Nature Microbiology最新文献_第2页

Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria 来自完整噬菌体感染的 Synechococcus 的代谢物具有吸引海洋异养菌的化学作用

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-15 DOI: 10.1038/s41564-024-01843-2

Richard J. Henshaw, Jonathan Moon, Michael R. Stehnach, Benjamin P. Bowen, Suzanne M. Kosina, Trent R. Northen, Jeffrey S. Guasto, Sheri A. Floge

{"title":"Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria","authors":"Richard J. Henshaw, Jonathan Moon, Michael R. Stehnach, Benjamin P. Bowen, Suzanne M. Kosina, Trent R. Northen, Jeffrey S. Guasto, Sheri A. Floge","doi":"10.1038/s41564-024-01843-2","DOIUrl":"https://doi.org/10.1038/s41564-024-01843-2","url":null,"abstract":"Chemical cues mediate interactions between marine phytoplankton and bacteria, underpinning ecosystem-scale processes including nutrient cycling and carbon fixation. Phage infection alters host metabolism, stimulating the release of chemical cues from intact plankton, but how these dynamics impact ecology and biogeochemistry is poorly understood. Here we determine the impact of phage infection on dissolved metabolite pools from marine cyanobacteria and the subsequent chemotactic response of heterotrophic bacteria using time-resolved metabolomics and microfluidics. Metabolites released from intact, phage-infected Synechococcus elicited strong chemoattraction from Vibrio alginolyticus and Pseudoalteromonas haloplanktis, especially during early infection stages. Sustained bacterial chemotaxis occurred towards live-infected Synechococcus, contrasted by no discernible chemotaxis towards uninfected cyanobacteria. High-throughput microfluidics identified 5′-deoxyadenosine and 5′-methylthioadenosine as key attractants. Our findings establish that, before lysis, phage-infected picophytoplankton release compounds that attract motile heterotrophic bacteria, suggesting a mechanism for resource transfer that might impact carbon and nutrient fluxes across trophic levels.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142637054","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

Single-cell imaging of the Mycobacterium tuberculosis cell cycle reveals linear and heterogenous growth 结核分枝杆菌细胞周期的单细胞成像揭示了线性和异质生长过程

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-15 DOI: 10.1038/s41564-024-01846-z

Eun Seon Chung, Prathitha Kar, Maliwan Kamkaew, Ariel Amir, Bree B. Aldridge

引用次数: 0

Estimates of microbiome heritability across hosts 不同宿主微生物组遗传率的估计值

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-15 DOI: 10.1038/s41564-024-01865-w

Andrew H. Morris, Brendan J. M. Bohannan

引用次数: 0

A method to detect origin of transfer sequences for plasmid conjugation 一种检测质粒共轭转移序列起源的方法

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-13 DOI: 10.1038/s41564-024-01845-0

引用次数: 0

Microbial solutions must be deployed against climate catastrophe 必须采用微生物解决方案应对气候灾难

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-11 DOI: 10.1038/s41564-024-01861-0

Raquel Peixoto, Christian R. Voolstra, Lisa Y. Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A. Amin, Max Häggblom, Ann Gregory, Thulani P. Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T. Lennon, Antonio Ventosa, Patrik M. Bavoil, Virginia Miller, Jack A. Gilbert

引用次数: 0

Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids 扩大可移动质粒中含转移序列起源的多样性

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2024-11-08 DOI: 10.1038/s41564-024-01844-1

Manuel Ares-Arroyo, Amandine Nucci, Eduardo P. C. Rocha

{"title":"Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids","authors":"Manuel Ares-Arroyo, Amandine Nucci, Eduardo P. C. Rocha","doi":"10.1038/s41564-024-01844-1","DOIUrl":"https://doi.org/10.1038/s41564-024-01844-1","url":null,"abstract":"Conjugative plasmids are important drivers of bacterial evolution. Most plasmids lack genes for conjugation and characterized origins of transfer (oriT), which has hampered our understanding of plasmid mobility. Here we used bioinformatic analyses to characterize occurrences of known oriT families across 38,057 plasmids, confirming that most conjugative and mobilizable plasmids lack identifiable oriTs. Recognizable oriT sequences tend to be intergenic, upstream of relaxase genes and specifically associated with relaxase types. We used these criteria to develop a computational method to search for and identify 21 additional families of oriT-containing sequences in plasmids from the pathogens Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. Sequence analyses found 3,072 occurrences of these oriT-containing sequences across 2,976 plasmids, many of which encoded antimicrobial resistance genes. Six candidate oriT-containing sequences were validated experimentally and were shown to facilitate conjugation in E. coli. These findings expand our understanding of plasmid mobility.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"36 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142597656","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 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":"13 1","pages":""},"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":"27 1","pages":""},"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":"9 11","pages":"2847-2861"},"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

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