Nature Microbiology最新文献_第5页

Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation 细菌利用外源性肽聚糖作为危险信号触发生物膜的形成

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-03 DOI: 10.1038/s41564-024-01886-5

Sanika Vaidya, Dibya Saha, Daniel K. H. Rode, Gabriel Torrens, Mads F. Hansen, Praveen K. Singh, Eric Jelli, Kazuki Nosho, Hannah Jeckel, Stephan Göttig, Felipe Cava, Knut Drescher

{"title":"Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation","authors":"Sanika Vaidya, Dibya Saha, Daniel K. H. Rode, Gabriel Torrens, Mads F. Hansen, Praveen K. Singh, Eric Jelli, Kazuki Nosho, Hannah Jeckel, Stephan Göttig, Felipe Cava, Knut Drescher","doi":"10.1038/s41564-024-01886-5","DOIUrl":"10.1038/s41564-024-01886-5","url":null,"abstract":"For any organism, survival is enhanced by the ability to sense and respond to threats in advance. For bacteria, danger sensing among kin cells has been observed, but the presence or impacts of general danger signals are poorly understood. Here we show that different bacterial species use exogenous peptidoglycan fragments, which are released by nearby kin or non-kin cell lysis, as a general danger signal. Using microscopy and gene expression profiling of Vibrio cholerae, we find that even brief signal exposure results in a regulatory response that causes three-dimensional biofilm formation, which protects cells from a broad range of stresses, including bacteriophage predation. A diverse set of species (Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis) also respond to exogenous peptidoglycan by forming biofilms. As peptidoglycan from different Gram-negative and Gram-positive species triggered three-dimensional biofilm formation, we propose that this danger signal and danger response are conserved among bacteria. Peptidoglycan released by neighbouring kin or non-kin cell lysis induces physiological changes that protect from a range of stresses, including phage predation.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"144-157"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01886-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917087","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

Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium tRNA基因表达的适应性缺失导致海洋蓝聚球菌的噬菌体抗性

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-03 DOI: 10.1038/s41564-024-01877-6

Sophia Zborowsky, Ran Tahan, Debbie Lindell

{"title":"Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium","authors":"Sophia Zborowsky, Ran Tahan, Debbie Lindell","doi":"10.1038/s41564-024-01877-6","DOIUrl":"10.1038/s41564-024-01877-6","url":null,"abstract":"Synechococcus is a significant primary producer in the oceans, coexisting with cyanophages, which are important agents of mortality. Bacterial resistance against phage infection is a topic of significant interest, yet little is known for ecologically relevant systems. Here we use exogenous gene expression and gene disruption to investigate mechanisms underlying intracellular resistance of marine Synechococcus WH5701 to the Syn9 cyanophage. The restriction–modification and Gabija defence systems possessed by Synechococcus WH5701 did not contribute to resistance. Instead, resistance was primarily driven by insufficient levels of LeuTAA tRNA, preventing translation of key phage genes in a passive, intracellular mode of resistance. Restoring cellular tRNA expression rendered the cyanobacterium sensitive to infection. We propose an evolutionary scenario whereby changes in cell codon usage, acquisition of tRNAs by the phage and loss of cell and phage tRNA expression resulted in an effective means of resistance, highlighting the dynamic interplay between bacteria and phages in shaping their co-evolutionary trajectories. Depletion of host LeuTAA tRNA levels prevents the translation of key cyanophage genes during infection and represents a passive, intracellular mode of resistance with implications for co-evolution.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"66-76"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01877-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917088","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

Two decades of bacterial ecology and evolution in a freshwater lake 一个淡水湖20年的细菌生态和进化

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-03 DOI: 10.1038/s41564-024-01888-3

Robin R. Rohwer, Mark Kirkpatrick, Sarahi L. Garcia, Matthew Kellom, Katherine D. McMahon, Brett J. Baker

{"title":"Two decades of bacterial ecology and evolution in a freshwater lake","authors":"Robin R. Rohwer, Mark Kirkpatrick, Sarahi L. Garcia, Matthew Kellom, Katherine D. McMahon, Brett J. Baker","doi":"10.1038/s41564-024-01888-3","DOIUrl":"10.1038/s41564-024-01888-3","url":null,"abstract":"Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities. A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response to environmental extremes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"246-257"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917051","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

Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic COVID-19大流行期间SARS-CoV-2尖峰的表型进化

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-03 DOI: 10.1038/s41564-024-01878-5

Wilhelm Furnon, Vanessa M. Cowton, Giuditta De Lorenzo, Richard Orton, Vanessa Herder, Diego Cantoni, Georgios Ilia, Diogo Correa Mendonca, Karen Kerr, Jay Allan, Nicole Upfold, Gavin R. Meehan, Siddharth Bakshi, Udeet Ranjan Das, Sergi Molina Arias, Marion McElwee, Sarah Little, Nicola Logan, Kirsty Kwok, Katherine Smollett, Brian J. Willett, Ana Da Silva Filipe, David L. Robertson, Joe Grove, Arvind H. Patel, Massimo Palmarini

