Nature Microbiology最新文献_第2页

Author Correction: Unbinned contigs expand known diversity in the global microbiome. 作者更正：未分类的基因扩展了全球微生物群的已知多样性。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-27 DOI: 10.1038/s41564-026-02354-y

Vishnu Prasoodanan Pk,Oleksandr M Maistrenko,Anthony Fullam,Daniel R Mende,Ece Kartal,Luis Pedro Coelho,Anja Spang,Peer Bork,Thomas S B Schmidt

引用次数: 0

Plant pathogen invasion through extracellular defence evasion. 植物病原体通过细胞外防御逃避入侵。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-24 DOI: 10.1038/s41564-026-02343-1

Baoye He

引用次数: 0

Community context reshapes microbial proteomes and reduces functional overlap. 群落环境重塑微生物蛋白质组，减少功能重叠。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-24 DOI: 10.1038/s41564-026-02310-w

Sarah Moraïs,Michael Mazor,Itai Amit,Philip Gerth,Anke Trautwein-Schult,Sandra Maaß,Ido Grinshpan,Yehonatan Shelly,Liron Levin,Dörte Becher,Itzhak Mizrahi

{"title":"Community context reshapes microbial proteomes and reduces functional overlap.","authors":"Sarah Moraïs,Michael Mazor,Itai Amit,Philip Gerth,Anke Trautwein-Schult,Sandra Maaß,Ido Grinshpan,Yehonatan Shelly,Liron Levin,Dörte Becher,Itzhak Mizrahi","doi":"10.1038/s41564-026-02310-w","DOIUrl":"https://doi.org/10.1038/s41564-026-02310-w","url":null,"abstract":"Microbial coexistence in complex communities requires mechanisms that minimize competition and optimize resource use. However, the mechanisms by which these ecological strategies are executed remain poorly understood. Here we show that bacteria modulate protein abundance in response to specific community members, reducing functional redundancy and promoting metabolic complementarity. Using synthetic gut-derived consortia exposed to distinct carbon sources, we systematically profiled proteomic responses of individual species across isolate, pairwise and 4-member communities. We found that biotic interactions, rather than abiotic conditions, were the dominant drivers of proteomic variation. These interactions led to reproducible, partner-specific expression shifts that significantly reduced functional overlap and were frequently associated with increased community productivity. Together, these findings highlight gene expression as a means by which microbes implement ecological strategies in community contexts. Through this regulatory plasticity, microbes dynamically reshape their realized niche through protein abundance modulation, enabling them to partition metabolic space and stabilize community structure.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"25 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147738950","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

Strain-level transmission inference across multi-kingdom metagenomic data using TRACS. 使用TRACS跨多界宏基因组数据的菌株水平传播推断。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-24 DOI: 10.1038/s41564-026-02339-x

Gerry Tonkin-Hill,Yan Shao,Alexander E Zarebski,Sudaraka Mallawaarachchi,Ouli Xie,Tommi Mäklin,Harry A Thorpe,Mark R Davies,Stephen D Bentley,Trevor D Lawley,Jukka Corander

{"title":"Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.","authors":"Gerry Tonkin-Hill,Yan Shao,Alexander E Zarebski,Sudaraka Mallawaarachchi,Ouli Xie,Tommi Mäklin,Harry A Thorpe,Mark R Davies,Stephen D Bentley,Trevor D Lawley,Jukka Corander","doi":"10.1038/s41564-026-02339-x","DOIUrl":"https://doi.org/10.1038/s41564-026-02339-x","url":null,"abstract":"Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmision Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"54 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147738951","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

Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires. 开曼能够大规模分析肠道微生物组碳水化合物活性酶谱。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-24 DOI: 10.1038/s41564-026-02318-2

Quinten R Ducarmon,Nicolai Karcher,Samir Giri,Hanne L P Tytgat,Omar Delannoy-Bruno,Selin Pekel,Fabian Springer,Patrick Wörz,Christian Schudoma,Athanasios Typas,Georg Zeller

{"title":"Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.","authors":"Quinten R Ducarmon,Nicolai Karcher,Samir Giri,Hanne L P Tytgat,Omar Delannoy-Bruno,Selin Pekel,Fabian Springer,Patrick Wörz,Christian Schudoma,Athanasios Typas,Georg Zeller","doi":"10.1038/s41564-026-02318-2","DOIUrl":"https://doi.org/10.1038/s41564-026-02318-2","url":null,"abstract":"Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"19 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147738952","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

Benchmarking shotgun metagenomics. 霰弹枪宏基因组的基准测试。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2026-04-24 DOI: 10.1038/s41564-026-02344-0

引用次数: 0

In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules 计算机分型绘制了大肠杆菌转运蛋白依赖胶囊的自然多样性

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-23 DOI: 10.1038/s41564-026-02323-5

Samuel Miravet-Verde, Elisabetta Cacace, Carine Roese Mores, Christoph Rutschmann, Chia-wei Lin, Hans-Joachim Ruscheweyh, Aline Cuénod, Elisa Cappio Barazzone, Enora Marrec, Kateryna Vershynina, Raffael Schumann, Dan J. Bower, Mario Schubert, Adrian Egli, Timm Fiebig, Emma Slack, Shinichi Sunagawa, Timothy G. Keys

