Nature Microbiology最新文献

Technological innovations in microbiology. 微生物学的技术创新。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-06 DOI: 10.1038/s41564-026-02364-w

引用次数: 0

Author Correction: An emerging human eye disease is associated with aquatic virus zoonotic infection. 作者更正：一种新出现的人眼疾病与水生病毒人畜共患感染有关。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-05 DOI: 10.1038/s41564-026-02376-6

Shuang Liu, Die Hu, Tingting Xu, Jia Yin, Xinmiao Shan, Jitao Xia, Zhaoxi Wang, Ruidong Xu, Chong Wang, Danielle E Anderson, Peipei Wu, Qianwen Bu, Xiuzhen Liu, Yingjie Liu, Wenjie Tan, Ting Wang, Can Zhao, Hai Zhu, Lin-Fa Wang, Lixin Xie, Xiaojing Pan, Qingli Zhang

引用次数: 0

Practical lessons from microbiome citizen-science projects. 微生物组公民科学项目的实践经验。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-04 DOI: 10.1038/s41564-026-02345-z

Sarah Lebeer, Sofie Goormachtig

引用次数: 0

Bridging continuous and discrete evolution through a controllable, hypermutagenic phage-bacteria system. 通过一个可控的、高诱变的噬菌体-细菌系统连接连续和离散的进化。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-01 DOI: 10.1038/s41564-026-02346-y

Shujian Ong, Pramila Ghode, Ashvinath Narenderan, Shuxuan Lao, Fabian Willenborg, Tobias V Eden, Carl O Marsh, Wen Shan Yew, Julius Fredens

{"title":"Bridging continuous and discrete evolution through a controllable, hypermutagenic phage-bacteria system.","authors":"Shujian Ong, Pramila Ghode, Ashvinath Narenderan, Shuxuan Lao, Fabian Willenborg, Tobias V Eden, Carl O Marsh, Wen Shan Yew, Julius Fredens","doi":"10.1038/s41564-026-02346-y","DOIUrl":"https://doi.org/10.1038/s41564-026-02346-y","url":null,"abstract":"Directed evolution methods face trade-offs between the control of discrete approaches and the throughput of modern continuous systems. Here, we engineered a method called lytic selection and evolution (LySE) for near-continuous evolution of bacterial gene clusters while maintaining discrete checkpoints. We developed a hypermutagenic T7 DNA polymerase variant fused to a dual adenine-cytosine deaminase to install all possible transition mutations at similar frequencies. By relieving pressure from maintaining genome fidelity, we obtained mutation rates of 3.82 × 10-5 substitutions per base. For biocontainment, the T7 DNA polymerase was encoded on an accessory plasmid, while the target gene cluster was encoded on a T7 DNA polymerase-lacking T7 phagemid. Alternating cycles of lysis and transduction enable selective replication and mutagenesis of target genes, while off-target genomic mutations are discarded. LySE evolved a 25-fold increase in tetA-encoded tigecycline resistance in 5 cycles, and a 50.9% increase in endpoint biomass of a bacterial strain that uses the polyethylene terephthalate monomer, ethylene glycol, as its sole carbon source. Our method balances speed and control for directed bacterial evolution.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":19.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817862","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}

引用次数: 0

Unravelling bacterial complexity at high resolution with single-cell transcriptomics. 利用单细胞转录组学在高分辨率下揭示细菌复杂性。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-01 DOI: 10.1038/s41564-026-02333-3

Anne E Clatworthy, Vincenzo P DiNatale, Emanuel Burgos-Robles, Fernando Lopes, Chris Smillie, Deborah T Hung

{"title":"Unravelling bacterial complexity at high resolution with single-cell transcriptomics.","authors":"Anne E Clatworthy, Vincenzo P DiNatale, Emanuel Burgos-Robles, Fernando Lopes, Chris Smillie, Deborah T Hung","doi":"10.1038/s41564-026-02333-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02333-3","url":null,"abstract":"Phenotypic heterogeneity, a feature of both bacteria and eukaryotic cells, arises from inherent cell-to-cell variability. In eukaryotes, single-cell RNA sequencing has led to an explosion in understanding how heterogeneity impacts different cell types and states in organs and tissues. While single-cell RNA sequencing analyses in bacteria have lagged behind eukaryotic studies, recent technological advances now enable similar, high-resolution studies to be performed at scale in bacteria, yielding fundamental insights into how heterogeneity influences bacterial physiology, metabolism, antibiotic resistance, pathogenesis and interactions within complex microbial communities. Here we review recent advances in bacterial single-cell RNA sequencing, including the methods developed so far and what has been learned from their application. We also discuss technological and computational challenges going forwards, the need for standardization and how that could be achieved, and how this emerging field is now poised to revolutionize our understanding of bacterial physiology, infection biology and interactions within bacterial communities, such as the microbiota.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":19.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817893","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}

引用次数: 0

Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice. 由人肠道共生体产生的硫酸胆汁酸减轻小鼠的儿科败血症。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-05-01 DOI: 10.1038/s41564-026-02351-1

Xiang Liu, Haobo Zhang, Yan-Zhen Wang, Xinyu Tu, Jiejie Wen, Shu Lei, Nian Liu, Xinyi Wei, Changzhen Li, Yiwei Li, Bifeng Liu, Yu-Qi Feng, Quan-Fei Zhu, Xin Liu, Kang Ning

