Nature Microbiology最新文献_第5页

A transatlantic joint lab model for interdisciplinary research 跨大西洋跨学科研究联合实验室模式。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-22 DOI: 10.1038/s41564-025-02127-z

Angelique Hoelzemer, Wilfredo F. Garcia-Beltran

引用次数: 0

Phages with a broad host range are common across ecosystems 宿主范围广泛的噬菌体在生态系统中很常见。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-19 DOI: 10.1038/s41564-025-02108-2

Amaury Bignaud, Devon E. Conti, Agnès Thierry, Jacques Serizay, Karine Labadie, Julie Poulain, Olivia Cheny, Maritrini Colón-González, Laurent Debarbieux, Marianna Guerrero-Osornio, Sophie Helaine, Peter Hill, Gwenaelle Le Tinier, Gael A. Millot, Lucia Morales, Andrés Parada, Nadia Riera, Gregorio Iraola, Romain Koszul, Martial Marbouty

{"title":"Phages with a broad host range are common across ecosystems","authors":"Amaury Bignaud, Devon E. Conti, Agnès Thierry, Jacques Serizay, Karine Labadie, Julie Poulain, Olivia Cheny, Maritrini Colón-González, Laurent Debarbieux, Marianna Guerrero-Osornio, Sophie Helaine, Peter Hill, Gwenaelle Le Tinier, Gael A. Millot, Lucia Morales, Andrés Parada, Nadia Riera, Gregorio Iraola, Romain Koszul, Martial Marbouty","doi":"10.1038/s41564-025-02108-2","DOIUrl":"10.1038/s41564-025-02108-2","url":null,"abstract":"Phages are diverse and abundant within microbial communities, where they play major roles in their evolution and adaptation. Phage replication, and multiplication, is generally thought to be restricted within a single or narrow host range. Here we use published and newly generated proximity-ligation-based metagenomic Hi-C (metaHiC) data from various environments to explore virus–host interactions. We reconstructed 4,975 microbial and 6,572 phage genomes of medium quality or higher. MetaHiC yielded a contact network between genomes and enabled assignment of approximately half of phage genomes to their hosts, revealing that a substantial proportion of these phages interact with multiple species in environments as diverse as the oceanic water column or the human gut. This observation challenges the traditional view of a narrow host spectrum of phages by unveiling that multihost associations are common across ecosystems, with implications for how they might impact ecology and evolution and phage therapy approaches. Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 10","pages":"2537-2549"},"PeriodicalIF":19.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089896","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 dominant subgroup of marine Bathyarchaeia assimilates organic and inorganic carbon into unconventional membrane lipids 海洋深海古菌的一个优势亚群将有机和无机碳同化成非常规的膜脂。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-19 DOI: 10.1038/s41564-025-02121-5

Liang Dong, Yunge Jing, Jialin Hou, Jiaming Zhou, Tiantian Yu, Shijie Chen, Lewen Liang, Pengfei Zhu, Xiaoxiao Zhao, Kai-Uwe Hinrichs, Fengping Wang

{"title":"A dominant subgroup of marine Bathyarchaeia assimilates organic and inorganic carbon into unconventional membrane lipids","authors":"Liang Dong, Yunge Jing, Jialin Hou, Jiaming Zhou, Tiantian Yu, Shijie Chen, Lewen Liang, Pengfei Zhu, Xiaoxiao Zhao, Kai-Uwe Hinrichs, Fengping Wang","doi":"10.1038/s41564-025-02121-5","DOIUrl":"10.1038/s41564-025-02121-5","url":null,"abstract":"Bathyarchaeia, an abundant and ecologically versatile archaea found commonly in marine sediments, has a key role in the global carbon cycle. However, its lipid biomarkers and carbon assimilation mechanisms are poorly understood. Here, using a highly enriched Bathyarchaeia culture (>95% archaea) obtained from estuarine sediment of the East China Sea, we show that Baizosediminiarchaeum (formerly subgroup Bathy-8), the most abundant and widespread Bathyarchaeia group on Earth, synthesizes butanetriol dialkyl glycerol tetraethers (BDGTs) as its dominant membrane lipids. BDGTs are unusual archaeal tetraether lipids characterized by a butanetriol backbone instead of the typical glycerol, challenging fundamental assumptions in archaeal lipid biochemistry. Although BDGTs have been previously identified in the methanogen Methanomassiliicoccus luminyensis, we now provide direct evidence that Bathyarchaeia also synthesizes BDGTs, definitively establishing this globally abundant group as a natural BDGT producer. Stable isotope probing with 13C-bicarbonate shows that Baizosediminiarchaeum assimilates carbon into BDGTs from both inorganic carbon and lignin. These unique carbon assimilation strategies suggest the biogeochemical importance of Baizosediminarchaeum in marine carbon cycling and organic matter decomposition. Baizosediminiarchaeum, a key player in the deep biosphere, builds butanetriol dialkyl glycerol tetraether (BDGT) membrane lipids and feeds on both CO2 and lignin, revealing a survival strategy in low-energy environments and a unique lipid biomarker for this group.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 10","pages":"2579-2590"},"PeriodicalIF":19.4,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145089900","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 nitrogen-fixing bacterium forms symbioses on land and at sea 固氮细菌在陆地和海洋中形成共生体。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-17 DOI: 10.1038/s41564-025-02131-3

