Yiheng Hu, Johanna Bode, Daniel Gómez-Pérez, Marco Alexandre Guerreiro, Alfredo Mari, Kun Wang, Sinja Niemann, Maryam Mahmoudi, Ariane Kemen, Paloma Duran, Oskar Wacker, Daniel Straub, Sven Nahnsen, Benjamin Schwessinger, Fabrice Roux, Carlos Alonso-Blanco, Jon Ågren, Stéphane Hacquard, Eva H. Stukenbrock, Eric Kemen
{"title":"Thiamine cross-feeding drives microbial coexistence in the leaf microbiome","authors":"Yiheng Hu, Johanna Bode, Daniel Gómez-Pérez, Marco Alexandre Guerreiro, Alfredo Mari, Kun Wang, Sinja Niemann, Maryam Mahmoudi, Ariane Kemen, Paloma Duran, Oskar Wacker, Daniel Straub, Sven Nahnsen, Benjamin Schwessinger, Fabrice Roux, Carlos Alonso-Blanco, Jon Ågren, Stéphane Hacquard, Eva H. Stukenbrock, Eric Kemen","doi":"10.1038/s41564-026-02499-w","DOIUrl":"https://doi.org/10.1038/s41564-026-02499-w","url":null,"abstract":"Microbiome homeostasis is crucial for host health and ecosystem function, yet the molecular and ecological mechanisms underlying community assembly and stability remain elusive. Here we uncover a conserved yeast–oomycete association that promotes their coexistence in the leaf microbiome. Using a continental-scale microbiome survey, we identified an asymmetric mutualistic interaction between two eukaryotic hub microbes: the yeast Dioszegia hungarica and the obligate oomycete Albugo laibachii. We show that Dioszegia facilitates Albugo colonization by supplying thiamine via a dedicated membrane permease, alleviating Albugo’s auxotrophy. Genomic and transcriptomic analyses indicate that natural selection has acted on thiamine production in Dioszegia, shaping this metabolic complementation. In planta assays further suggest that Albugo presence supports Dioszegia persistence under glasshouse conditions. Our study illustrates how the evolution of nutrient cross-feeding mediates microbial coexistence and microbiome stability. Targeting microbial nutrient flows offers new strategies for engineering microbiomes and enhancing plant resilience in natural and agricultural systems.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087883","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}
Marta Mendonça Cova, Lucas Morley, Marjorie Maynadier, Jason Delabre, Arnault Graindorge, Laurence Berry-Sterkers, Shrawan Kumar Mageswaran, Valérie Rofidal, Cameron J. Powell, Martin J. Boulanger, Yi-Wei Chang, Daniela Sparvoli, Maryse Lebrun
{"title":"A conserved GTPase complex gates exocytosis for defence and parasitism across alveolates","authors":"Marta Mendonça Cova, Lucas Morley, Marjorie Maynadier, Jason Delabre, Arnault Graindorge, Laurence Berry-Sterkers, Shrawan Kumar Mageswaran, Valérie Rofidal, Cameron J. Powell, Martin J. Boulanger, Yi-Wei Chang, Daniela Sparvoli, Maryse Lebrun","doi":"10.1038/s41564-026-02501-5","DOIUrl":"https://doi.org/10.1038/s41564-026-02501-5","url":null,"abstract":"Regulated protein secretion is a fundamental process by which eukaryotic cells respond to and interact with their dynamic environments, yet its mechanism outside metazoans remains largely unknown. Here we uncover an atypical small GTPase complex (Nd-GTPase–Nd9–NdP1) conserved across the Alveolata—a major eukaryotic clade encompassing ciliates and apicomplexan parasites—that gates organelle exocytosis for diverse functions ranging from cellular defence to host invasion. Using Tetrahymena thermophila and Toxoplasma gondii as comparative models, we combine functional genetics, cryo-electron tomography and integrative structural modelling to show that this complex maintains the organelle secretory apparatus in a pre-secretion state and permits activation upon stimulation. Comparative analysis further reveals that apicomplexan parasites rely on an apical vesicle to tighten control over secretion. These findings define a unifying principle of gated alveolate exocytosis, illustrating how evolution remodels an ancient secretion system to meet specialized cellular demands, and underlie key mechanisms of parasite virulence.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"476 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087659","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}
Caroline Tawk, Youssef El Mouali, Kun D. Huang, Sebastiaan Valkiers, Vitor Heidrich, Achim Gronow, Lisa Osbelt, Johanna Rapp, Hannes Link, Nicola Segata, Athanasios Typas, Till Strowig
