Benjamin A. Adler, Muntathar J. Al-Shimary, Jaymin R. Patel, Emily G. Armbruster, David Colognori, Emeric J. Charles, Kate V. Miller, Arushi Lahiri, Michael L. Cui, Agnès Oromí-Bosch, Angela Voelker, Marena Trinidad, Jina Lee, Sebastien Beurnier, Ron Boger, Jason Nomburg, Rodolphe Barrangou, Vivek K. Mutalik, Joseph S. Schoeniger, Joseph A. Pogliano, David F. Savage, Jennifer A. Doudna, Brady F. Cress
{"title":"CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d","authors":"Benjamin A. Adler, Muntathar J. Al-Shimary, Jaymin R. Patel, Emily G. Armbruster, David Colognori, Emeric J. Charles, Kate V. Miller, Arushi Lahiri, Michael L. Cui, Agnès Oromí-Bosch, Angela Voelker, Marena Trinidad, Jina Lee, Sebastien Beurnier, Ron Boger, Jason Nomburg, Rodolphe Barrangou, Vivek K. Mutalik, Joseph S. Schoeniger, Joseph A. Pogliano, David F. Savage, Jennifer A. Doudna, Brady F. Cress","doi":"10.1038/s41564-025-01935-7","DOIUrl":"https://doi.org/10.1038/s41564-025-01935-7","url":null,"abstract":"<p>Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"185 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495273","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}
Yonatan Chemla, Connor J. Sweeney, Christopher A. Wozniak, Christopher A. Voigt
{"title":"Publisher Correction: Design and regulation of engineered bacteria for environmental release","authors":"Yonatan Chemla, Connor J. Sweeney, Christopher A. Wozniak, Christopher A. Voigt","doi":"10.1038/s41564-025-01956-2","DOIUrl":"https://doi.org/10.1038/s41564-025-01956-2","url":null,"abstract":"<p>Correction to: <i>Nature Microbiology</i> https://doi.org/10.1038/s41564-024-01918-0, published online 4 February 2025.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"18 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477667","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":"Planning and describing a microbiome data analysis","authors":"Amy D. Willis, David S. Clausen","doi":"10.1038/s41564-025-01944-6","DOIUrl":"https://doi.org/10.1038/s41564-025-01944-6","url":null,"abstract":"We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"18 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462488","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}
Ming-Yuan Li, Kao Deng, Xiao-He Cheng, Lewis Yu-Lam Siu, Zhuo-Ran Gao, Trupti Shivaprasad Naik, Viktoriya G. Stancheva, Peter Pak-Hang Cheung, Qi-Wen Teo, Sophie W. van Leur, Ho-Him Wong, Yun Lan, Tommy Tsan-Yuk Lam, Meng-Xu Sun, Na-Na Zhang, Yue Zhang, Tian-Shu Cao, Fan Yang, Yong-Qiang Deng, Sumana Sanyal, Cheng-Feng Qin
{"title":"ARF4-mediated intracellular transport as a broad-spectrum antiviral target","authors":"Ming-Yuan Li, Kao Deng, Xiao-He Cheng, Lewis Yu-Lam Siu, Zhuo-Ran Gao, Trupti Shivaprasad Naik, Viktoriya G. Stancheva, Peter Pak-Hang Cheung, Qi-Wen Teo, Sophie W. van Leur, Ho-Him Wong, Yun Lan, Tommy Tsan-Yuk Lam, Meng-Xu Sun, Na-Na Zhang, Yue Zhang, Tian-Shu Cao, Fan Yang, Yong-Qiang Deng, Sumana Sanyal, Cheng-Feng Qin","doi":"10.1038/s41564-025-01940-w","DOIUrl":"https://doi.org/10.1038/s41564-025-01940-w","url":null,"abstract":"<p>Host factors that are involved in modulating cellular vesicular trafficking of virus progeny could be potential antiviral drug targets. ADP-ribosylation factors (ARFs) are GTPases that regulate intracellular vesicular transport upon GTP binding. Here we demonstrate that genetic depletion of ARF4 suppresses viral infection by multiple pathogenic RNA viruses including Zika virus (ZIKV), influenza A virus (IAV) and SARS-CoV-2. Viral infection leads to ARF4 activation and virus production is rescued upon complementation with active ARF4, but not with inactive mutants. Mechanistically, ARF4 deletion disrupts translocation of virus progeny into the Golgi complex and redirects them for lysosomal degradation, thereby blocking virus release. More importantly, peptides targeting ARF4 show therapeutic efficacy against ZIKV and IAV challenge in mice by inhibiting ARF4 activation. Our findings highlight the role of ARF4 during viral infection and its potential as a broad-spectrum antiviral target for further development.