Nature Microbiology最新文献_第2页

Micro-engineering the future 微工程的未来

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-27 DOI: 10.1038/s41564-026-02481-6

引用次数: 0

Large eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling. 大型真核DNA病毒为膜重构编码ESCRT机制。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-26 DOI: 10.1038/s41564-026-02470-9

Sofia Medvedeva, Ulysse Guyet, Eugene V Koonin, Tom O Delmont, Mart Krupovic

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Desiccation promotes DNA damage and rifampin resistance in Mycobacterium tuberculosis. 干燥促进结核分枝杆菌DNA损伤和利福平耐药性。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-26 DOI: 10.1038/s41564-026-02437-w

Christopher D Brown, Brendon M Lee, Hannah M Liu, Amy M Wu, Andrea Tellez, Harry Zou, Prabhat Ranjan Singh, Kohta Saito, Saurabh Mishra, Megan Brown, Anas Saleh, Narineh M Odjourian, Melissa Cristaldo, Mingyu Gan, Qingyun Liu, Martin Gengenbacher, Seth A Darst, Elizabeth A Campbell, Carl Nathan, Kyu Y Rhee

{"title":"Desiccation promotes DNA damage and rifampin resistance in Mycobacterium tuberculosis.","authors":"Christopher D Brown, Brendon M Lee, Hannah M Liu, Amy M Wu, Andrea Tellez, Harry Zou, Prabhat Ranjan Singh, Kohta Saito, Saurabh Mishra, Megan Brown, Anas Saleh, Narineh M Odjourian, Melissa Cristaldo, Mingyu Gan, Qingyun Liu, Martin Gengenbacher, Seth A Darst, Elizabeth A Campbell, Carl Nathan, Kyu Y Rhee","doi":"10.1038/s41564-026-02437-w","DOIUrl":"https://doi.org/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.","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":"148830699","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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A roadmap to create FAIR collections of microbial strains 建立公平微生物菌株收集的路线图。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-26 DOI: 10.1038/s41564-026-02446-9

Thomas C. A. Hitch, Mitsuo Sakamoto, Jörg Overmann, Thomas Clavel

{"title":"A roadmap to create FAIR collections of microbial strains","authors":"Thomas C. A. Hitch, Mitsuo Sakamoto, Jörg Overmann, 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}

引用次数: 0

A Zika virus vaccine with E protein fusion loop mutations protects via CD8⁺ T cells. 携带E蛋白融合环突变的寨卡病毒疫苗通过CD8+ T细胞提供保护。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-26 DOI: 10.1038/s41564-026-02465-6

Kantinan Chuensirikulchai, Qin Hui Li, Hsueh-Han Lu, Julia Timis, Manuel Montano, Luke Eder, Pradip Bhandari, Dawid Zyla, Maximilian Bunz, Henry Madany, Rubens Prince Dos Santos Alves, Paolla Beatriz Almeida Pinto, Erin Maule, Michael Nguyen, Erica Ollmann Saphire, Lakshmanane Premkumar, Annie Elong Ngono, Sujan Shresta

{"title":"A Zika virus vaccine with E protein fusion loop mutations protects via CD8+ T cells.","authors":"Kantinan Chuensirikulchai, Qin Hui Li, Hsueh-Han Lu, Julia Timis, Manuel Montano, Luke Eder, Pradip Bhandari, Dawid Zyla, Maximilian Bunz, Henry Madany, Rubens Prince Dos Santos Alves, Paolla Beatriz Almeida Pinto, Erin Maule, Michael Nguyen, Erica Ollmann Saphire, Lakshmanane Premkumar, Annie Elong Ngono, Sujan Shresta","doi":"10.1038/s41564-026-02465-6","DOIUrl":"https://doi.org/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.","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":"148830689","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

Metabolic dependencies are common among soil bacteria 代谢依赖性在土壤细菌中很常见。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-25 DOI: 10.1038/s41564-026-02456-7

引用次数: 0

Colibactin beyond carcinogenesis 大肠杆菌素超越致癌作用。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-24 DOI: 10.1038/s41564-026-02448-7

Patrick Gallagher, Layla M. Jeries, Kasie Raymann

引用次数: 0

Candida auris uses nutrient sensing to modulate virulence and host immune responses 耳念珠菌利用营养感测调节毒力和宿主免疫反应。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-24 DOI: 10.1038/s41564-026-02454-9

Irma Tedja, Harshini Weerasinghe, Garrett Bryak, Helen Stölting, Tricia L. Lo, Claudia Simm, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Paul F. Harrison, Françios A. B. Olivier, Michael J. McDonald, Shankar Thangamani, Traude H. Beilharz, Ana Traven

