, ESCRT-III and ATPase Vps4, in mirusviruses and some viruses in the phylum Nucleocytoviricota that infect unicellular eukaryotes. Mirusviruses seem to have hijacked host ESCRT machinery early in their evolution.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148830660","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":"A roadmap to create FAIR collections of microbial strains","authors":"Thomas C. A. Hitch,&nbsp;Mitsuo Sakamoto,&nbsp;Jörg Overmann,&nbsp;Thomas Clavel","doi":"10.1038/s41564-026-02446-9","DOIUrl":"10.1038/s41564-026-02446-9","url":null,"abstract":"Microbiology is in the midst of a cultivation renaissance and this is particularly true in microbiome research, where access to isolates enables mechanistic studies. However, to reach that goal, isolates and their (meta)data must be findable, accessible, interoperable and reproducible (FAIR). Many studies have reported the isolation of thousands of microbial strains, but few are publicly accessible. This is partly due to the hurdles faced in creating FAIR resources, such as the additional workload involved in organizing submission to culture collections and curating metadata for each strain. In addition, inconsistent strain identifiers reduce the findability of strains by preventing their use by the community being tracked. These limitations hinder the sustainable growth of scientific knowledge and innovations in microbiome research. Here we propose a roadmap to help scientists create FAIR collections of microbial strains. We provide guidance on the process of establishing a state-of-the-art collection of microorganisms, from project planning to strain deposition and how to name new taxa. By creating FAIR collections of microbial strains, we can safeguard Earth’s microbial heritage for future generations. Here the authors propose guidance on the process of establishing a state-of-the-art collection of microorganisms, including project planning, strain deposition and the naming of new taxa.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2399-2407"},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148830721","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":"Desiccation promotes DNA damage and rifampin resistance in Mycobacterium tuberculosis","authors":"Christopher D. Brown,&nbsp;Brendon M. Lee,&nbsp;Hannah M. Liu,&nbsp;Amy M. Wu,&nbsp;Andrea Tellez,&nbsp;Harry Zou,&nbsp;Prabhat Ranjan Singh,&nbsp;Kohta Saito,&nbsp;Saurabh Mishra,&nbsp;Megan Brown,&nbsp;Anas Saleh,&nbsp;Narineh M. Odjourian,&nbsp;Melissa Cristaldo,&nbsp;Mingyu Gan,&nbsp;Qingyun Liu,&nbsp;Martin Gengenbacher,&nbsp;Seth A. Darst,&nbsp;Elizabeth A. Campbell,&nbsp;Carl Nathan,&nbsp;Kyu Y. Rhee","doi":"10.1038/s41564-026-02437-w","DOIUrl":"10.1038/s41564-026-02437-w","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that depends on its ability to spread from host to host to survive as a species. Knowledge of traits supporting transmission is lacking. Here, because desiccation occurs during the generation of Mtb-transmitting aerosol droplets, we exposed Mtb mounted atop a filter platform to varying degrees of humidity to characterize its transcriptomic and metabolomic responses to desiccation and rehydration. Desiccation increased levels of oxidative stress, oxidative damage and double-stranded DNA breaks, activating DNA repair responses required for survival. Expression of the transcription-coupled repair factor, mfd, also increased but this buffered the fitness cost of specific resistance-conferring mutations in rpoB, the target of the frontline drug rifampin. Silencing mfd during aerosolization specifically impaired survival of strains harbouring the most common rifampin resistance allele, S450L. This function is epidemiologically supported by whole-genome sequence analysis of 51,229 clinically circulating strains. These studies suggest that transmission-associated desiccation-induced DNA damage is a potential source of genetic diversification that can potentiate antibiotic resistance. Analysis of desiccation stress responses in Mycobacterium tuberculosis reveals increased oxidative stress and DNA damage, leading to upregulation of the transcription-coupled repair factor, Mfd, which buffers fitness costs associated with specific rpoB mutations conferring rifampin resistance.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2738-2750"},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02437-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148830699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Zika virus vaccine with E protein fusion loop mutations protects via CD8+ T cells","authors":"Kantinan Chuensirikulchai,&nbsp;Qin Hui Li,&nbsp;Hsueh-han Lu,&nbsp;Julia Timis,&nbsp;Manuel Montano,&nbsp;Luke Eder,&nbsp;Pradip Bhandari,&nbsp;Dawid Zyla,&nbsp;Maximilian Bunz,&nbsp;Henry Madany,&nbsp;Rubens Prince Dos Santos Alves,&nbsp;Paolla Beatriz Almeida Pinto,&nbsp;Erin Maule,&nbsp;Michael Nguyen,&nbsp;Erica Ollmann Saphire,&nbsp;Lakshmanane Premkumar,&nbsp;Annie Elong Ngono,&nbsp;Sujan Shresta","doi":"10.1038/s41564-026-02465-6","DOIUrl":"10.1038/s41564-026-02465-6","url":null,"abstract":"There are currently no effective vaccines against Zika virus (ZIKV). Candidate vaccines target the ZIKV envelope (E) protein, the major target of anti-ZIKV neutralizing antibodies (nAbs). Here we utilized DNA and RNA platforms to compare virus-like particle vaccines with premembrane (prM) and E expressed either in the wild-type form (Z-prM/E-WT) or with fusion loop (FL) mutations (Z-prM/E-FLM), which limit antibody-dependent enhancement of infection. Both vaccines induced effective protection against infection in C57BL/6 Ifnar1−/− mice but with different mechanisms. The Z-prM/E-WT vaccine elicited nAbs against both immature and mature ZIKV virions, whereas mutations in the Z-prM/E-FLM vaccine impaired prM cleavage, resulting in a suboptimal antibody response failing to neutralize mature virions. Serum transfer and T cell depletion experiments in two mouse models demonstrated that CD8+ T cells were necessary and sufficient for short-term protection by Z-prM/E-FLM, whereas both antibodies and CD8+ T cells contributed to Z-prM/E-WT-induced long-term protection. Our results identify unexpected roles for CD8+ T cells in protection mediated by predominantly nAb-directed prM/E-based ZIKV vaccines. They also reveal that protection conferred by antibody-centric ZIKV vaccines that rely on CD8+ T cells alone is transient, whereas protection afforded by those that elicit both protective antibodies and CD8+ T cells is durable. A Zika vaccine that minimizes pathogenic antibodies provides short-term protection via CD8+ T cells despite suboptimal neutralizing antibodies, whereas an antibody-centric vaccine that induces both antibody and CD8+ T cell responses confers durable protection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2867-2882"},"PeriodicalIF":18.7,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02465-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148830689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}