{"title":"Synergy between Enterobacteriaceae and diet mediates competition between dominant Bacteroidales in the human gut","authors":"Caroline Tawk, Youssef El Mouali, Kun D. Huang, Sebastiaan Valkiers, Vitor Heidrich, Achim Gronow, Lisa Osbelt, Johanna Rapp, Hannes Link, Nicola Segata, Athanasios Typas, Till Strowig","doi":"10.1038/s41564-026-02500-6","DOIUrl":"https://doi.org/10.1038/s41564-026-02500-6","url":null,"abstract":"Healthy human gut microbiota is dominated by Bacteroidaceae in industrialized populations and by Prevotellaceae in those with traditional lifestyles, but diet alone is insufficient to explain this dominance of different Bacteroidota. Here we screened 94 dietary components in synthetic gut communities and find that these two bacterial families compete for overlapping nutritional niches. Segatella copri, a key member of Prevotellaceae-rich communities, outcompeted Bacteroidaceae when preferred polysaccharides such as arabinan were available, but this advantage depended on community composition, particularly the presence of Enterobacteriaceae. Metatranscriptomics and targeted metabolomics further revealed that Enterobacteriaceae synergized with dietary components to promote Segatella dominance in human and mouse gut communities. These interactions were validated by using multiple E. coli and Segatella isolates. Analyses of global metagenomes also showed a positive correlation between Segatella-rich non-industrialized microbiomes and Enterobacteriaceae abundance. Our results establish an ecosystem-level dynamic interplay between dietary components and key gut commensals that favour the dominance of Prevotellaceae.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"32 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087631","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}
Yue Zhang, Ying Zhao, Lu Zhang, Baoqin Xuan, Zhenyu Wang, Bin Yu, Weixun Li, Xiaowen Huang, Yilu Zhou, Lijun Ning, Jinmei Ding, Yi Jiang, Muni Hu, Yuqi Shao, Lingxi Li, Xiang Gao, Shengliang Chen, Haoyan Chen, Fei Wang, Zhe Cui, Jing-Yuan Fang, Jie Hong
{"title":"Fusobacterium nucleatum enhances enterotoxigenic Bacteroides fragilis-mediated neuron loss and intestinal motility dysfunction","authors":"Yue Zhang, Ying Zhao, Lu Zhang, Baoqin Xuan, Zhenyu Wang, Bin Yu, Weixun Li, Xiaowen Huang, Yilu Zhou, Lijun Ning, Jinmei Ding, Yi Jiang, Muni Hu, Yuqi Shao, Lingxi Li, Xiang Gao, Shengliang Chen, Haoyan Chen, Fei Wang, Zhe Cui, Jing-Yuan Fang, Jie Hong","doi":"10.1038/s41564-026-02497-y","DOIUrl":"https://doi.org/10.1038/s41564-026-02497-y","url":null,"abstract":"Gut dysmotility is a common long-term effect of enterotoxigenic Bacteroides fragilis (ETBF) colonization but the underlying mechanisms are not clear. Here, using mouse colonization models, we found that ETBF-secreted B. fragilis toxin (BFT) causes loss of colonic myenteric neurons, which are crucial regulators of intestinal motility. BFT induced apoptosis in these neurons through the NOD1–RIPK2–CASP9–CASP3 pathway, leading to gut dysmotility that persisted even after the clearance of ETBF. Analyses of human inflammatory bowel disease and colorectal cancer patient cohorts showed a positive correlation between ETBF and Fusobacterium nucleatum abundance. In mice, F. nucleatum-derived 2-hydroxybutyric acid enhanced BFT production in ETBF by alleviating RprY-mediated suppression and aggravated neurotoxicity and dysmotility. This enteric neuron loss and dysmotility enhanced susceptibility to dextran sulfate sodium-induced colitis in mice. Therapeutically, a Bifidobacterium-based probiotic attenuated neuron toxicity and improved intestinal motility. Our findings reveal bacterial interactions regulating intestinal function and a potential clinical therapeutic approach to preventing outcomes of ETBF colonization.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"8 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087884","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}
Ram-Sevak Raja-Kumar, Fantin Mesny, Arpan Kumar Basak, Jacy Newfeld, Guillaume Chesneau, Frederickson Entila, Tak Lee, Linda Rigerte, Stephanie Carvajal Acevedo, Bruno Hüttel, Pedro W. Crous, Jose G. Maciá-Vicente, Helen Stewart, Matthew Ryan, Ahmad M. Fakhoury, Soledad Sacristán, Meriem Aitouguinane, Isabelle Batisson, Stefano Dumontet, Wade H. Elmer, Jana Henzelyová, Joanna S. Kruszewska, Jessica M. Nelson, Cara M. Santelli, Markus Pauly, Antonio Molina, Kei Hiruma, Stéphane Hacquard