{"title":"Candida auris uses nutrient sensing to modulate virulence and host immune responses","authors":"Irma Tedja, Harshini Weerasinghe, Garrett Bryak, Helen Stölting, Tricia L. Lo, Claudia Simm, Angavai Swaminathan, Calvin A. Kraupner-Taylor, Paul F. Harrison, Françios A. B. Olivier, Michael J. McDonald, Shankar Thangamani, Traude H. Beilharz, Ana Traven","doi":"10.1038/s41564-026-02454-9","DOIUrl":"10.1038/s41564-026-02454-9","url":null,"abstract":"The emergence of Candida auris as a pathogen required host adaptation and evasion of mammalian immunity, but the mechanisms are poorly understood. We discovered that C. auris uses nutrient sensing to tune its virulence traits and modulate immune activation in changing environments. In glucose-rich conditions (relevant to blood), C. auris suppresses its virulence traits and evades immune detection. Conversely, non-fermentable carbon sources prevalent in skin activate adhesion and filamentation, thereby triggering macrophage responses. Activation of adhesion by non-fermentable carbon sources is recapitulated across diverse C. auris strains, while filamentation is heterogeneous. In-depth phenotyping of multiple clinical strains revealed that C. auris generates phenotypic heterogeneity by titrating expression of key transcriptional regulators dependent on nutrient inputs and genetic background. This modulates its virulence potential and controls proportional immune responses. Therefore, metabolic flexibility enables C. auris to optimize a critical trade-off: expressing virulence traits while minimizing immune recognition to colonize host tissues. Candida auris colonizes metabolically diverse host niches and modulates immunity to its advantage. This study shows that carbon source availability regulates C. auris adhesion and cell morphology, thereby controlling immune activation.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2448-2463"},"PeriodicalIF":18.7,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02454-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813619","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}

引用次数: 0

Colibactin produced by a honeybee gut symbiont mediates pathogen defence 由蜜蜂肠道共生体产生的大肠杆菌蛋白介导病原体防御。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-24 DOI: 10.1038/s41564-026-02438-9

Yulin Song, J. Elijah Powell, Joel W. H. Wong, Yunxi Liu, Miguel A. Aguilar Ramos, Tyler De Jong, Patrick J. Lariviere, Jayaditya Maganti, Emily P. Balskus, Nancy A. Moran

{"title":"Colibactin produced by a honeybee gut symbiont mediates pathogen defence","authors":"Yulin Song, J. Elijah Powell, Joel W. H. Wong, Yunxi Liu, Miguel A. Aguilar Ramos, Tyler De Jong, Patrick J. Lariviere, Jayaditya Maganti, Emily P. Balskus, Nancy A. Moran","doi":"10.1038/s41564-026-02438-9","DOIUrl":"10.1038/s41564-026-02438-9","url":null,"abstract":"Colibactin is a bacterial genotoxin that damages DNA and is linked to colorectal cancer. It is implicated in interbacterial competition but its role in natural microbiomes is unclear. Here we show that Frischella perrara, a colibactin-producing symbiont restricted to honeybee guts, lowers bee lifespan but increases survivorship following challenge with the opportunistic bee pathogen Serratia marcescens. F. perrara mutants lacking colibactin production fail to improve survivorship following challenge. The symbiont reduces pathogen loads by causing colibactin-dependent DNA damage and prophage induction. Colibactin is toxic to the pathogen under anoxic conditions, reflecting the bee gut. clbS, a gene conferring protection from colibactin, is ubiquitous among bacteria restricted to bee guts but absent from opportunistic colonizers, including pathogens. Indeed, F. perrara colonization representing colibactin pressure had limited impact on the bee gut microbiome where strains encode clbS. Our findings suggest that colibactin functions in interbacterial competition and protects against pathogens while permitting co-evolved symbionts to persist. A colibactin-producing symbiont in honeybee guts defends against opportunistic pathogens and confers protection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2408-2422"},"PeriodicalIF":18.7,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813575","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

Obligate cross-feeding of metabolites is common in soil microbial communities 代谢物的专性交叉取食在土壤微生物群落中很常见。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-24 DOI: 10.1038/s41564-026-02457-6

Ghada Yousif, Francisco Zorrilla, Swagatika Dash, Leonardo Oña, Aditi Shekhar, Samir Giri, Rui Guan, Sharvari Harshe, Michael Itermann, Daphne Welter, Vladimir Benes, Kiran R. Patil, Christian Kost

{"title":"Obligate cross-feeding of metabolites is common in soil microbial communities","authors":"Ghada Yousif, Francisco Zorrilla, Swagatika Dash, Leonardo Oña, Aditi Shekhar, Samir Giri, Rui Guan, Sharvari Harshe, Michael Itermann, Daphne Welter, Vladimir Benes, Kiran R. Patil, Christian Kost","doi":"10.1038/s41564-026-02457-6","DOIUrl":"10.1038/s41564-026-02457-6","url":null,"abstract":"Ecological theory predicts that obligate cross-feeding of metabolites is common in microbial communities. However, systematic studies testing this prediction in natural microbial communities such as soil are missing, thus hindering the understanding of these ecologically important ecosystems. Here we address this gap by analysing 6,931 bacterial isolates from 27 soil microbial communities sampled in Germany. We find that the growth of up to 50% of community members depended on supplementation with amino acids, vitamins or nucleobases. For 73% of isolates, supplementation with multiple amino acids was necessary. Genomic analysis of 62 strains revealed that accumulation of insertion sequences and gene loss was associated with the observed auxotrophic phenotypes. Genome-scale metabolic models, computational analyses and cocultivation experiments suggest other co-occurring genotypes complement the metabolic needs of auxotrophs, thus enabling their growth and survival. Together, our results indicate that soil bacteria probably exist within integrated metabolic networks rather than as metabolically autonomous units. Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecological metabolic networks.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2436-2447"},"PeriodicalIF":18.7,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813656","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