Nature Microbiology最新文献

A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems 一种广泛存在的噬菌体编码激酶能够躲避多种宿主抗噬菌体防御系统的攻击

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-06 DOI: 10.1038/s41564-024-01851-2

Susu Jiang, Chao Chen, Wanqiu Huang, Yue He, Xuan Du, Yi Wang, Hongda Ou, Zixin Deng, Congrui Xu, Lixu Jiang, Lianrong Wang, Shi Chen

{"title":"A widespread phage-encoded kinase enables evasion of multiple host antiphage defence systems","authors":"Susu Jiang, Chao Chen, Wanqiu Huang, Yue He, Xuan Du, Yi Wang, Hongda Ou, Zixin Deng, Congrui Xu, Lixu Jiang, Lianrong Wang, Shi Chen","doi":"10.1038/s41564-024-01851-2","DOIUrl":"https://doi.org/10.1038/s41564-024-01851-2","url":null,"abstract":"DNA degradation (Dnd) is a widespread bacterial antiphage defence system that relies on DNA phosphorothioate (PT) modification for self/non-self discrimination and subsequent degradation of unmodified DNA. Phages employ counterstrategies to evade host immunity, but anti-Dnd immunity has not been characterized. Here we report an immune evasion protein encoded by the Salmonella phage JSS1 that contributes to subverting Dnd and other defence systems. Using quantitative proteomic and phosphoproteomic analyses, we show that the protein JSS1_004 employs N-terminal Ser/Thr/Tyr protein kinase activity to catalyse the multisite phosphorylation of host DndFGH. Notably, JSS1_004 also phosphorylates other bacterial immune systems to varying degrees, including CRISPR‒Cas, QatABCD, SIR2+HerA and DUF4297+HerA. Given that JSS1_004 and its homologues are widespread in phylogenetically diverse phages, we suggest that this strategy constitutes a family of immune evasion proteins that increases the chances of phage proliferation even when a host deploys multiple defence systems.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":28.3,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588686","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

Submicrometre spatiotemporal characterization of the Toxoplasma adhesion strategy for gliding motility 弓形虫滑行运动粘附策略的亚微米级时空特性分析

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-04 DOI: 10.1038/s41564-024-01818-3

Luis Vigetti, Bastien Touquet, Delphine Debarre, Thierry Rose, Lionel Bureau, Dima Abdallah, Galina V. Dubacheva, Isabelle Tardieux

{"title":"Submicrometre spatiotemporal characterization of the Toxoplasma adhesion strategy for gliding motility","authors":"Luis Vigetti, Bastien Touquet, Delphine Debarre, Thierry Rose, Lionel Bureau, Dima Abdallah, Galina V. Dubacheva, Isabelle Tardieux","doi":"10.1038/s41564-024-01818-3","DOIUrl":"https://doi.org/10.1038/s41564-024-01818-3","url":null,"abstract":"Toxoplasma gondii is a protozoan apicomplexan parasite that uses an adhesion-dependent mode of motility termed gliding to access host cells and disseminate into tissues. Previous studies on Apicomplexa motile morphotypes, including the T. gondii tachyzoite, have identified a cortical actin–myosin motor system that drives the rearward translocation of transmembrane adhesins, thus powering forward movement. However, this model is currently questioned. Here, combining micropatterning and tunable surface chemistry (to edit parasite surface ligands) with flow force and live or super-resolution imaging, we show that tachyzoites build only one apical anchoring contact with the substrate, over which it slides. Furthermore, we show that glycosaminoglycan–parasite interactions are sufficient to promote such force-productive contact and find that the apicobasal flow is set up independent of adhesin release and surface interactions. These findings should enable further characterization of the molecular functions at the T. gondii–substrate mechanosensitive interface and their comparison across apicomplexans.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":28.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574466","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

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information 仅利用基因组信息预测整个埃希氏菌属的菌株级噬菌体-宿主相互作用

