Emma J Banks, Pavol Bárdy, Ngat T Tran, Phuong M Nguyen, Boris Stojilković, Kevin Gozzi, Abbas Maqbool, Tung B K Le
{"title":"A bacterial CARD-NLR-like immune system controls the release of gene transfer agents.","authors":"Emma J Banks, Pavol Bárdy, Ngat T Tran, Phuong M Nguyen, Boris Stojilković, Kevin Gozzi, Abbas Maqbool, Tung B K Le","doi":"10.1038/s41564-026-02316-4","DOIUrl":"10.1038/s41564-026-02316-4","url":null,"abstract":"<p><p>Bacteria use immune systems to detect and defend against mobile genetic elements including phages. Gene transfer agents (GTAs) are domesticated prophages with phage-like characteristics including the ability to induce host cell lysis for gene transfer. Whether GTAs elicit or avoid bacterial immune systems is poorly understood. Here, a transposon mutagenesis with deep sequencing screen in Caulobacter crescentus identified a tripartite system, LypABC, essential for GTA-mediated cell lysis and gene transfer. LypABC resembles a caspase recruitment domain-nucleotide-binding leucine-rich repeat (CARD-NLR) anti-phage defence system. LypABC is dispensable for DNA packaging into GTA particles but required for host cell lysis, involving the peptidase domains of LypA and LypC, and the ATPase domain of LypB. As LypABC overproduction is toxic, strict regulation through the transcriptional repressor CdxB is required. CdxB binds the promoters of lypABC and of essential GTA activator genes, coupling GTA activation to host cell lysis. Our findings suggest that bacterial immune systems can be co-opted to support horizontal gene transfer by GTAs.</p>","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":" ","pages":""},"PeriodicalIF":19.4,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147699024","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":"Structure of Crimean-Congo haemorrhagic fever virus RNA polymerase.","authors":"Dong Wang,Ge Yang,Bin Liu","doi":"10.1038/s41564-026-02319-1","DOIUrl":"https://doi.org/10.1038/s41564-026-02319-1","url":null,"abstract":"Crimean-Congo haemorrhagic fever virus (CCHFV) is a highly pathogenic member of the Nairoviridae and causes severe disease with high fatality rates. Currently, there are no approved antivirals for CCHFV, but resolving the structure of its RNA-dependent RNA polymerase, termed L protein, could help drug development. Here we report cryogenic electron microscopy structures of the CCHFV L protein in both apo and RNA-bound states at 2.62 Å and 2.53 Å, respectively. These structures define the molecular architecture of the PA-, PB1- and PB2-like domains within the polymerase core, elucidate the mechanism of promoter recognition and reveal RNA-induced conformational changes that stabilize catalytic elements. Together, these insights provide a structural framework for understanding nairovirus replication and enable structure-based development of polymerase inhibitors.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"112 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147695176","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}
Anders Eivind Myhre,Malin Holm Meyer-Myklestad,Hanne Hestdal Gullaksen,Ole S Søgaard,Martin Tolstrup,Maria Salgado,Javier Martinez-Picado,Mona Holberg-Petersen,Anna Karina Juhl,Mariane H Schleimann,Jesper D Gunst,Astrid Thomsen,Katie Fisher,Jagjit Singh Bhamra,Anne-Marte Bakken Kran,Bente Halvorsen,Anne Ma Dyrhol-Riise,Dag Henrik Reikvam,Pål Aukrust,Tobias Gedde-Dahl, ,Tuva Børresdatter Dahl,Mari Kaarbø,Marius Trøseid
{"title":"Long-term HIV-1 remission achieved through allogeneic haematopoietic stem cell transplant from a CCR5Δ32/Δ32 sibling donor.","authors":"Anders Eivind Myhre,Malin Holm Meyer-Myklestad,Hanne Hestdal Gullaksen,Ole S Søgaard,Martin Tolstrup,Maria Salgado,Javier Martinez-Picado,Mona Holberg-Petersen,Anna Karina Juhl,Mariane H Schleimann,Jesper D Gunst,Astrid Thomsen,Katie Fisher,Jagjit Singh Bhamra,Anne-Marte Bakken Kran,Bente Halvorsen,Anne Ma Dyrhol-Riise,Dag Henrik Reikvam,Pål Aukrust,Tobias Gedde-Dahl, ,Tuva Børresdatter Dahl,Mari Kaarbø,Marius Trøseid","doi":"10.1038/s41564-026-02304-8","DOIUrl":"https://doi.org/10.1038/s41564-026-02304-8","url":null,"abstract":"Only few cases of human immunodeficiency virus (HIV) remission have been reported after allogeneic haematopoietic stem cell transplantation (HSCT), mostly involving stem cell donors with the homozygous CCR5Δ32 (CCR5Δ32/Δ32) mutation, which confers resistance to CCR5-tropic HIV-1. Here we report the case of a 63-year-old man in off-treatment HIV remission, 5 years after HSCT with a CCR5Δ32/Δ32 sibling donor for myelodysplastic syndrome. In-depth clinical characterization including virological and immunological analyses of peripheral blood, gut and bone marrow samples revealed that full donor chimerism was achieved. Antiretroviral therapy was discontinued after 24 months, and 48 months after HSCT, no intact HIV DNA was detected in blood or gut biopsies. Replication-competent virus and HIV-specific T cell responses were absent, and HIV antibody responses showed a gradual decline. Full donor chimerism in the gut, which is the primary viral reservoir, underscores the likelihood of a cure.