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"1 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443318","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":"Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid","authors":"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","doi":"10.1038/s41564-025-01937-5","DOIUrl":"https://doi.org/10.1038/s41564-025-01937-5","url":null,"abstract":"<p>Intestinal crypts harbour a specific microbiota but whether and how these bacteria regulate intestinal stem cells (ISCs) or influence colorectal cancer (CRC) development is unclear. Here we screened crypt-resident bacteria in organoids and found that indole acetic acid (IAA) secreted by <i>Acinetobacter radioresistens</i> inhibits ISC turnover. <i>A. radioresistens</i> inhibited cellular proliferation in tumour slices from CRC patients and inhibited intestinal tumorigenesis and spheroid initiation in APC<sup>Min/+</sup> mice. Targeted clearance of <i>A. radioresistens</i> from colonic crypts using bacteriophage increased EphB2 expression and consequently promoted cellular proliferation, ISC turnover and tumorigenesis in mouse models of CRC. The protective effects of <i>A. radioresistens</i> were abrogated upon deletion of <i>trpC</i> to prevent IAA production, or upon intestine-specific aryl hydrocarbon receptor (AhR) knockout, identifying an IAA-AhR-Wnt-β-catenin signalling axis that promotes ISC homeostasis. Our findings reveal a protective role for an intestinal crypt-resident microbiota member in tumorigenesis.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"29 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443314","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":"ILC3s regulate the gut microbiota via host intestinal galactosylation to limit pathogen infection in mice","authors":"Wenyan Wang, Na Li, Hongkai Xu, Siting Wei, Yiping Li, Jiayao Ou, Jiacheng Hao, Jing Zhang, Liyou Dong, Ying Qiu, Xiaoyu Hu, Yang-Xin Fu, Xiaohuan Guo","doi":"10.1038/s41564-025-01933-9","DOIUrl":"https://doi.org/10.1038/s41564-025-01933-9","url":null,"abstract":"<p>Host immunity and commensal bacteria synergistically maintain intestinal homeostasis and mediate colonization resistance against pathogens. However, the molecular and cellular mechanisms remain unclear. Here, with a mouse infection model of <i>Citrobacter rodentium</i>, a natural mouse intestinal pathogen that mimics human enteropathogenic <i>Escherichia coli</i> and enterohaemorrhagic <i>Escherichia coli</i>, we find that group 3 innate lymphoid cells (ILC3s) can protect the host from infection by regulating gut microbiota. Mechanistically, ILC3s can control gut dysbiosis through IL-22-dependent regulation of intestinal galactosylation in mice. ILC3 deficiency led to an increase in intestinal galactosylation and the expansion of commensal <i>Akkermansia muciniphila</i> in colonic mucus. The increased <i>A. muciniphila</i> and <i>A. muciniphila</i>-derived metabolic product succinate further promoted the expression of pathogen virulence factors <i>tir</i> and <i>ler</i>, resulting in increased susceptibility to <i>C. rodentium</i> infection. Together, our data reveal a mechanism for ILC3s in protecting against pathogen infection through the regulation of intestinal glycosylation and gut microbiota metabolism.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426988","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}
Riccardo Vernuccio, Alejandro Martínez León, Chetan S. Poojari, Julian Buchrieser, Christopher N. Selverian, Yakin Jaleta, Annalisa Meola, Florence Guivel-Benhassine, Françoise Porrot, Ahmed Haouz, Maelenn Chevreuil, Bertrand Raynal, Jason Mercer, Etienne Simon-Loriere, Kartik Chandran, Olivier Schwartz, Jochen S. Hub, Pablo Guardado-Calvo
{"title":"Structural insights into tecovirimat antiviral activity and poxvirus resistance","authors":"Riccardo Vernuccio, Alejandro Martínez León, Chetan S. Poojari, Julian Buchrieser, Christopher N. Selverian, Yakin Jaleta, Annalisa Meola, Florence Guivel-Benhassine, Françoise Porrot, Ahmed Haouz, Maelenn Chevreuil, Bertrand Raynal, Jason Mercer, Etienne Simon-Loriere, Kartik Chandran, Olivier Schwartz, Jochen S. Hub, Pablo Guardado-Calvo","doi":"10.1038/s41564-025-01936-6","DOIUrl":"https://doi.org/10.1038/s41564-025-01936-6","url":null,"abstract":"<p>Mpox is a zoonotic disease endemic to Central and West Africa. Since 2022, two human-adapted monkeypox virus (MPXV) strains have caused large outbreaks outside these regions. Tecovirimat is the most widely used drug to treat mpox. It