{"title":"Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.","authors":"Xiang Liu, Haobo Zhang, Yan-Zhen Wang, Xinyu Tu, Jiejie Wen, Shu Lei, Nian Liu, Xinyi Wei, Changzhen Li, Yiwei Li, Bifeng Liu, Yu-Qi Feng, Quan-Fei Zhu, Xin Liu, Kang Ning","doi":"10.1038/s41564-026-02351-1","DOIUrl":"https://doi.org/10.1038/s41564-026-02351-1","url":null,"abstract":"Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":19.4,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817828","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}

引用次数: 0

Escherichia coli capsules enjoy a genomic revival. 大肠杆菌胶囊迎来了基因组学的复兴。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-04-30 DOI: 10.1038/s41564-026-02337-z

Melissa J Martin, Francois Lebreton

引用次数: 0

Streptomyces produce a diphtheria toxin-like exotoxin that targets insects. 链霉菌产生一种类似白喉毒素的外毒素，以昆虫为目标。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-04-30 DOI: 10.1038/s41564-026-02315-5

Ying Xu, Reed M Stubbendieck, Raghuvir Viswanatha, Ajda Krč, Lisa S Baik, Won Se Suh, Yanhui Hu, Huan Wang, Linxiang Yin, Enzo Mameli, Anne van der Meij, John R Carlson, Andrew C Doxey, Pål Stenmark, Norbert Perrimon, Cameron R Currie, Min Dong

{"title":"Streptomyces produce a diphtheria toxin-like exotoxin that targets insects.","authors":"Ying Xu, Reed M Stubbendieck, Raghuvir Viswanatha, Ajda Krč, Lisa S Baik, Won Se Suh, Yanhui Hu, Huan Wang, Linxiang Yin, Enzo Mameli, Anne van der Meij, John R Carlson, Andrew C Doxey, Pål Stenmark, Norbert Perrimon, Cameron R Currie, Min Dong","doi":"10.1038/s41564-026-02315-5","DOIUrl":"https://doi.org/10.1038/s41564-026-02315-5","url":null,"abstract":"Streptomyces and insects engage in complex interactions shaped by millions of years of evolution. While many beneficial relationships are well recognized, it remains unknown whether Streptomyces produce virulence factors targeting insects specifically. Here, through bioinformatic analysis, we identified diphtheria toxin (DT) homologues, which we named Streptomyces antiquus insecticidal proteins (SAIP), within a monophyletic lineage of Streptomyces that emerged more than 100 million years ago. SAIP is cytotoxic to insect cells and lethal to Drosophila melanogaster, suppressing neuronal activity and immune responses in vivo. Structural and functional studies validated that SAIP is homologous to DT and acts by ADP ribosylation of eukaryotic elongation factor 2. CRISPR-Cas9 screening identified the insect protein Flower as the SAIP receptor across a range of insects. Toxigenic Streptomyces can consume dead insects and produce bioactive secondary metabolites while growing on insect carcasses. These findings establish an insecticidal toxin in Streptomyces and demonstrate that Streptomyces have evolved highly specific virulence factors against insects.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":19.4,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817904","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}

引用次数: 0

Prioritizing prenatal screening to prevent Chagas disease. 优先进行产前筛查以预防恰加斯病。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-04-30 DOI: 10.1038/s41564-026-02342-2

Cass D Condray, Kira L Newman

引用次数: 0

Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity 核酸酶- ntpase噬菌体防御系统利用保守的分子特征来控制细菌免疫

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-27 DOI: 10.1038/s41564-026-02312-8

Adelyn E. Ragucci, Sadie P. Antine, Ethan M. Leviss, Sarah E. Mooney, Jasmine M. Garcia, Lena Shyrokova, Vasili Hauryliuk, Amy S. Y. Lee, Philip J. Kranzusch

{"title":"Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity","authors":"Adelyn E. Ragucci, Sadie P. Antine, Ethan M. Leviss, Sarah E. Mooney, Jasmine M. Garcia, Lena Shyrokova, Vasili Hauryliuk, Amy S. Y. Lee, Philip J. Kranzusch","doi":"10.1038/s41564-026-02312-8","DOIUrl":"https://doi.org/10.1038/s41564-026-02312-8","url":null,"abstract":"Bacteria encode diverse defence systems, including restriction–modification and CRISPR–Cas, that cleave nucleic acid to protect against phage infection. Bioinformatic analyses demonstrate that many recently identified antiphage defence operons comprise a nuclease and NTPase protein, suggesting that additional nucleic acid-targeting systems remain to be understood. Here we develop large-scale comparative cell biology and biochemical approaches to analyse 16 nuclease–NTPase systems and define molecular features that control antiphage defence. Purification, biochemical characterization and in vitro reconstitution of nucleic acid degradation demonstrates that protein–protein complex formation is a shared feature of multigene nuclease–NTPase systems. We show that PaAbpAB, BtHachiman and EcPD-T4-8 system nucleases use highly degenerate recognition site preferences to enable broad nucleic acid degradation, and the Azaca system exhibits specific phage targeting through the recognition of modified phage genomic DNA. Our results uncover principles of antiphage defence system function and highlight the mechanistic diversity of nuclease–NTPase systems in bacterial immunity.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"29 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147751832","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}

引用次数: 0