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147666546","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}
Xue Li,Grace A Arya,Aung Myint Thu,Jordi Landier,Daniel M Parker,Gilles Delmas,Ann Reyes,Khin Maung Lwin,Kanlaya Sriprawat,François Nosten,Timothy J C Anderson
{"title":"Impact of intensive control on malaria population genomics under elimination settings in Southeast Asia.","authors":"Xue Li,Grace A Arya,Aung Myint Thu,Jordi Landier,Daniel M Parker,Gilles Delmas,Ann Reyes,Khin Maung Lwin,Kanlaya Sriprawat,François Nosten,Timothy J C Anderson","doi":"10.1038/s41564-026-02327-1","DOIUrl":"https://doi.org/10.1038/s41564-026-02327-1","url":null,"abstract":"The malaria elimination programme in Kayin State (Myanmar) uses malaria posts for rapid detection and treatment, together with mass drug administration in high-transmission villages, which has reduced transmission by 97%. Here we examine the impact of control on parasite genomic parameters to inform future control efforts. Using 2,270 genome-sequenced Plasmodium falciparum infections from 283 malaria posts, sampled over 58 months (2015-2020), we find that parasite effective population size decreased over the study period, but there was minimal change in artemisinin resistance allele frequency until 2020, when just one predominant genotype (carrying kelch13-R561H) remained. We observed sustained localized transmission of unique parasite genotypes revealing transmission chains and positive correlations in parasite relatedness for ≤20 km. Mass drug administration resulted in parasite founder effects, providing genomic evidence for the efficacy of this control tool. These results reveal changes in population structure driven by control and rapid shifts in allele frequency in a parasite population close to elimination.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"65 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147666497","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}
Ian M Gois,Connor M Bowers,Byung-Chul Kim,Robert Flick,Christopher E Lawson
{"title":"Acetate utilization strategy in chain-elongating bacteria determines butyrate versus medium-chain carboxylate production.","authors":"Ian M Gois,Connor M Bowers,Byung-Chul Kim,Robert Flick,Christopher E Lawson","doi":"10.1038/s41564-026-02320-8","DOIUrl":"https://doi.org/10.1038/s41564-026-02320-8","url":null,"abstract":"Chain-elongating bacteria (CEB) are a unique guild of anaerobes that upcycle organic waste into valuable short- and medium-chain carboxylic acids (MCCAs), enabling a circular bioeconomy. However, the metabolic rules that determine product chain length have remained elusive. Here we combine 13C isotope tracing, proteomics, enzyme assays and metabolic modelling to show that distinct acetate utilization strategies underlie the divergence between MCCA-producing CEB and those solely producing less valuable, short-chain butyrate. MCCA-producing strains recycle acetate to maximize lactate use under acetate limitation, but at the cost of slower growth. In contrast, butyrate-producing strains grow faster by favouring acetate assimilation, at the cost of restricted lactate utilization when acetate is scarce. These physiological trade-offs are encoded in the substrate specificity of coenzyme A transferase, the terminal enzyme in reverse β-oxidation. Our findings uncover a fundamental constraint shaping chain-length selectivity in CEB and offer strategies that could optimize MCCA production from organic waste streams.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147666545","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}
Tsuyoshi Uehara, Allison L. Zulli, Brittany Miller, Lindsay M. Avery, Steven A. Boyd, Cassandra L. Chatwin, Guo-Hua Chu, Anthony S. Drager, Mitchell Edwards, Susan G. Emeigh Hart, Nathan J. Line, Cullen L. Myers, Gopinath Rongala, Annie Stevenson, Kyoko Uehara, Fan Yi, Bibo Wang, Zhenwu Liu, Mingyue Wang, Zhichao Zhao, Xinming Zhou, Haiyan Zhao, Caleb M. Stratton, Sandeepchowdary Bala, Christopher Davies, Rok Tkavc, Ann E. Jerse, Daniel C. Pevear, Christopher J. Burns, Denis M. Daigle, Stephen M. Condon
