Nature Microbiology最新文献_第6页

Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice 肠obactin抑制微生物依赖的AhR激活，促进小鼠细菌性败血症

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-08 DOI: 10.1038/s41564-024-01882-9

Robert C. Keskey, Jason Xiao, Sanjiv Hyoju, Adam Lam, Daniel Kim, Ashley M. Sidebottom, Alexander Zaborin, Anne Dijkstra, Rebecca Meltzer, Abhimanyu Thakur, Kui Zhang, Huanhuan Joyce Chen, Natalia V. Beloborodova, Alisa K. Pautova, Krysta Wolfe, Bhakti Patel, Renee Thewissen, Olga Zaborina, John C. Alverdy

{"title":"Enterobactin inhibits microbiota-dependent activation of AhR to promote bacterial sepsis in mice","authors":"Robert C. Keskey, Jason Xiao, Sanjiv Hyoju, Adam Lam, Daniel Kim, Ashley M. Sidebottom, Alexander Zaborin, Anne Dijkstra, Rebecca Meltzer, Abhimanyu Thakur, Kui Zhang, Huanhuan Joyce Chen, Natalia V. Beloborodova, Alisa K. Pautova, Krysta Wolfe, Bhakti Patel, Renee Thewissen, Olga Zaborina, John C. Alverdy","doi":"10.1038/s41564-024-01882-9","DOIUrl":"10.1038/s41564-024-01882-9","url":null,"abstract":"Sepsis is a major cause of morbidity and mortality, but our understanding of the mechanisms underlying survival or susceptibility is limited. Here, as pathogens often subvert host defence mechanisms, we hypothesized that this might influence the outcome of sepsis. We used microbiota analysis, faecal microbiota transplantation, antibiotic treatment and caecal metabolite analysis to show that gut-microbiota-derived tryptophan metabolites including indoles increased host survival in a mouse model of Serratia marcescens sepsis. Infection in macrophage-specific aryl hydrocarbon receptor (AhR) knockout mice revealed that AhR activation induced transcriptional reprogramming in macrophages and increased bacterial clearance and host survival. However, culture supernatants from multiple bacterial pathogens inhibited AhR activation in vitro. We showed that the secreted siderophore, enterobactin, inhibited AhR activation in vitro and increased sepsis mortality in vivo. By contrast, oral or systemic tryptophan supplementation increased survival. These findings show that sepsis survival depends upon the interplay between pathogen inhibition and the activation of AhR by a microbiota-derived metabolite. Bacterial pathogens produce enterobactin, which suppresses microbiota-derived indole activation of Ahr in macrophages to inhibit bacterial clearance and increase the severity of bacterial sepsis.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"388-404"},"PeriodicalIF":20.5,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142935884","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

Dietary exclusion of major food groups shapes the gut microbiome and may influence health 排除主要食物群的饮食会塑造肠道微生物群，并可能影响健康

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-07 DOI: 10.1038/s41564-024-01875-8

引用次数: 0

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals 21561个人的纯素食、素食和杂食饮食的肠道微生物特征及其相关的健康结果

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-06 DOI: 10.1038/s41564-024-01870-z

Gloria Fackelmann, Paolo Manghi, Niccolò Carlino, Vitor Heidrich, Gianmarco Piccinno, Liviana Ricci, Elisa Piperni, Alberto Arrè, Elco Bakker, Alice C. Creedon, Lucy Francis, Joan Capdevila Pujol, Richard Davies, Jonathan Wolf, Kate M. Bermingham, Sarah E. Berry, Tim D. Spector, Francesco Asnicar, Nicola Segata

{"title":"Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals","authors":"Gloria Fackelmann, Paolo Manghi, Niccolò Carlino, Vitor Heidrich, Gianmarco Piccinno, Liviana Ricci, Elisa Piperni, Alberto Arrè, Elco Bakker, Alice C. Creedon, Lucy Francis, Joan Capdevila Pujol, Richard Davies, Jonathan Wolf, Kate M. Bermingham, Sarah E. Berry, Tim D. Spector, Francesco Asnicar, Nicola Segata","doi":"10.1038/s41564-024-01870-z","DOIUrl":"10.1038/s41564-024-01870-z","url":null,"abstract":"As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology. Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"41-52"},"PeriodicalIF":20.5,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01870-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142934992","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

Crucial stepping stones in freshwater microbiology 淡水微生物学的重要基石

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-06 DOI: 10.1038/s41564-024-01898-1

David A. Pearce, James E. Lawrence, Maria Luisa Avila Jimenez

引用次数: 0

Zinc-dependent β-lactam resistance at a cost 锌依赖性β-内酰胺抗性的代价

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-06 DOI: 10.1038/s41564-024-01892-7

Jacob E. Choby, David S. Weiss

引用次数: 0

Oropouche virus and the urgent need for global surveillance Oropouche病毒和全球监测的迫切需要

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-06 DOI: 10.1038/s41564-024-01897-2

Marta Giovanetti

引用次数: 0

Unravelling viral ecology and evolution over 20 years in a freshwater lake 解开淡水湖20多年来的病毒生态学和进化

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-03 DOI: 10.1038/s41564-024-01876-7

Zhichao Zhou, Patricia Q. Tran, Cody Martin, Robin R. Rohwer, Brett J. Baker, Katherine D. McMahon, Karthik Anantharaman

{"title":"Unravelling viral ecology and evolution over 20 years in a freshwater lake","authors":"Zhichao Zhou, Patricia Q. Tran, Cody Martin, Robin R. Rohwer, Brett J. Baker, Katherine D. McMahon, Karthik Anantharaman","doi":"10.1038/s41564-024-01876-7","DOIUrl":"10.1038/s41564-024-01876-7","url":null,"abstract":"As freshwater lakes undergo rapid anthropogenic change, long-term studies reveal key microbial dynamics, evolutionary shifts and biogeochemical interactions, yet the vital role of viruses remains overlooked. Here, leveraging a 20 year time series from Lake Mendota, WI, USA, we characterized 1.3 million viral genomes across time, seasonality and environmental factors. Double-stranded DNA phages from the class Caudoviricetes dominated the community. We identified 574 auxiliary metabolic gene families representing over 140,000 auxiliary metabolic genes, including important genes such as psbA (photosynthesis), pmoC (methane oxidation) and katG (hydrogen peroxide decomposition), which were consistently present and active across decades and seasons. Positive associations and niche differentiation between virus–host pairs, including keystone Cyanobacteria, methanotrophs and Nanopelagicales, emerged during seasonal changes. Inorganic carbon and ammonium influenced viral abundances, underscoring viral roles in both ‘top-down’ and ‘bottom-up’ interactions. Evolutionary processes favoured fitness genes, reduced genomic heterogeneity and dominant sub-populations. This study transforms understanding of viral ecology and evolution in Earth’s microbiomes. A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":"231-245"},"PeriodicalIF":20.5,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917052","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

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