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-31 DOI: 10.1038/s41564-024-01832-5

Baptiste Gaborieau, Hugo Vaysset, Florian Tesson, Inès Charachon, Nicolas Dib, Juliette Bernier, Tanguy Dequidt, Héloïse Georjon, Olivier Clermont, Pascal Hersen, Laurent Debarbieux, Jean-Damien Ricard, Erick Denamur, Aude Bernheim

{"title":"Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information","authors":"Baptiste Gaborieau, Hugo Vaysset, Florian Tesson, Inès Charachon, Nicolas Dib, Juliette Bernier, Tanguy Dequidt, Héloïse Georjon, Olivier Clermont, Pascal Hersen, Laurent Debarbieux, Jean-Damien Ricard, Erick Denamur, Aude Bernheim","doi":"10.1038/s41564-024-01832-5","DOIUrl":"10.1038/s41564-024-01832-5","url":null,"abstract":"Predicting bacteriophage infection of specific bacterial strains promises advancements in phage therapy and microbial ecology. Whether the dynamics of well-established phage–host model systems generalize to the wide diversity of microbes is currently unknown. Here we show that we could accurately predict the outcomes of phage–bacteria interactions at the strain level in natural isolates from the genus Escherichia using only genomic data (area under the receiver operating characteristic curve (AUROC) of 86%). We experimentally established a dataset of interactions between 403 diverse Escherichia strains and 96 phages. Most interactions are explained by adsorption factors as opposed to antiphage systems which play a marginal role. We trained predictive algorithms and pinpoint poorly predicted interactions to direct future research efforts. Finally, we established a pipeline to recommend tailored phage cocktails, demonstrating efficiency on 100 pathogenic E. coli isolates. This work provides quantitative insights into phage–host specificity and supports the use of predictive algorithms in phage therapy. Phage–host interactions are computationally predicted using only genomic information, highlighting future research directions and enabling generation of custom phage cocktails.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":20.5,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555784","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

Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function SARS-CoV-2 急性后遗症的心血管症状与影响心肌细胞功能的痕量细胞因子有关

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-10-30 DOI: 10.1038/s41564-024-01838-z

Jane E. Sinclair, Courtney Vedelago, Feargal J. Ryan, Meagan Carney, Meredith A. Redd, Miriam A. Lynn, Branka Grubor-Bauk, Yuanzhao Cao, Anjali K. Henders, Keng Yih Chew, Deborah Gilroy, Kim Greaves, Larisa Labzin, Laura Ziser, Katharina Ronacher, Leanne M. Wallace, Yiwen Zhang, Kyle Macauslane, Daniel J. Ellis, Sudha Rao, Lucy Burr, Amanda Bain, Anjana Karawita, Benjamin L. Schulz, Junrong Li, David J. Lynn, Nathan Palpant, Alain Wuethrich, Matt Trau, Kirsty R. Short

{"title":"Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function","authors":"Jane E. Sinclair, Courtney Vedelago, Feargal J. Ryan, Meagan Carney, Meredith A. Redd, Miriam A. Lynn, Branka Grubor-Bauk, Yuanzhao Cao, Anjali K. Henders, Keng Yih Chew, Deborah Gilroy, Kim Greaves, Larisa Labzin, Laura Ziser, Katharina Ronacher, Leanne M. Wallace, Yiwen Zhang, Kyle Macauslane, Daniel J. Ellis, Sudha Rao, Lucy Burr, Amanda Bain, Anjana Karawita, Benjamin L. Schulz, Junrong Li, David J. Lynn, Nathan Palpant, Alain Wuethrich, Matt Trau, Kirsty R. Short","doi":"10.1038/s41564-024-01838-z","DOIUrl":"https://doi.org/10.1038/s41564-024-01838-z","url":null,"abstract":"An estimated 65 million people globally suffer from post-acute sequelae of COVID-19 (PASC), with many experiencing cardiovascular symptoms (PASC-CVS) like chest pain and heart palpitations. This study examines the role of chronic inflammation in PASC-CVS, particularly in individuals with symptoms persisting over a year after infection. Blood samples from three groups—recovered individuals, those with prolonged PASC-CVS and SARS-CoV-2-negative individuals—revealed that those with PASC-CVS had a blood signature linked to inflammation. Trace-level pro-inflammatory cytokines were detected in the plasma from donors with PASC-CVS 18 months post infection using nanotechnology. Importantly, these trace-level cytokines affected the function of primary human cardiomyocytes. Plasma proteomics also demonstrated higher levels of complement and coagulation proteins in the plasma from patients with PASC-CVS. This study highlights chronic inflammation’s role in the symptoms of PASC-CVS.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":28.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536902","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 path to better practices in microbiology 改进微生物学实践的途径