{"title":"A penicillin-binding protein inhibitor series to target drug-resistant Neisseria gonorrhoeae","authors":"Tsuyoshi Uehara, Allison L. Zulli, Brittany Miller, Lindsay M. Avery, Steven A. Boyd, Cassandra L. Chatwin, Guo-Hua Chu, Anthony S. Drager, Mitchell Edwards, Susan G. Emeigh Hart, Nathan J. Line, Cullen L. Myers, Gopinath Rongala, Annie Stevenson, Kyoko Uehara, Fan Yi, Bibo Wang, Zhenwu Liu, Mingyue Wang, Zhichao Zhao, Xinming Zhou, Haiyan Zhao, Caleb M. Stratton, Sandeepchowdary Bala, Christopher Davies, Rok Tkavc, Ann E. Jerse, Daniel C. Pevear, Christopher J. Burns, Denis M. Daigle, Stephen M. Condon","doi":"10.1038/s41564-026-02309-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02309-3","url":null,"abstract":"Emerging multidrug-resistant Neisseria gonorrhoeae strains possessing altered penA alleles (encoding penicillin-binding protein 2, PBP2) threaten the utility of ceftriaxone, the last remaining outpatient antibiotic for gonorrhoea treatment, posing a global health emergency. Here we report a benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) developed to address penA-mediated ceftriaxone resistance. Optimization of boro-PBPi led to the identification of compound 21 (VNRX-14079), which exhibited potent antibacterial activity against multidrug-resistant N. gonorrhoeae through high-affinity binding to the PBP2 target. Boro-PBPi–PBP2 complex structures confirmed the covalent interaction of the boron atom with the catalytic residue Ser310 and the importance of the β3–β4 loop mobility for improved affinity. Boro-PBPi 21 elicits bactericidal activity, a low frequency of resistance, a good safety profile, suitable pharmacokinetic properties and in vivo efficacy in a murine infection model against ceftriaxone-resistant N. gonorrhoeae. Boro-PBPi 21 is therefore a promising antigonorrhoea agent poised for further advancement.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"5 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147631132","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}
Jiabao Liu, Hao Li, Yintai Tian, Miao Guo, Cigdem Sahin, Shotaro Kamata, Akihiro Honda, Jhenielle Campbell, Jin Shi, Emine Dide Yurtal, Diwen Yang, Matthew Jachimowicz, Shian Hu, Yufeng Gong, William Navarre, Isao Ishii, Carolyn L. Cummins, Hui Peng, Shengpeng Wang, Xiaojuan Wang, Sridhar Mani, Henry M. Krause
{"title":"Microbial 10-oxostearic acid protects mice against colitis via the nuclear receptor PPARα","authors":"Jiabao Liu, Hao Li, Yintai Tian, Miao Guo, Cigdem Sahin, Shotaro Kamata, Akihiro Honda, Jhenielle Campbell, Jin Shi, Emine Dide Yurtal, Diwen Yang, Matthew Jachimowicz, Shian Hu, Yufeng Gong, William Navarre, Isao Ishii, Carolyn L. Cummins, Hui Peng, Shengpeng Wang, Xiaojuan Wang, Sridhar Mani, Henry M. Krause","doi":"10.1038/s41564-026-02321-7","DOIUrl":"https://doi.org/10.1038/s41564-026-02321-7","url":null,"abstract":"Interactions between the host, diet and intestinal microbiota are critical for metabolic and immune homeostasis, but the intersecting metabolites and receptors remain poorly defined. Here we identify 10-oxostearic acid (10-oxoSA), a microbial metabolite derived from oleic acid, the most abundant fatty acid in nature, as a potent and selective agonist of the lipid-sensing nuclear receptor peroxisome proliferator-activated receptor alpha (PPARα). Biochemical and structural analyses reveal that 10-oxoSA binds PPARα with higher affinity than previously identified endogenous ligands. In a mouse model of colitis, 10-oxoSA confers protection in a PPARα-dependent manner. Multi-tissue transcriptomics show that 10-oxoSA upregulates beneficial PPARα target genes in the ileum and colon, many in previously unrecognized pathways, while also circumventing deleterious hepatic responses. Multi-omics analyses also show that prolonged oral 10-oxoSA administration is well tolerated in the gut and liver with minimal impact on gut microbiota composition. These findings establish a natural diet–microbiota–host axis with potential for anti-inflammatory interventions.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"18 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147631129","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}
