Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall, Gene W. Tyson
{"title":"Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper","authors":"Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall, Gene W. Tyson","doi":"10.1038/s41587-025-02738-1","DOIUrl":"https://doi.org/10.1038/s41587-025-02738-1","url":null,"abstract":"<p>Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website ‘Sandpiper’ collates microbial community profiles from 248,559 publicly available metagenomes.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"669 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639831","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}
{"title":"Clinical trials gain intelligence","authors":"","doi":"10.1038/s41587-025-02754-1","DOIUrl":"10.1038/s41587-025-02754-1","url":null,"abstract":"As governments around the world begin to embrace artificial intelligence in healthcare, clinical trials are entering a new phase — faster, smarter and more inclusive. With regulatory momentum building to adapt new technologies, artificial intelligence is no longer just a promise for the future but a powerful tool reshaping how trials are designed, conducted and analyzed today.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1017-1018"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41587-025-02754-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144629931","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}
{"title":"Biotech news from around the world","authors":"","doi":"10.1038/s41587-025-02749-y","DOIUrl":"10.1038/s41587-025-02749-y","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1026-1026"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630237","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}
{"title":"A new impact framework for investors in life sciences bridges financial returns and patient outcomes","authors":"Philip Brainin","doi":"10.1038/s41587-025-02726-5","DOIUrl":"10.1038/s41587-025-02726-5","url":null,"abstract":"A new model for quantifying the impact of capital investments in life science interventions could help investors, policymakers and healthcare stakeholders to assess, monitor and optimize the societal impact of their investments.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1041-1046"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630294","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}
Sarah M. E. Gabriele, Matthew J. Martin, Aaron S. Kesselheim, S. Sean Tu
{"title":"The strength and importance of government-funded patents for approved drugs","authors":"Sarah M. E. Gabriele, Matthew J. Martin, Aaron S. Kesselheim, S. Sean Tu","doi":"10.1038/s41587-025-02724-7","DOIUrl":"10.1038/s41587-025-02724-7","url":null,"abstract":"Understanding the strength and importance of US government-sponsored patents can help to limit high drug prices as well as constitute a justification to enact reasonable pricing clauses and exercise march-in rights.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1050-1052"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630141","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}
{"title":"De-extinction: debate continues around tech to ‘resurrect’ lost species","authors":"Michael Eisenstein","doi":"10.1038/s41587-025-02745-2","DOIUrl":"10.1038/s41587-025-02745-2","url":null,"abstract":"Experts disagree about the extent to which hybrids based on dire wolves reflect the original extinct species, and the broader role of de-extinction technologies in ecosystem restoration.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1023-1026"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630289","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}
{"title":"Innovation to investment: how to build your first life sciences pitch deck","authors":"Katherine E. Reuther, Darren Cooke, Mark Kessel","doi":"10.1038/s41587-025-02730-9","DOIUrl":"10.1038/s41587-025-02730-9","url":null,"abstract":"A strong pitch deck can help make a good first impression, establish credibility and build the confidence to secure the support and financial resources needed for eventual commercial success.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"43 7","pages":"1204-1207"},"PeriodicalIF":41.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630285","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}
{"title":"Inducing bacterial calcification for systematic treatment and immunomodulation against methicillin-resistant Staphylococcus aureus","authors":"Wanying Zhang, Liang Liu, Qingyan Zhang, Huidan Lu, Anyao Li, Yuqiao Huang, Wenting Zhang, Hanhui Li, Xiaoyan Lu, Xinliang Ming, Ze Yang, Hao Shou, Yilin Wang, Jingyan Xia, Feng Xu, Ben Wang","doi":"10.1038/s41587-025-02736-3","DOIUrl":"https://doi.org/10.1038/s41587-025-02736-3","url":null,"abstract":"<p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) has become one of the deadliest bacteria globally due to antibiotic resistance. In this study, we crosslinked antigen-binding fragments of monoclonal antibodies against the wall-teichoic acid of <i>S. aureus</i> with polysialic acid to form an antibody‒PSA conjugate, which can effectively target and induce calcification on the surface of MRSA. This process eliminates bacteria by hindering the energy metabolism and multiple essential metabolic pathways of MRSA. We found that bacterial calcification leads to increased expression of calprotectin, S100A8/S100A9, in macrophages and monocytes in vivo and can stimulate the activation of macrophages to an inflammatory state, thereby promoting bacterial eradication as an immunomodulator. Systemic administration of the antibody‒PSA conjugate demonstrates high efficacy and safety for treating chronic lung infections and chronic osteomyelitis caused by MRSA in mice. This study offers a promising therapy for treating drug-resistant bacteria and related refractory pathogenic infections.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"45 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144629714","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}