{"title":"Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts","authors":"Ram-Sevak Raja-Kumar, Fantin Mesny, Arpan Kumar Basak, Jacy Newfeld, Guillaume Chesneau, Frederickson Entila, Tak Lee, Linda Rigerte, Stephanie Carvajal Acevedo, Bruno Hüttel, Pedro W. Crous, Jose G. Maciá-Vicente, Helen Stewart, Matthew Ryan, Ahmad M. Fakhoury, Soledad Sacristán, Meriem Aitouguinane, Isabelle Batisson, Stefano Dumontet, Wade H. Elmer, Jana Henzelyová, Joanna S. Kruszewska, Jessica M. Nelson, Cara M. Santelli, Markus Pauly, Antonio Molina, Kei Hiruma, Stéphane Hacquard","doi":"10.1038/s41564-026-02492-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02492-3","url":null,"abstract":"The root microbiome includes fungal pathogens capable of colonizing multiple plant hosts, yet the underlying genetic determinants remain unknown. Here we report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota, which displays pathogenic potential across multiple hosts. Using a collection of 72 Plectosphaerella isolates and whole-genome sequencing, we observed subtle phenotypic and genotypic variation associated with fungal phylogeny but not host plant identity. Transcriptome profiling of a P. cucumerina isolate in roots of diverse plants revealed core and host-specific fungal responses, including induction of carbohydrate-active enzymes (CAZymes) involved in root cell wall deconstruction. A fungal gene encoding a candidate β-1,3-glucanase (GH64) was identified as a key genetic factor driving multihost infection. This gene is present across plant-colonizing fungi and functions as a disease determinant in both P. cucumerina and a Colletotrichum root pathogen. Our results indicate that host-induced CAZymes can couple fungal virulence with multihost compatibility.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"1 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087809","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":"Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency","authors":"Jingjing Chang, Dianwen Wang, Zongmu Yao, Yingnan Pang, Hengfei Zhang, Changji Wang, Yuanbo Xie, Yu Sun, Jianfeng Zhang, Weiqiang Li, Aizhen Liang, Xiangnan Li, Dazhou Chen, Hongping Chen, Xuewen Chen, Enze Wang, Lam-Son Phan Tran, Jilin Wang, Jos M. Raaijmakers, Chunjie Tian, Eiko E. Kuramae","doi":"10.1038/s41564-026-02498-x","DOIUrl":"https://doi.org/10.1038/s41564-026-02498-x","url":null,"abstract":"Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"58 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087635","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}
Ana Rodrigues, António M. Mendes, Rute Gonçalves, Helena Nunes-Cabaço, Sofia Marques, Nuno Valente-Leal, Daniel Gomes da Costa, Cristina Ferreira, Marc Veldhoen, Miguel Prudêncio, Maria M. Mota, Ângelo Ferreira Chora
{"title":"Host cell traversal by Plasmodium parasites drives sterilizing T cell-mediated immunity following immunization","authors":"Ana Rodrigues, António M. Mendes, Rute Gonçalves, Helena Nunes-Cabaço, Sofia Marques, Nuno Valente-Leal, Daniel Gomes da Costa, Cristina Ferreira, Marc Veldhoen, Miguel Prudêncio, Maria M. Mota, Ângelo Ferreira Chora","doi":"10.1038/s41564-026-02477-2","DOIUrl":"https://doi.org/10.1038/s41564-026-02477-2","url":null,"abstract":"The development of a vaccine capable of conferring sterile protection against Plasmodium, the causative agent of malaria, is a major priority for global eradication efforts. Whole-organism vaccines using liver-infective sporozoites provide high levels of sterile protection against pre-erythrocytic infection. Yet, determinants of sporozoite immunogenicity remain poorly characterized. Here we demonstrate, using rodent models of vaccination, that the ability of Plasmodium sporozoites to actively migrate through multiple host cells before infecting hepatocytes is required for sterilizing immunity, regardless of the extent of intrahepatic development of immunizing parasites. We further establish host cell traversal as a dominant contributor to the induction of sterile protection. Impaired cell traversal precludes protective liver-resident memory CD8 T cell responses following vaccination but not the production of antiplasmodial antibodies. Our findings show that intrahepatic parasite development alone does not fully account for the magnitude and durability of protection induced by whole-sporozoite vaccination, and highlight parasite behaviour traits as critical immunogenic events shaping sterilizing cellular immunity against Plasmodium liver stages.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"31 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087665","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}