{"title":"Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic","authors":"Wilhelm Furnon, Vanessa M. Cowton, Giuditta De Lorenzo, Richard Orton, Vanessa Herder, Diego Cantoni, Georgios Ilia, Diogo Correa Mendonca, Karen Kerr, Jay Allan, Nicole Upfold, Gavin R. Meehan, Siddharth Bakshi, Udeet Ranjan Das, Sergi Molina Arias, Marion McElwee, Sarah Little, Nicola Logan, Kirsty Kwok, Katherine Smollett, Brian J. Willett, Ana Da Silva Filipe, David L. Robertson, Joe Grove, Arvind H. Patel, Massimo Palmarini","doi":"10.1038/s41564-024-01878-5","DOIUrl":"10.1038/s41564-024-01878-5","url":null,"abstract":"SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform. Here we generated a panel of recombinant viruses carrying different spike proteins from 27 variants circulating between 2020 and 2024 in the same genomic background. We then assessed several of their phenotypic traits both in vitro and in vivo. We found distinct phenotypic trajectories of spike among and between variants circulating before and after the emergence of Omicron variants. Spike of post-Omicron variants maintained enhanced tropism for the nasal epithelium and large airways but displayed, over time, several phenotypic traits typical of the pre-Omicron variants. Hence, spike with phenotypic features of both pre- and post-Omicron variants may continue to emerge in the future. Systematic comparison of SARS-CoV-2 spike proteins from pre- and post-Omicron variants in cell lines, primary respiratory epithelial cells and Syrian hamsters show distinct phenotypic trajectories in replication kinetics, cell tropism, cell-to-cell fusion, spike processing, cell entry routes and virulence.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"77-93"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01878-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917050","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

Gut–liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice 病原体肺炎克雷伯菌的肠-肝易位促进小鼠肝细胞癌

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-02 DOI: 10.1038/s41564-024-01890-9

Xueliang Wang, Yi Fang, Wei Liang, Yuhong Cai, Chi Chun Wong, Junlin Wang, Na Wang, Harry Cheuk-Hay Lau, Ying Jiao, Xingyu Zhou, Liufang Ye, Mengmiao Mo, Tao Yang, Miao Fan, Lei Song, Heming Zhou, Qiang Zhao, Eagle Siu-Hong Chu, Meinong Liang, Weixin Liu, Xin Liu, Shuaiyin Zhang, Haitao Shang, Hong Wei, Xiaoxing Li, Lixia Xu, Bing Liao, Joseph J. Y. Sung, Ming Kuang, Jun Yu

{"title":"Gut–liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice","authors":"Xueliang Wang, Yi Fang, Wei Liang, Yuhong Cai, Chi Chun Wong, Junlin Wang, Na Wang, Harry Cheuk-Hay Lau, Ying Jiao, Xingyu Zhou, Liufang Ye, Mengmiao Mo, Tao Yang, Miao Fan, Lei Song, Heming Zhou, Qiang Zhao, Eagle Siu-Hong Chu, Meinong Liang, Weixin Liu, Xin Liu, Shuaiyin Zhang, Haitao Shang, Hong Wei, Xiaoxing Li, Lixia Xu, Bing Liao, Joseph J. Y. Sung, Ming Kuang, Jun Yu","doi":"10.1038/s41564-024-01890-9","DOIUrl":"10.1038/s41564-024-01890-9","url":null,"abstract":"Hepatocellular carcinoma (HCC) is accompanied by an altered gut microbiota but whether the latter contributes to carcinogenesis is unclear. Here we show that faecal microbiota transplantation (FMT) using stool samples from patients with HCC spontaneously initiate liver inflammation, fibrosis and dysplasia in wild-type mice, and accelerate disease progression in a mouse model of HCC. We find that HCC-FMT results in gut barrier injury and translocation of live bacteria to the liver. Metagenomic analyses and bacterial culture of liver tissues reveal enrichment of the gut pathogen Klebsiella pneumoniae in patients with HCC and mice transplanted with the HCC microbiota. Moreover, K. pneumoniae monocolonization recapitulates the effect of HCC-FMT in promoting liver inflammation and hepatocarcinogenesis. Mechanistically, K. pneumoniae surface protein PBP1B interacts with and activates TLR4 on HCC cells, leading to increased cell proliferation and activation of oncogenic signalling. Targeting gut colonization using K. oxytoca or TLR4 inhibition represses K. pneumoniae-induced HCC progression. These findings indicate a role for an altered gut microbiota in hepatocarcinogenesis. Transfer of faecal microbiota from hepatocellular carcinoma patients to mice promotes carcinogenesis via live gut pathogenic Klebsiella pneumoniae translocating to the liver.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"169-184"},"PeriodicalIF":20.5,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01890-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911428","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

Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons 细菌IS110转座子中古细菌和真核生物RNA引导RNA修饰的进化起源

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-02 DOI: 10.1038/s41564-024-01889-2

Hugo Vaysset, Chance Meers, Jean Cury, Aude Bernheim, Samuel H. Sternberg

引用次数: 0

Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut 宏基因组免疫球蛋白测序揭示了健康人体肠道微生物菌株的IgA包被