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-30 DOI: 10.1038/s41564-024-01864-x

引用次数: 0

A cross-systems primer for synthetic microbial communities 合成微生物群落的跨系统入门指南

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-30 DOI: 10.1038/s41564-024-01827-2

Elijah C. Mehlferber, Gontran Arnault, Bishnu Joshi, Laila P. Partida-Martinez, Kathryn A. Patras, Marie Simonin, Britt Koskella

{"title":"A cross-systems primer for synthetic microbial communities","authors":"Elijah C. Mehlferber, Gontran Arnault, Bishnu Joshi, Laila P. Partida-Martinez, Kathryn A. Patras, Marie Simonin, Britt Koskella","doi":"10.1038/s41564-024-01827-2","DOIUrl":"10.1038/s41564-024-01827-2","url":null,"abstract":"The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research. Here the authors outline best practices for the development, implementation and evaluation of synthetic microbial communities (or SynComs) across different systems.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":20.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541486","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

Community standards and future opportunities for synthetic communities in plant–microbiota research 植物微生物群落研究中的群落标准和合成群落的未来机遇

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-30 DOI: 10.1038/s41564-024-01833-4

Trent R. Northen, Manuel Kleiner, Marta Torres, Ákos T. Kovács, Mette Haubjerg Nicolaisen, Dorota M. Krzyżanowska, Shilpi Sharma, George Lund, Lars Jelsbak, Oliver Baars, Nikolaj Lunding Kindtler, Kathrin Wippel, Caja Dinesen, Jessica A. Ferrarezi, Malek Marian, Adele Pioppi, Xinming Xu, Tonni Andersen, Niko Geldner, Paul Schulze-Lefert, Julia A. Vorholt, Ruben Garrido-Oter

{"title":"Community standards and future opportunities for synthetic communities in plant–microbiota research","authors":"Trent R. Northen, Manuel Kleiner, Marta Torres, Ákos T. Kovács, Mette Haubjerg Nicolaisen, Dorota M. Krzyżanowska, Shilpi Sharma, George Lund, Lars Jelsbak, Oliver Baars, Nikolaj Lunding Kindtler, Kathrin Wippel, Caja Dinesen, Jessica A. Ferrarezi, Malek Marian, Adele Pioppi, Xinming Xu, Tonni Andersen, Niko Geldner, Paul Schulze-Lefert, Julia A. Vorholt, Ruben Garrido-Oter","doi":"10.1038/s41564-024-01833-4","DOIUrl":"10.1038/s41564-024-01833-4","url":null,"abstract":"Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research. To address this gap, we recommend three actions: (1) defining reference SynComs; (2) establishing community standards, protocols and benchmark data for constructing and using SynComs; and (3) creating an infrastructure for sharing strains and data. We also outline opportunities to develop SynCom research through technical advances, linking to field studies, and filling taxonomic blind spots to move towards fully representative SynComs. Here the authors discuss the use of synthetic communities, or SynComs, in plant–microbiome research and propose steps to develop community standards that will support future research.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":20.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541482","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

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome 从饮食和肠道微生物组的角度设计和报告益生菌和益生菌临床试验

