Nature Microbiology最新文献_第7页

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

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 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

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

Quinone-transporting filaments expand bioenergetic capacity in Gram-positive Bacillota 在革兰氏阳性杆菌中，醌转运丝扩大了生物能量容量

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-17 DOI: 10.1038/s41564-026-02450-z

Ashleigh Kropp, Kazem Asadollahi, Jamie A. Stapleton, Luka Simsive, Pok Man Leung, Rachel L. Darnell, Christopher K. Barlow, Benjamin G. Hartmann, Nicholas D. J. Yates, Tasha Lumbantobing, Daniel R. Fox, Chris Greening, Oleksii Zdorevskyi, Vivek Sharma, James N. Blaza, Alison Parkin, Rhys Grinter

{"title":"Quinone-transporting filaments expand bioenergetic capacity in Gram-positive Bacillota","authors":"Ashleigh Kropp, Kazem Asadollahi, Jamie A. Stapleton, Luka Simsive, Pok Man Leung, Rachel L. Darnell, Christopher K. Barlow, Benjamin G. Hartmann, Nicholas D. J. Yates, Tasha Lumbantobing, Daniel R. Fox, Chris Greening, Oleksii Zdorevskyi, Vivek Sharma, James N. Blaza, Alison Parkin, Rhys Grinter","doi":"10.1038/s41564-026-02450-z","DOIUrl":"10.1038/s41564-026-02450-z","url":null,"abstract":"Cellular respiration depends on transferring electrons to hydrophobic quinones in membrane bilayers, meaning bioenergetic capacity is constrained by available membrane surface area. While Gram-negative bacteria expand this capacity through internal membrane invaginations and eukaryotes use membrane-bound organelles, whether Gram-positive bacteria have alternative capacity-generating mechanisms is unknown. Here we show that Bacillus subtilis forms a quinone-transporting pseudomembrane composed of filaments of the NADH dehydrogenase Ndh and the quinone-transporting protein Ncp. Cryo-EM, lipidomics and molecular dynamics reveal that Ndh and Ncp co-assemble with lipids into a 4:4 stoichiometric complex with a solvent-excluded hydrophobic lumen containing phospholipids, which sequesters quinones. These complexes further assemble into filaments, linking chambers into a continuous conduit that amplifies quinone reduction. Phylogenetic analysis suggests that this capacity is widespread in Bacillota. Quinone-transporting filaments thus reveal a strategy to expand the quinone pool and bioenergetic capacity while occupying minimal membrane space. Bacillus subtilis Ncp and NADH dehydrogenase form tube-like filaments with phospholipid-lined chambers that associate with quinones, which can expand bioenergetic capacity and support respiratory electron transfer.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2543-2561"},"PeriodicalIF":18.7,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02450-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148769134","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

Global microbial DNA signatures of temperature and nutrient limitation across ecosystems 整个生态系统温度和营养限制的全球微生物DNA特征

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-14 DOI: 10.1038/s41564-026-02451-y

Tomer Antman, Ohad Lewin-Epstein, Tamir Yerushalmi, Yonatan S. Broder, David Zeevi

{"title":"Global microbial DNA signatures of temperature and nutrient limitation across ecosystems","authors":"Tomer Antman, Ohad Lewin-Epstein, Tamir Yerushalmi, Yonatan S. Broder, David Zeevi","doi":"10.1038/s41564-026-02451-y","DOIUrl":"10.1038/s41564-026-02451-y","url":null,"abstract":"Microbial genomes continuously adapt to environmental conditions, but identifying universal signatures of adaptation remains challenging. Here we show that environmental temperature can be accurately predicted across ecosystems from DNA composition alone (R2 = 0.75), using tetranucleotide frequencies from 1,235 marine and soil metagenomes and a machine learning approach. This predictive signal was also apparent within individual taxa, consistent with a fundamental temperature-associated signature. By contrast, GC content exhibited opposite correlations with temperature in soil (positive) and marine (negative) environments. This phenomenon was probably driven by differences in nutrient availability, as GC content increases with nutrients while nutrients decrease with temperature in marine samples. By integrating these observations, we identified specific tetranucleotides, with 50% GC, that displayed consistent and robust temperature correlations across environments and may have contributed to the stability of predictions. This work highlights metagenome-wide DNA–temperature associations, relevant for understanding microbial community responses to global changes. Machine learning on tetranucleotide frequencies from marine and soil metagenomes shows how environmental conditions imprint on the genome, which could be used to understand microbial community responses to global changes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2794-2804"},"PeriodicalIF":18.7,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148728905","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