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-02 DOI: 10.1038/s41564-024-01887-4

Matthew R. Olm, Sean P. Spencer, Tadashi Takeuchi, Evelyn Lemus Silva, Justin L. Sonnenburg

{"title":"Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut","authors":"Matthew R. Olm, Sean P. Spencer, Tadashi Takeuchi, Evelyn Lemus Silva, Justin L. Sonnenburg","doi":"10.1038/s41564-024-01887-4","DOIUrl":"10.1038/s41564-024-01887-4","url":null,"abstract":"IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host–microbe interactions. Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"112-125"},"PeriodicalIF":20.5,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911425","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

Receptor-binding proteins from animal viruses are broadly compatible with human cell entry factors 来自动物病毒的受体结合蛋白与人类细胞进入因子广泛兼容

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-02 DOI: 10.1038/s41564-024-01879-4

Jérémy Dufloo, Iván Andreu-Moreno, Jorge Moreno-García, Ana Valero-Rello, Rafael Sanjuán

{"title":"Receptor-binding proteins from animal viruses are broadly compatible with human cell entry factors","authors":"Jérémy Dufloo, Iván Andreu-Moreno, Jorge Moreno-García, Ana Valero-Rello, Rafael Sanjuán","doi":"10.1038/s41564-024-01879-4","DOIUrl":"10.1038/s41564-024-01879-4","url":null,"abstract":"Cross-species transmission of animal viruses poses a threat to human health. However, systematic experimental assessments of these risks remain scarce. A critical step in viral infection is cellular internalization mediated by viral receptor-binding proteins (RBPs). Here we constructed viral pseudotypes bearing the RBPs of 102 enveloped RNA viruses and assayed their infectivity across 5,202 RBP–cell combinations. This showed that most of the tested viruses have the potential to enter human cells. Pseudotype infectivity varied widely among the 14 viral families examined and was influenced by RBP characteristics, host of origin and target cell type. Cellular gene expression data revealed that the availability of specific cell-surface receptors is not necessarily the main factor limiting viral entry and that additional host factors must be considered. Altogether, these results suggest weak interspecies barriers in the early stages of infection and advance our understanding of the molecular interactions driving viral zoonosis. Functional systematic pseudotype virus-based analysis of the ability of diverse animal viruses to enter into a panel of well-characterized human cell lines shows a broad compatibility between animal virus receptor-binding proteins and human cell entry factors.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"405-419"},"PeriodicalIF":20.5,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01879-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142911427","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

Potato crop performance is predicted by tuber microbiome 马铃薯块茎微生物组预测马铃薯作物生产性能

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-12-30 DOI: 10.1038/s41564-024-01893-6

引用次数: 0

Seed tuber microbiome can predict growth potential of potato varieties 块茎微生物组可以预测马铃薯品种的生长潜力

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2024-12-27 DOI: 10.1038/s41564-024-01872-x

Yang Song, Elisa Atza, Juan J. Sánchez-Gil, Doretta Akkermans, Ronnie de Jonge, Peter G. H. de Rooij, David Kakembo, Peter A. H. M. Bakker, Corné M. J. Pieterse, Neil V. Budko, Roeland L. Berendsen

{"title":"Seed tuber microbiome can predict growth potential of potato varieties","authors":"Yang Song, Elisa Atza, Juan J. Sánchez-Gil, Doretta Akkermans, Ronnie de Jonge, Peter G. H. de Rooij, David Kakembo, Peter A. H. M. Bakker, Corné M. J. Pieterse, Neil V. Budko, Roeland L. Berendsen","doi":"10.1038/s41564-024-01872-x","DOIUrl":"10.1038/s41564-024-01872-x","url":null,"abstract":"Potato vigour, the growth potential of seed potatoes, is a key agronomic trait that varies significantly across production fields due to factors such as genetic background and environmental conditions. Seed tuber microbiomes are thought to influence plant health and crop performance, yet the precise relationships between microbiome composition and potato vigour remain unclear. Here we conducted microbiome sequencing on seed tuber eyes and heel ends from 6 potato varieties grown in 240 fields. By using time-resolved drone imaging of three trial fields in the next season to track crop development, we were able to link microbiome composition with potato vigour. We used microbiome data at varying taxonomic resolutions to build random forest predictive models and found that amplicon sequence variants provided the highest predictive accuracy for potato vigour. The model revealed variety-specific relationships between the seed tuber microbiome and next season’s crop vigour in independent trial fields. With a coefficient of determination value of 0.69 for the best-performing variety, the model accurately predicted vigour in seed tubers from fields not previously included in the analysis. Moreover, the model identified key microbial indicators of vigour from which a Streptomyces, an Acinetobacter and a Cellvibrio amplicon sequence variant stood out as the most important contributors to the model’s accuracy. This study shows that seed potato vigour can be reliably predicted based on the microbiota associated with seed tuber eyes, potentially guiding future microbiome-informed breeding strategies. Time-resolved drone imaging of potato crop development and seed tuber microbiome data can be used to predict potato vigour, or growth potential, in next-season crops in trial fields.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"28-40"},"PeriodicalIF":20.5,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887345","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