Nature Microbiology最新文献_第5页

Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice 代谢模型揭示了小鼠宿主-微生物组代谢相互作用的衰老相关下降

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-26 DOI: 10.1038/s41564-025-01959-z

Lena Best, Thomas Dost, Daniela Esser, Stefano Flor, Andy Mercado Gamarra, Madlen Haase, A. Samer Kadibalban, Georgios Marinos, Alesia Walker, Johannes Zimmermann, Rowena Simon, Silvio Schmidt, Jan Taubenheim, Sven Künzel, Robert Häsler, Sören Franzenburg, Marco Groth, Silvio Waschina, Philip Rosenstiel, Felix Sommer, Otto W. Witte, Philippe Schmitt-Kopplin, John F. Baines, Christiane Frahm, Christoph Kaleta

{"title":"Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice","authors":"Lena Best, Thomas Dost, Daniela Esser, Stefano Flor, Andy Mercado Gamarra, Madlen Haase, A. Samer Kadibalban, Georgios Marinos, Alesia Walker, Johannes Zimmermann, Rowena Simon, Silvio Schmidt, Jan Taubenheim, Sven Künzel, Robert Häsler, Sören Franzenburg, Marco Groth, Silvio Waschina, Philip Rosenstiel, Felix Sommer, Otto W. Witte, Philippe Schmitt-Kopplin, John F. Baines, Christiane Frahm, Christoph Kaleta","doi":"10.1038/s41564-025-01959-z","DOIUrl":"10.1038/s41564-025-01959-z","url":null,"abstract":"Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host–microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome–host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies. A multi-omics approach reveals host–microbiome interactions in aging in mice.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 4","pages":"973-991"},"PeriodicalIF":20.5,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-025-01959-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703196","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

Combining antibiotics to tackle antimicrobial resistance 联合使用抗生素解决抗菌素耐药性问题

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-26 DOI: 10.1038/s41564-025-01969-x

William Hope, Sumathi Nambiar, Seamus O’Brien, Michael Sharland, David L. Paterson, Mo Yin, Ian H. Gilbert, Michael Ferguson, Sharon J. Peacock, Iain Buchan, Nada Reza, Vineet Dubey, Christopher A. Darlow, Alessandro Gerada, Alex Howard, on behalf of Pre-X Investigators

引用次数: 0

Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation 种传细菌通过生态位分配和促进作用驱动小麦根际微生物组组装

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-03-26 DOI: 10.1038/s41564-025-01973-1

Daniel Garrido-Sanz, Christoph Keel

{"title":"Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation","authors":"Daniel Garrido-Sanz, Christoph Keel","doi":"10.1038/s41564-025-01973-1","DOIUrl":"https://doi.org/10.1038/s41564-025-01973-1","url":null,"abstract":"<p>Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"29 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143703195","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

Decoding microbe–diet–host synergy in colorectal cancer 解读结直肠癌中的微生物-饮食-宿主协同作用

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-21 DOI: 10.1038/s41564-025-01971-3

Alvaro Quevedo-Olmos, Shihan Wang, Thomas F. Meyer

引用次数: 0

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium 细菌素的产生促进了万古霉素耐药屎肠球菌在医院的出现

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-21 DOI: 10.1038/s41564-025-01958-0

Emma G. Mills, Katharine Hewlett, Alexander B. Smith, Marissa P. Griffith, Lora Pless, Alexander J. Sundermann, Lee H. Harrison, Joseph P. Zackular, Daria Van Tyne

{"title":"Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium","authors":"Emma G. Mills, Katharine Hewlett, Alexander B. Smith, Marissa P. Griffith, Lora Pless, Alexander J. Sundermann, Lee H. Harrison, Joseph P. Zackular, Daria Van Tyne","doi":"10.1038/s41564-025-01958-0","DOIUrl":"10.1038/s41564-025-01958-0","url":null,"abstract":"Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 VREfm clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed a polyclonal VREfm population, although 46% of isolates formed genetically related clusters, suggesting a high transmission rate. Comparing these data to a global collection of 15,631 publicly available VREfm genomes collected between 2002 and 2022 identified replacement of the sequence type (ST) 17 VREfm lineage by emergent ST80 and ST117 lineages at the local and global level. Comparative genomic and functional analyses revealed that emergent lineages encoded bacteriocin T8, which conferred a competitive advantage over bacteriocin T8-negative strains in vitro and upon colonization of the mouse gut. Bacteriocin T8 carriage was also strongly associated with strain emergence in the global genome collection. These data suggest that bacteriocin T8-mediated competition may have contributed to VREfm lineage replacement. Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in vitro and in vivo.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 4","pages":"871-881"},"PeriodicalIF":20.5,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-025-01958-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666282","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

Malaria vectors with leaky guts 肠道渗漏的疟疾病媒

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-20 DOI: 10.1038/s41564-025-01970-4

George K. Christophides

引用次数: 0

Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice 药物- fc偶联CD388靶向流感病毒神经氨酸酶，在小鼠中具有广泛的保护作用

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-17 DOI: 10.1038/s41564-025-01955-3

Simon Döhrmann, James Levin, Jason N. Cole, Allen Borchardt, Karin Amundson, Amanda Almaguer, Elizabeth Abelovski, Rajvir Grewal, Douglas Zuill, Nicholas Dedeic, Grayson Hough, Joanne Fortier, Joanna Donatelli, Thanh Lam, Zhi-Yong Chen, Wanlong Jiang, Travis Haussener, Alain Noncovich, James M. Balkovec, Daniel C. Bensen, Voon Ong, Thomas P. Brady, Jeffrey B. Locke, Shawn Flanagan, Robert M. Hughes, Jeffrey L. Stein, Leslie W. Tari