Ruben Garrido-Oter

引用次数: 0

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum 绿藻门细菌中一个功能性古菌的结构。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-17 DOI: 10.1038/s41564-025-02110-8

Shamphavi Sivabalasarma, Najwa Taib, Clara L. Mollat, Marie Joest, Stefan Steimle, Simonetta Gribaldo, Sonja-Verena Albers

{"title":"Structure of a functional archaellum in Bacteria of the Chloroflexota phylum","authors":"Shamphavi Sivabalasarma, Najwa Taib, Clara L. Mollat, Marie Joest, Stefan Steimle, Simonetta Gribaldo, Sonja-Verena Albers","doi":"10.1038/s41564-025-02110-8","DOIUrl":"10.1038/s41564-025-02110-8","url":null,"abstract":"Motility in Archaea is driven by the archaellum, a rotary ATP-driven machinery unrelated to the bacterial flagellum. To date, archaella have been described exclusively in archaea; however, recent work reported archaellum genes in bacterial strains of the SAR202 clade (Chloroflexota). Here, using MacSyFinder, we show that bona fide archaellum gene clusters are widespread in several members of the Chloroflexota. Analysis of archaellum-encoding loci and Alphafold3-predicted structures show similarity to the archaellum machinery. Using cryo electron microscopy single-particle analysis, we solved the structure of the bacterial archaellum from Litorilinea aerophila to 2.7 Å. We also show the expression and assembly of this machinery in bacteria and its function in swimming motility. Finally, a phylogenomic analysis revealed two horizontal gene transfer events from euryarchaeal members to Chloroflexota. In summary, our study shows that a functional and assembled archaellum machinery can be exchanged between the two prokaryotic domains. Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 10","pages":"2412-2424"},"PeriodicalIF":19.4,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-025-02110-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145078217","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

Publisher Correction: Future ocean warming may cause large reductions in Prochlorococcus biomass and productivity 出版者更正：未来海洋变暖可能导致原绿球藻生物量和生产力大幅减少。

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-16 DOI: 10.1038/s41564-025-02145-x

François Ribalet, Stephanie Dutkiewicz, Erwan Monier, E. Virginia Armbrust

引用次数: 0

Ecological function of phenazine in soil 非那嗪在土壤中的生态功能

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-12 DOI: 10.1038/s41564-025-02125-1

María Negre Rodríguez, Ákos T. Kovács

引用次数: 0

Author Correction: Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease 作者更正：维也纳病毒衣壳蛋白模仿自身抗原，并有助于Sjögren疾病的自身免疫

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-09-12 DOI: 10.1038/s41564-025-02143-z

Xinwei Zhang, Yan Li, Yang Qin, Zhangdi Liao, Chaoqiong Deng, Yangchun Chen, Yan Li, Hongyan Qian, Yan He, Shiju Chen, Guixiu Shi, Yuan Liu

引用次数: 0

Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity 成立世界自然保护联盟微生物保护专家组，作为全球微生物生物多样性的保障

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-12 DOI: 10.1038/s41564-025-02113-5

Jack A. Gilbert, Raquel S. Peixoto, Amber Hartman Scholz, Maria Gloria Dominguez Bello, Lise Korsten, Gabriele Berg, Brajesh Singh, Antje Boetius, Fengping Wang, Chris Greening, Kelly Wrighton, Seth Bordenstein, Janet K. Jansson, Jay T. Lennon, Valeria Souza, Torsten Thomas, Don Cowan, Thomas W. Crowther, Nguyen Nguyen, Lucy Harper, Louis-Patrick Haraoui, Suzanne L. Ishaq, Kent Redford

引用次数: 0

Phenazines contribute to microbiome dynamics by targeting topoisomerase IV 非那嗪类药物通过靶向拓扑异构酶IV促进微生物组动力学

IF 19.4 1区生物学

Nature Microbiology Pub Date : 2025-09-11 DOI: 10.1038/s41564-025-02118-0

Yaqi Zhou, Hongkai Wang, Jiaxin Sun, Wisnu Adi Wicaksono, Chao Liu, Yinghao He, Yuxuan Qin, Gabriele Berg, Lei Li, Houwen Lin, Yunrong Chai, Yang Bai, Zhonghua Ma, Tomislav Cernava, Yun Chen

{"title":"Phenazines contribute to microbiome dynamics by targeting topoisomerase IV","authors":"Yaqi Zhou, Hongkai Wang, Jiaxin Sun, Wisnu Adi Wicaksono, Chao Liu, Yinghao He, Yuxuan Qin, Gabriele Berg, Lei Li, Houwen Lin, Yunrong Chai, Yang Bai, Zhonghua Ma, Tomislav Cernava, Yun Chen","doi":"10.1038/s41564-025-02118-0","DOIUrl":"10.1038/s41564-025-02118-0","url":null,"abstract":"Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol. Computational analysis and pairwise assays reveal that bacterial topoisomerase IV is a target of microbially produced phenazines, which informs synthetic-community design to treat fungal crop infection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 10","pages":"2396-2411"},"PeriodicalIF":19.4,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031951","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