Claude Kwe Yinda, John-Sebastian Eden, Erica T. Prates, Anna Vlot, Sarah van Tol, Sarah L. Anzick, Jianning Wang, Kim Halpin, Benny Borremans, Tamika J. Lunn, Kent Barbian, Brown Bulloch, Benjamin Greene, Kimberly Meade-White, Trenton Bushmaker, Caylee A. Falvo, Daniel E. Crowley, Devin N. Jones-Slobodian, Manesh Shah, Mirko Pavicic, William Carr, Craig Martens, Daniel Jacobson, Raina K. Plowright, Alison J. Peel, Vincent J. Munster
{"title":"Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats","authors":"Claude Kwe Yinda, John-Sebastian Eden, Erica T. Prates, Anna Vlot, Sarah van Tol, Sarah L. Anzick, Jianning Wang, Kim Halpin, Benny Borremans, Tamika J. Lunn, Kent Barbian, Brown Bulloch, Benjamin Greene, Kimberly Meade-White, Trenton Bushmaker, Caylee A. Falvo, Daniel E. Crowley, Devin N. Jones-Slobodian, Manesh Shah, Mirko Pavicic, William Carr, Craig Martens, Daniel Jacobson, Raina K. Plowright, Alison J. Peel, Vincent J. Munster","doi":"10.1038/s41564-025-02254-7","DOIUrl":"10.1038/s41564-025-02254-7","url":null,"abstract":"Hendra virus (HeV) was discovered in 1994 in Australia. Limited genomic data have hindered comprehensive understanding of HeV’s evolutionary dynamics. Here we recovered 48 HeV genomes from bats and 9 from horses from Australia between 2016 and 2020, revealing four distinct clades. Each clade was distributed over a large spatial area with multiple clades co-circulating within a single bat roost on the same day and over consecutive years. The diversity and temporal stability of co-circulating clades suggest that viral dynamics are driven by episodic shedding of existing lineages maintained at the population level, rather than immune-driven strain-replacement dynamics. HeV isolates of different clades displayed variation in phenotypic properties but minimal antigenic differences. We provide an overview of evolutionary dynamics, phenotypic properties and assessment of countermeasures for HeV, and provide insights into the processes that maintain virus diversity in bats and influence the potential for viral emergence. Recovery of 48 bat and 9 horse HeV genomes from Australia (2016–2020) identified four Hendra virus clades, offering insights into evolutionary dynamics.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 4","pages":"851-866"},"PeriodicalIF":19.4,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-025-02254-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626395","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":"Local peptidoglycan composition defines division site selection in Streptococcus pneumoniae.","authors":"Adrien Ducret,Cassandra Falcou,Céline Freton,Sathya Narayanan Nagarajan,Christophe Grangeasse","doi":"10.1038/s41564-026-02322-6","DOIUrl":"https://doi.org/10.1038/s41564-026-02322-6","url":null,"abstract":"Accurate division site placement is essential for bacteria to produce viable daughter cells. In the ovoid-shaped Streptococcus pneumoniae, previous work showed that division site placement depends on both the protein MapZ and chromosome segregation, although specific mechanisms remain unclear. Here we imaged fluorescently labelled S. pneumoniae, observing division site placement at the cell equator, the widest part of the cell, not at the mid-cell. Disruption of chromosome segregation neither affected MapZ nor divisome positioning, suggesting that division site selection can occur independently of chromosome segregation. MapZ localization depends on the sequential recruitment of two peptidoglycan decarboxylases, DacA and DacB, to the division site. DacA and DacB activity during early peptidoglycan synthesis generates a distinctive, tetrapeptide signature required for MapZ binding. As the cell cycle progresses, this signature becomes enriched at cell equators, recruiting MapZ so that these equators eventually serve as the division site in daughter cells. These findings update the mechanism of division site placement in S. pneumoniae.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"64 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147630267","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":"Advancing microbiology through foundational science","authors":"","doi":"10.1038/s41564-026-02335-1","DOIUrl":"10.1038/s41564-026-02335-1","url":null,"abstract":"Microorganisms have tremendous potential to impact humanity, but such revelations are only possible in the light of foundational, discovery-based microbiology research.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"11 4","pages":"837-838"},"PeriodicalIF":19.4,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41564-026-02335-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626394","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}