Nature Microbiology最新文献

{"title":"Translating soil microbiome knowledge into agricultural decisions.","authors":"Vitor Luciano Costa da Silva, Bárbara Caroline Niza Silva de Alvarenga, Francisco Dini-Andreote, Victor Satler Pylro","doi":"10.1038/s41564-026-02495-0","DOIUrl":"https://doi.org/10.1038/s41564-026-02495-0","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970067","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":"Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa","authors":"Sophie Belman, Cebile Lekhuleni, Jackie Kleynhans, Giovenale Moirano, Daniela Lührsen, Cristina Carnerero, Susan Meiring, Stephanie W. Lo, Mignon du Plessis, Anne von Gottberg, Rachel Lowe","doi":"10.1038/s41564-026-02458-5","DOIUrl":"10.1038/s41564-026-02458-5","url":null,"abstract":"Streptococcus pneumoniae is highly diverse, comprising over 100 serotypes and hundreds of genomic lineages amid widespread vaccination. While it can cause invasive pneumococcal disease (IPD) which exhibits pronounced seasonal spikes, the interplay between pneumococcal diversity and environmental drivers remains unexplored. Here we analysed 59,017 IPD cases over 19 years from South Africa, incorporating 4,350 genome-sequenced isolates, using Bayesian spatiotemporal models to link environmental exposure and pneumococcal diversity. Cumulatively, across an 8-week period, moderate relative humidity (33–49%) and cold minimum temperatures (4–10 °C) increased IPD risk by 5% and 4%, respectively. Conversely, warm maximum temperatures (27–38 °C) were associated with up to a 10% increased risk within a week of exposure. There was a positive association between air pollution (PM2.5) and IPD, although it varied by age, disease presentation, and most notably serotype and lineage. Specifically, the lag time between PM2.5 exposure and disease onset varied by serotype, with only serotypes 4, 8 and 23F conferring an immediate IPD risk. High prevalence of GPSC21 lineage (serotype 19F) also modified the pollution response, shifting the lag structure to produce immediate risk of disease following high PM2.5 exposure. Our results demonstrate that pneumococcal population structure shapes air quality risk which in turn can shape the fitness landscape of microbial populations. Integration of these data may inform public health policy. Air quality and climate factors alter the risk of invasive pneumococcal diseases such as meningitis. Importantly, the lineage and serotype (population structure) of circulating bacteria can alter how quickly disease risk rises in the weeks following exposure.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2723-2737"},"PeriodicalIF":18.7,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02458-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970069","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":"Modelling air pollution impacts on infectious disease","authors":"John S. Ji","doi":"10.1038/s41564-026-02488-z","DOIUrl":"10.1038/s41564-026-02488-z","url":null,"abstract":"Air pollution increases the risk of invasive pneumococcal disease and bacterial lineage changes the timing of that risk, making pathogen genomic diversity an effect modifier.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2676-2677"},"PeriodicalIF":18.7,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148970108","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":"Publisher Correction: Unique adaptations in sulfatases underpin colonic mucin degradation by Akkermansia muciniphila.","authors":"Debajit Dey, Naba D Salman, Charles W E Tomlinson, Chunsheng Jin, Grete Raba, Sadie R Schaus, Marcus Nilsson, Zak McIver, Reyme Herman, Adam Simpkin, Matthew Davy, Daniel J Rigden, Mirjam Czjzek, Dominic P Byrne, Mihai Oltean, Alexander Case, Christoph G Baumann, Gareth S A Wright, Sjoerd van der Post, Edwin A Yates, Eric C Martens, Lauren Davey, Ana S Luis, Alan Cartmell","doi":"10.1038/s41564-026-02504-2","DOIUrl":"https://doi.org/10.1038/s41564-026-02504-2","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920581","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":"Author Correction: Longitudinal plasma metabolomics reveals a role for taurine in asymptomatic malaria and seasonal persistence.","authors":"Gretchen Diffendall, Perine Millot, Patty Chen, Balotin Fogang, Dominique Dorin-Semblat, Fanny Aprahamian, Sylvère Durand, Benoît Gamain, Antoine Claessens, Artur Scherf","doi":"10.1038/s41564-026-02503-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02503-3","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920648","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":"IL-17A-producing γδ T cells control pulmonary Mycobacterium abscessus infection in mice.","authors":"Xiaoqian Hu, Siran Lin, Wenchang Meng, Haoye Liu, Zhijie Qin, Zhihao Wu, Yaqi Wan, Shuai Ma, Xuguang Yang, Zhinan Yin, Yiwei Chu, Wenhong Zhang, Lingyun Shao, Yuli Lin","doi":"10.1038/s41564-026-02466-5","DOIUrl":"https://doi.org/10.1038/s41564-026-02466-5","url":null,"abstract":"<p><p>The specific role of γδ T cells in non-tuberculous mycobacteria (NTM) infections remains incompletely understood. Here we characterized the immune landscape of pulmonary tissues from a Mycobacterium abscessus-infected NTM mice model. Interleukin-17 (IL-17)A⁺ γδ T cells were essential for controlling M. abscessus infection by directly eliminating extracellular bacteria. These cells conferred protective immunity in two mouse models of infection combined with either pulmonary fibrosis or a lack of functional interferon-gamma (IFNγ)-mediated immunity. IL-17A⁺ γδ T cells exerted bactericidal activity via granzyme B-dependent cytotoxic pathways. Absence of IL-17A substantially impaired bacterial recognition and cytotoxic function of IL-17A⁺ γδ T cells, highlighting the cell-intrinsic requirement for IL-17A signalling in γδ T cell activation. M. abscessus recognition through Toll-like receptor 2 induced macrophage production of IL-1β and IL-23, promoting the expansion and activation of IL-17A⁺ γδ T cells. Single-cell RNA sequencing on human peripheral blood mononuclear cells suggests that anti-IFNγ autoantibodies compromise γδ T cell function. Our findings establish IL-17A⁺ γδ T cells as a promising therapeutic target for NTM infections, particularly when IFNγ-dependent immunity is compromised.