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-30 DOI: 10.1038/s41564-024-01831-6

Kevin Whelan, Margaret Alexander, Claire Gaiani, Genelle Lunken, Andrew Holmes, Heidi M. Staudacher, Stephan Theis, Maria L. Marco

{"title":"Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome","authors":"Kevin Whelan, Margaret Alexander, Claire Gaiani, Genelle Lunken, Andrew Holmes, Heidi M. Staudacher, Stephan Theis, Maria L. Marco","doi":"10.1038/s41564-024-01831-6","DOIUrl":"10.1038/s41564-024-01831-6","url":null,"abstract":"Diet is a major determinant of the gastrointestinal microbiome composition and function, yet our understanding of how it impacts the efficacy of prebiotics and probiotics is limited. Here we examine current evidence of dietary influence on prebiotic and probiotic efficacy in human studies, including potential mechanisms. We propose that habitual diet be included as a variable in prebiotic and probiotic intervention studies. This recommendation is based on the potential mechanisms via which diet can affect study outcomes, either directly or through the gut microbiome. We consider the challenges and opportunities of dietary assessment in this context. Lastly, we provide recommendations for the design, conduct and reporting of human clinical trials of prebiotics and probiotics (and other biotic interventions) to account for any effect of diet and nutrition. Here the authors make recommendations for the design of clinical trials for prebiotics and probiotics that includes consideration of diet and the gut microbiome.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":20.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541483","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

Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris 附带敏感性抵消了白色念珠菌抗真菌药物耐药性的演变

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-29 DOI: 10.1038/s41564-024-01811-w

Hans Carolus, Dimitrios Sofras, Giorgio Boccarella, Stef Jacobs, Vladislav Biriukov, Louise Goossens, Alicia Chen, Ina Vantyghem, Tibo Verbeeck, Siebe Pierson, Celia Lobo Romero, Hans Steenackers, Katrien Lagrou, Pieter van den Berg, Judith Berman, Toni Gabaldón, Patrick Van Dijck

{"title":"Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris","authors":"Hans Carolus, Dimitrios Sofras, Giorgio Boccarella, Stef Jacobs, Vladislav Biriukov, Louise Goossens, Alicia Chen, Ina Vantyghem, Tibo Verbeeck, Siebe Pierson, Celia Lobo Romero, Hans Steenackers, Katrien Lagrou, Pieter van den Berg, Judith Berman, Toni Gabaldón, Patrick Van Dijck","doi":"10.1038/s41564-024-01811-w","DOIUrl":"10.1038/s41564-024-01811-w","url":null,"abstract":"Antifungal drug resistance represents a serious global health threat, necessitating new treatment strategies. Here we investigated collateral sensitivity (CS), in which resistance to one drug increases sensitivity to another, and cross-resistance (XR), in which one drug resistance mechanism reduces susceptibility to multiple drugs, since CS and XR dynamics can guide treatment design to impede resistance development, but have not been systematically explored in pathogenic fungi. We used experimental evolution and mathematical modelling of Candida auris population dynamics during cyclic and combined drug exposures and found that especially CS-based drug cycling can effectively prevent the emergence of drug resistance. In addition, we found that a CS-based treatment switch can actively select against or eradicate resistant sub-populations, highlighting the potential to consider CS in therapeutic decision-making upon resistance detection. Furthermore, we show that some CS trends are robust among different strains and resistance mechanisms. Overall, these findings provide a promising direction for improved antifungal treatment approaches. Collateral-sensitivity-based drug cycling effectively prevents and impedes the evolution of antifungal drug resistance in Candida auris.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":null,"pages":null},"PeriodicalIF":20.5,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520171","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

Persistent viral RNA and protein contribute to post-acute pathology 持续存在的病毒 RNA 和蛋白质导致了急性期后的病理变化

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-10-28 DOI: 10.1038/s41564-024-01837-0

Keng Yih Chew, Kirsty R. Short

引用次数: 0