blocks viral egress by targeting the viral phospholipase F13; however, the structural details are unknown, and mutations in the F13 gene can result in resistance against tecovirimat, raising public health concerns. Here we report the structure of an F13 homodimer using X-ray crystallography, both alone (2.1 Å) and in complex with tecovirimat (2.6 Å). Combined with molecular dynamics simulations and dimerization assays, we show that tecovirimat acts as a molecular glue that promotes dimerization of the phospholipase. Tecovirimat resistance mutations identified in clinical MPXV isolates map to the F13 dimer interface and prevent drug-induced dimerization in solution and in cells. These findings explain how tecovirimat works, allow for better monitoring of resistant MPXV strains and pave the way for developing more potent and resilient therapeutics.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"22 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393189","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}
Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang
{"title":"Publisher Correction: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome","authors":"Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang","doi":"10.1038/s41564-025-01951-7","DOIUrl":"https://doi.org/10.1038/s41564-025-01951-7","url":null,"abstract":"<p>Correction to: <i>Nature Microbiology</i> https://doi.org/10.1038/s41564-024-01914-4, published online 3 February 2025.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"50 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393363","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}
Chinmay Dwibedi, Annika S. Axelsson, Birgitta Abrahamsson, Jed W. Fahey, Olof Asplund, Ola Hansson, Emma Ahlqvist, Valentina Tremaroli, Fredrik Bäckhed, Anders H. Rosengren
{"title":"Effect of broccoli sprout extract and baseline gut microbiota on fasting blood glucose in prediabetes: a randomized, placebo-controlled trial","authors":"Chinmay Dwibedi, Annika S. Axelsson, Birgitta Abrahamsson, Jed W. Fahey, Olof Asplund, Ola Hansson, Emma Ahlqvist, Valentina Tremaroli, Fredrik Bäckhed, Anders H. Rosengren","doi":"10.1038/s41564-025-01932-w","DOIUrl":"https://doi.org/10.1038/s41564-025-01932-w","url":null,"abstract":"<p>More effective treatments are needed for impaired fasting glucose or glucose intolerance, known as prediabetes. Sulforaphane is an isothiocyanate that reduces hepatic gluconeogenesis in individuals with type 2 diabetes and is well tolerated when provided as a broccoli sprout extract (BSE). Here we report a randomized, double-blind, placebo-controlled trial in which drug-naive individuals with prediabetes were treated with BSE (<i>n</i> = 35) or placebo (<i>n</i> = 39) once daily for 12 weeks. The primary outcome was a 0.3 mmol l<sup>−1</sup> reduction in fasting blood glucose compared with placebo from baseline to week 12. Gastro-intestinal side effects but no severe adverse events were observed in response to treatment. BSE did not meet the prespecified primary outcome, and the overall effect in individuals with prediabetes was a 0.2 mmol l<sup>−1</sup> reduction in fasting blood glucose (95% confidence interval −0.44 to −0.01; <i>P</i> = 0.04). Exploratory analyses to identify subgroups revealed that individuals with mild obesity, low insulin resistance and reduced insulin secretion had a pronounced response (0.4 mmol l<sup>−1</sup> reduction) and were consequently referred to as responders. Gut microbiota analysis further revealed an association between baseline gut microbiota and pathophysiology and that responders had a different gut microbiota composition. Genomic analyses confirmed that responders had a higher abundance of a <i>Bacteroides</i>-encoded transcriptional regulator required for the conversion of the inactive precursor to bioactive sulforaphane. The abundance of this gene operon correlated with sulforaphane serum concentration. These findings suggest a combined influence of host pathophysiology and gut microbiota on metabolic treatment response, and exploratory analyses need to be confirmed in future trials. ClinicalTrials.gov registration: NCT03763240.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"41 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375380","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}