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888144","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":"High-throughput recovery of integron cassettes for gene discovery screens.","authors":"Filipa Trigo da Roza, André Carvalho, Amalia Prieto, Paula Blanco, Ester Vergara, Rocío López-Igual, Modesto Redrejo-Rodríguez, Melanie Blokesch, José Antonio Escudero","doi":"10.1038/s41564-026-02474-5","DOIUrl":"https://doi.org/10.1038/s41564-026-02474-5","url":null,"abstract":"<p><p>Integrons capture functional genes in mobile genetic elements called integron cassettes, which represent an untapped source of genes of biotechnological interest. Here we present two tools, cassette gatherer and cassette hunter, that enable high-throughput establishment of gene libraries either from genetically tractable strains or directly from DNA. We re-engineered a class 1 integron into counterselection markers on a plasmid or on the chromosome of a naturally competent Vibrio cholerae, which enabled capture of single cassettes in a sequence- and function-independent manner. When applied to Vibrio strains and genomic libraries, our tools recovered hundreds of single cassettes per assay with more than 99% specificity. We further subjected the library of cassettes generated by the hunter and gatherer tools to screens against phages ICP2 and T4, and identified nine phage-defence systems, including five previously undescribed. These tools enable rapid and large-scale recovery of integron cassettes that could be leveraged for functional gene discovery.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":18.7,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888025","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":"BCL-2 inhibition at antiretroviral therapy initiation reduces the intact SIV reservoir in macaques","authors":"Tomas Raul Wiche Salinas,&nbsp;Justin Harper,&nbsp;Claire Deleage,&nbsp;Kevin Nguyen,&nbsp;James Auger,&nbsp;Hannah R. Flores,&nbsp;Sandeep R. Kaushik,&nbsp;Amelia C. Wilkes,&nbsp;Rachelle L. Stammen,&nbsp;Jennifer S. Wood,&nbsp;Kirk A. Easley,&nbsp;Sydney Nelson,&nbsp;Gregory K. Tharp,&nbsp;Steven E. Bosinger,&nbsp;Mackenzie L. Cottrell,&nbsp;Emek Kose,&nbsp;Taina T. Immonen,&nbsp;Jeffrey D. Lifson,&nbsp;Gregory M. Laird,&nbsp;Brandon F. Keele,&nbsp;R. Brad Jones,&nbsp;Andrew D. Badley,&nbsp;Guido Silvestri,&nbsp;Deanna A. Kulpa,&nbsp;Mirko Paiardini","doi":"10.1038/s41564-026-02464-7","DOIUrl":"10.1038/s41564-026-02464-7","url":null,"abstract":"The anti-apoptotic molecule BCL-2 favours the maintenance of the CD4+ T-cell reservoir during HIV infection. Whether inhibition of BCL-2 can lead to long-term reduction of the HIV reservoir is unclear. Here we initiated antiretroviral therapy (ART) in 24 simian immunodeficiency virus (SIV)-infected rhesus macaques at 14 days post infection (p.i.), alone or combined with a 10-day treatment of venetoclax or venetoclax and CD8α depletion, with a follow-up to day 294 p.i. We report a rapid and sustained reduction of the intact SIV reservoir in venetoclax-treated rhesus macaques in blood and lymph nodes. CD4+ T cells that persisted after venetoclax treatment showed partial reduction in apoptotic sensitivity in ex vivo assays. These exhibited elevated expression of anti-apoptotic BCL-2 and BCL-xL, and showed reduced expression of pro-apoptotic molecules such as PUMA. These findings support the rationale for extended venetoclax dosing and suggest that combining BCL-2 inhibition with agents targeting additional anti-apoptotic molecules could enhance clearance of the viral reservoir in HIV cure strategies. Inhibition of the pro-survival protein BCL-2 at the initiation of antiretroviral therapy in macaques reduced persistent viral reservoirs in both blood and lymph nodes during SIV infection.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2707-2722"},"PeriodicalIF":18.7,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02464-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888040","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":"Grounding microbial conservation in ecological principles","authors":"Cinzia Corinaldesi,&nbsp;Karthik Anantharaman,&nbsp;James C. Aronson,&nbsp;Brett J. Baker,&nbsp;Marco Candela,&nbsp;Bradley Cardinale,&nbsp;Antonio Dell’Anno,&nbsp;Josep M. Gasol,&nbsp;Hans-Peter Grossart,&nbsp;Elisa Laiolo,&nbsp;Lisa A. Levin,&nbsp;Hidetaka Nomaki,&nbsp;Takuro Nunoura,&nbsp;Antonio Pusceddu,&nbsp;William J. Ripple,&nbsp;Paul V. R. Snelgrove,&nbsp;Curtis A. Suttle,&nbsp;Rui Zhang,&nbsp;Roberto Danovaro","doi":"10.1038/s41564-026-02462-9","DOIUrl":"10.1038/s41564-026-02462-9","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2669-2670"},"PeriodicalIF":18.7,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880970","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":"Reply to ‘Grounding microbial conservation in ecological principles’","authors":"Jack A. Gilbert,&nbsp;Chris Greening,&nbsp;Raquel S. Peixoto","doi":"10.1038/s41564-026-02463-8","DOIUrl":"10.1038/s41564-026-02463-8","url":null,"abstract":"","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 10","pages":"2671-2672"},"PeriodicalIF":18.7,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880959","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}