{"title":"In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules","authors":"Samuel Miravet-Verde, Elisabetta Cacace, Carine Roese Mores, Christoph Rutschmann, Chia-wei Lin, Hans-Joachim Ruscheweyh, Aline Cuénod, Elisa Cappio Barazzone, Enora Marrec, Kateryna Vershynina, Raffael Schumann, Dan J. Bower, Mario Schubert, Adrian Egli, Timm Fiebig, Emma Slack, Shinichi Sunagawa, Timothy G. Keys","doi":"10.1038/s41564-026-02323-5","DOIUrl":"https://doi.org/10.1038/s41564-026-02323-5","url":null,"abstract":"Serotyping identifies bacterial variants based on surface antigens, traditionally using antibody-based assays, but has been increasingly replaced by in silico methods that infer serotypes from genomic sequences for faster, scalable and more reproducible analyses. However, traditional Escherichia coli capsule serotyping has largely fallen out of use since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution and epidemiology. As capsules influence bacterial interactions with phages, host immune systems and the environment, this gap limits our understanding of E. coli ecology and pathogenicity as well as vaccine and diagnostic development. Here we established a definitive genotype–serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed 37,723 E. coli genomes, cataloguing 85 transporter-dependent capsule types (K-types), including 55 types that were not part of the reference collection. We leveraged this catalogue to develop a hidden Markov model-based in silico serotyping tool, kTYPr, and applied it to curated sets of 24,015 E. coli genomes and 2,762 metagenome-assembled genomes spanning diverse environmental and clinical sources. We found previously uncharacterized K-types enriched in undersampled environments and associated with E. coli disease. This study expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"39 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147734054","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

Emergence of distinct Streptococcus pyogenes emm1 and emm12 lineages in China 中国不同化脓性链球菌emm1和emm12谱系的出现

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-23 DOI: 10.1038/s41564-026-02324-4

Yuanhai You, Dingle Yu, Chao Yang, Xiaomin Peng, Ouli Xie, Hesheng Chang, Chunzhen Hua, Fei Zhao, Xiaomei Yan, Menghan Zhang, Xinwei Ruan, Jasmine E. J. Wells, Stephan Brouwer, Camila Duitama González, Ming Fang, Xiaojie Yu, Lu Sun, Xiaoyue Wei, Jie Liu, Daitao Zhang, Lihua He, Jiazheng Wang, Chuyang Sun, Yuejie Zheng, Sebastian Duchene, Mingming Zhou, Lifang Sun, Mark R. Davies, Mark J. Walker, Quanyi Wang, Jianzhong Zhang, Yonghong Yang

{"title":"Emergence of distinct Streptococcus pyogenes emm1 and emm12 lineages in China","authors":"Yuanhai You, Dingle Yu, Chao Yang, Xiaomin Peng, Ouli Xie, Hesheng Chang, Chunzhen Hua, Fei Zhao, Xiaomei Yan, Menghan Zhang, Xinwei Ruan, Jasmine E. J. Wells, Stephan Brouwer, Camila Duitama González, Ming Fang, Xiaojie Yu, Lu Sun, Xiaoyue Wei, Jie Liu, Daitao Zhang, Lihua He, Jiazheng Wang, Chuyang Sun, Yuejie Zheng, Sebastian Duchene, Mingming Zhou, Lifang Sun, Mark R. Davies, Mark J. Walker, Quanyi Wang, Jianzhong Zhang, Yonghong Yang","doi":"10.1038/s41564-026-02324-4","DOIUrl":"https://doi.org/10.1038/s41564-026-02324-4","url":null,"abstract":"Cases of scarlet fever have increased since 2011 across China. However, genomic epidemiological knowledge of Streptococcus pyogenes, the causative agent, is limited. Here we present a longitudinal analysis of S. pyogenes isolates (n = 1,029) across emm1 and emm12 genotypes collected from eight provinces across China between 1993 and 2024. Genomic data integrated with national scarlet fever incidence data confirmed emm12 and emm1 as dominant genotypes underlying five incidence peaks and disease resurgence in 2024. Phylogenetic analysis showed independent evolution of these genotypes in China compared to global epidemic lineages. Four emm12 clades were present in China before 2011 but were replaced by a single clade, Clade II, by 2020. A dominant emm1 clade, M1china, distinct from global lineages and the M1UK lineage, represents >98% of emm1 cases in China. Sub-clade expansion coincides with carriage of integrative conjugative elements containing macrolide and tetracycline resistance genes and virulence gene-encoding prophage. Ongoing maintenance of these elements in emm1 and emm12 populations likely underlies the resurgence of scarlet fever in China.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"23 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147734055","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

Giant viruses rewire control of cellular protein synthesis. 巨型病毒重新控制细胞蛋白质合成。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-23 DOI: 10.1038/s41564-026-02338-y

Mohammad Moniruzzaman,Danae Stephens

引用次数: 0

The ecology of bacterial attachment to phytoplankton. 细菌附着于浮游植物的生态学。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-22 DOI: 10.1038/s41564-026-02287-6

Mathieu Forget,Oliver Müller,Roman Stocker

引用次数: 0