{"title":"Drug–Fc conjugate CD388 targets influenza virus neuraminidase and is broadly protective in mice","authors":"Simon Döhrmann, James Levin, Jason N. Cole, Allen Borchardt, Karin Amundson, Amanda Almaguer, Elizabeth Abelovski, Rajvir Grewal, Douglas Zuill, Nicholas Dedeic, Grayson Hough, Joanne Fortier, Joanna Donatelli, Thanh Lam, Zhi-Yong Chen, Wanlong Jiang, Travis Haussener, Alain Noncovich, James M. Balkovec, Daniel C. Bensen, Voon Ong, Thomas P. Brady, Jeffrey B. Locke, Shawn Flanagan, Robert M. Hughes, Jeffrey L. Stein, Leslie W. Tari","doi":"10.1038/s41564-025-01955-3","DOIUrl":"10.1038/s41564-025-01955-3","url":null,"abstract":"The ability of influenza virus to undergo rapid antigenic shift to elude humoral immunity highlights the need for effective broad-spectrum influenza antivirals for treatment, prophylaxis and pandemic preparedness. Strategies providing durable, universal influenza protection in healthy and high-risk populations are urgently needed. Here we describe the design and preclinical characterization of CD388, a first-in-class antiviral drug–Fc conjugate (DFC), in mice and cynomolgus macaques. CD388 comprises a multivalent conjugate of the influenza virus neuraminidase inhibitor zanamivir, linked to a CH1–Fc hybrid domain of human IgG1 engineered for extended half-life. CD388 improves the antiviral activity of zanamivir, demonstrating potent, universal activity across influenza A and B viruses, including high pathogenicity and neuraminidase inhibitor resistant strains, a low potential for resistance development and potent efficacy in lethal mouse infection models. These results suggest that CD388 has the potential for universal prevention of influenza A and B in healthy and high-risk populations. CD388 is a first-in-class antiviral drug–Fc conjugate engineered for extended half-life that demonstrates potent prophylactic and therapeutic efficacy against lethal influenza A and B challenge in mice.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 4","pages":"912-926"},"PeriodicalIF":20.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-025-01955-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635165","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

Baloxavir improves disease outcomes in mice after intranasal or ocular infection with Influenza A virus H5N1-contaminated cow’s milk 巴洛昔韦改善小鼠鼻内或眼内感染甲型流感病毒h5n1污染的牛奶后的疾病结果

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-17 DOI: 10.1038/s41564-025-01961-5

Jeremy C. Jones, Konstantin Andreev, Thomas P. Fabrizio, Andrew S. Bowman, Elena A. Govorkova, Richard J. Webby

引用次数: 0

Publisher Correction: Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid 出版者更正：肠隐窝微生物群通过吲哚乙酸调节肠干细胞的更新和肿瘤发生

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-03-06 DOI: 10.1038/s41564-025-01976-y

Shuning Zhang, Lihua Peng, Shyamal Goswami, Yuchen Li, Haiyue Dang, Shuli Xing, Panpan Feng, Giulia Nigro, Yingying Liu, Yingfei Ma, Tianhao Liu, Jiahua Yang, Tinglei Jiang, Yingnan Yang, Nick Barker, Philippe Sansonetti, Parag Kundu

引用次数: 0

Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission 靶向蚊子前折叠蛋白-伴侣蛋白复合物阻断疟原虫传播

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-03-06 DOI: 10.1038/s41564-025-01947-3

Yuemei Dong, Seokyoung Kang, Simone L. Sandiford, Andrew Pike, Maria L. Simões, Ratawan Ubalee, Kevin Kobylinski, George Dimopoulos

{"title":"Targeting the mosquito prefoldin–chaperonin complex blocks Plasmodium transmission","authors":"Yuemei Dong, Seokyoung Kang, Simone L. Sandiford, Andrew Pike, Maria L. Simões, Ratawan Ubalee, Kevin Kobylinski, George Dimopoulos","doi":"10.1038/s41564-025-01947-3","DOIUrl":"10.1038/s41564-025-01947-3","url":null,"abstract":"The Plasmodium infection cycle in mosquitoes relies on numerous host factors in the vector midgut, which can be targeted with therapeutics. The mosquito prefoldin complex is needed to fold proteins and macromolecular complexes properly. Here we show that the conserved Anopheles mosquito prefoldin (PFDN)–chaperonin system is a potent transmission-blocking target for multiple Plasmodium species. Silencing any prefoldin subunit or its CCT/TRiC partner via RNA interference reduces Plasmodium falciparum oocyst loads in the mosquito midgut, as does co-feeding mosquitoes with PFDN6-specific antibody and gametocytes. Inhibition of the PFDN–CCT/TRiC chaperonin complex results in the loss of epithelial and extracellular matrix integrity, which triggers microorganism-mediated anti-Plasmodium immune priming and compromises the parasite’s laminin-based immune evasion. Mouse malaria transmission-blocking vaccine and antibody co-feeding assays support its potential as a multispecies transmission-blocking target for P. falciparum and Plasmodium vivax. Further study is needed to determine the potential of this system as a transmission-blocking vaccine target. Disrupting the prefoldin–chaperonin complex in various species of Anopheles mosquitoes results in a compromised intestinal barrier leading to an immune response that inhibits the malaria parasite.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 4","pages":"841-854"},"PeriodicalIF":20.5,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560757","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