Genomic catalogue of giant viruses reveals expanded diversity and functional potential 巨型病毒的基因组目录揭示了扩大的多样性和功能潜力

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-13 DOI: 10.1038/s41564-026-02435-y

Yumary M. Vasquez, Tiago Nardi, Gbocho Masato Terasaki, Petra Byl, Tomáš Brůna, Juan C. Villada, Miguel F. Romero-Gutiérrez, Thomas Mock, Timothy Y. James, GVMAGs data consortium, Tanja Woyke, Frederik Schulz

{"title":"Genomic catalogue of giant viruses reveals expanded diversity and functional potential","authors":"Yumary M. Vasquez, Tiago Nardi, Gbocho Masato Terasaki, Petra Byl, Tomáš Brůna, Juan C. Villada, Miguel F. Romero-Gutiérrez, Thomas Mock, Timothy Y. James, GVMAGs data consortium, Tanja Woyke, Frederik Schulz","doi":"10.1038/s41564-026-02435-y","DOIUrl":"10.1038/s41564-026-02435-y","url":null,"abstract":"Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus–host interactions and exploring viral evolution. This curated genome-resolved, metagenomic resource expands the known diversity of Nucleocytoviricota and Mirusviricota lineages.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2634-2646"},"PeriodicalIF":18.7,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02435-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148728980","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

Phage-encoded contingency loci enable bet-hedging against host defence mechanisms 噬菌体编码的偶然性基因座能够抵御宿主防御机制

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-13 DOI: 10.1038/s41564-026-02445-w

Jasper B. Gomez, Jeffrey E. Barrick, Christopher M. Waters

{"title":"Phage-encoded contingency loci enable bet-hedging against host defence mechanisms","authors":"Jasper B. Gomez, Jeffrey E. Barrick, Christopher M. Waters","doi":"10.1038/s41564-026-02445-w","DOIUrl":"10.1038/s41564-026-02445-w","url":null,"abstract":"Bacteriophages are the most diverse biological entities on Earth, but the processes influencing the evolution of genomic diversity in phages are poorly understood. Here, we show that phage genomes contain contingency loci, hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage on simple sequence repeats. Contingency loci have been extensively described in bacteria, archaea and eukaryotes, yet are understudied in phages. We use experimental evolution and genome sequencing to demonstrate that contingency loci in E. coli phages T2 and T4 reversibly generate genomic and phenotypic heterogeneity in progeny that allow them to hedge their bets against host defences. We find that simple sequence repeats are widespread in diverse E. coli phages and vary in abundance across genes with different functions. Collectively, our study describes a previously unappreciated facet of phage replication in which mutagenic simple sequence repeats drive genetic diversification and population heterogeneity, allowing phages to exploit hosts despite varying defence mechanisms. Diverse E. coli phage genomes have hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage, generating population heterogeneity that enables host exploitation.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 9","pages":"2515-2524"},"PeriodicalIF":18.7,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148728904","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

Recombitrons enable bacterial genome editing across phyla 重组子可以跨门编辑细菌基因组。

IF 18.7 1区生物学

Nature Microbiology Pub Date : 2026-08-10 DOI: 10.1038/s41564-026-02459-4

Sergio Gutiérrez, Edmar R. Oliveira-Filho

引用次数: 0