Rachel Colquhoun, Angie S. Hinrichs, Verity Hill, Christopher Ruis, Cornelius Roemer, Oliver G. Pybus, Andrew Rambaut, Áine O’Toole
{"title":"A generalized lineage nomenclature for viral genomic epidemiology","authors":"Rachel Colquhoun, Angie S. Hinrichs, Verity Hill, Christopher Ruis, Cornelius Roemer, Oliver G. Pybus, Andrew Rambaut, Áine O’Toole","doi":"10.1038/s41564-026-02468-3","DOIUrl":"10.1038/s41564-026-02468-3","url":null,"abstract":"Pathogen genomics has become increasingly integrated into outbreak response, with recent virus epidemics better characterized by large numbers of viral genetic sequences. Effective international communication of viral diversity requires a scalable, adaptable nomenclature, and existing systems may not accommodate rapid sequence generation. The Pango lineage nomenclature system was designed to address these problems and has been applied to SARS-CoV-2 since early 2020. Here we generalize the underlying principles into a framework for virus surveillance. Lineages are defined as epidemiologically meaningful clusters on a phylogenetic tree, initiated from founding lineages and expanded across a phylogeny through a hierarchical system of alphanumeric sublineage names. Six years on from the inception of the Pango system, we discuss challenges and considerations for implementation. We present a Pango lineage framework for chikungunya virus, providing an alternative to the geography-based clade system and designating 21 lineages across 8 founding lineages. This generalization provides a foundation for future genomic surveillance of many viruses, including for emerging outbreaks and the surveillance of endemic pathogens. This study extends the Pango lineage nomenclature system beyond SARS-CoV-2, introducing a dynamic framework for tracking and communicating viral diversity, demonstrated through its application to CHIKV.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2901-2910"},"PeriodicalIF":18.7,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02468-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087661","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}
Kai G. Pohl, Xin Gao, Jason McGowan, Parnika Mukherjee, Shirley Le, Patricia Carreira, Chinh Ngo, Henry J. Sutton, Sophia Brumhard, Anna Hiller, Hannah G. Kelly, Larissa Liow, Adrian Lo, Larissa Henze, Lucie Loyal, Rogerio Amino, Si Ming Man, Lynette Beattie, Leif Erik Sander, Ian A. Cockburn
{"title":"Innate immune sensing of Plasmodium sporozoite cell traversal drives protective T cell responses","authors":"Kai G. Pohl, Xin Gao, Jason McGowan, Parnika Mukherjee, Shirley Le, Patricia Carreira, Chinh Ngo, Henry J. Sutton, Sophia Brumhard, Anna Hiller, Hannah G. Kelly, Larissa Liow, Adrian Lo, Larissa Henze, Lucie Loyal, Rogerio Amino, Si Ming Man, Lynette Beattie, Leif Erik Sander, Ian A. Cockburn","doi":"10.1038/s41564-026-02460-x","DOIUrl":"https://doi.org/10.1038/s41564-026-02460-x","url":null,"abstract":"Attenuated Plasmodium sporozoites (SPZs) are being tested as a potential malaria vaccine as they elicit robust adaptive immune responses that protect against parasite challenge. Yet how they engage the innate immune system remains poorly understood. Here we isolated pure GFP+ Plasmodium berghei and Plasmodium falciparum SPZs, and sorted them onto mouse bone marrow-derived macrophages or human peripheral blood mononuclear cells to assess innate immune activation using bulk and single-cell RNA sequencing. SPZs induced a distinctive activation pattern in vitro resembling cell wounding responses, consistent with their ability to traverse host cells en route to the liver. Cell traversal-deficient SPZs failed to activate bone marrow-derived macrophages and showed impaired priming of protective CD8+ T cell immunity in vivo. The cell wounding response was independent of inflammasome or Toll-like receptor signalling but required γδ T cells, which are known to support CD8+ T cell responses against Plasmodium. This reveals an innate sensing mechanism triggered by parasite cell traversal that underpins the potent immunogenicity of Plasmodium SPZs.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"1 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149087633","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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