Nature Microbiology最新文献

{"title":"Working together with mutual respect","authors":"","doi":"10.1038/s41564-024-01828-1","DOIUrl":"10.1038/s41564-024-01828-1","url":null,"abstract":"We provide a brief insight into our roles as professional journal editors to facilitate mutually respectful relationships between scientists and editors.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2465-2465"},"PeriodicalIF":20.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01828-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361811","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":"Pathogen genomic surveillance status among lower resource settings in Asia","authors":"Marya Getchell, Suci Wulandari, Ruklanthi de Alwis, Shreya Agoramurthy, Yoong Khean Khoo, Tze-Minn Mak, La Moe, Anne-Claire Stona, Junxiong Pang, Muhd Haziq Fikry Haji Abdul Momin, Afreenish Amir, Lucia Rizka Andalucia, Ghows Azzam, Savuth Chin, Thanat Chookajorn, Govindakarnavar Arunkumar, Do Thai Hung, Aamer Ikram, Runa Jha, Erik A. Karlsson, Mai Quynh Le Thi, Surakameth Mahasirimongkol, Gathsaurie Neelika Malavige, Jessica E. Manning, Syarifah Liza Munira, Nguyen Vu Trung, Imran Nisar, Firdausi Qadri, Farah Naz Qamar, Matthew T. Robinson, Cynthia P. Saloma, Swe Setk, Tahmina Shirin, Le Van Tan, Timothy John R. Dizon, Ravindran Thayan, Hlaing Myat Thu, Hasitha Tissera, Phonepadith Xangsayarath, Zainun Zaini, John C. W. Lim, Sebastian Maurer-Stroh, Gavin J. D. Smith, Lin-Fa Wang, Paul Pronyk, On behalf of the Asia Pathogen Genomics Initiative (Asia PGI) consortium","doi":"10.1038/s41564-024-01809-4","DOIUrl":"10.1038/s41564-024-01809-4","url":null,"abstract":"Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in low-resource settings in South and Southeast Asia. Data collected between June 2022 and March 2023 from 42 institutions in 13 countries showed pathogen genomics capacity exists, but use is limited and under-resourced. All countries had NGS capacity and seven countries had strategic plans integrating pathogen genomics into wider surveillance efforts. Several pathogens were prioritized for human surveillance, but NGS application to environmental and human–animal interface surveillance was limited. Barriers to NGS implementation include reliance on external funding, supply chain challenges, trained personnel shortages and limited quality assurance mechanisms. Coordinated efforts are required to support national planning, address capacity gaps, enhance quality assurance and facilitate data sharing for decision making. Surveying next generation sequencing capabilities in 13 Asian countries identifies challenges to be met for improved implementation, pathogen surveillance and integration into public health decision-making.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2738-2747"},"PeriodicalIF":20.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01809-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142313713","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":"Specialized Listeria monocytogenes produce tailocins to provide a population-level competitive growth advantage","authors":"Nadejda Sigal, Rotem Lichtenstein-Wolfheim, Shai Schlussel, Gil Azulay, Ilya Borovok, Vered Holdengraber, Nadav Elad, Sharon G. Wolf, Ran Zalk, Raz Zarivach, Gabriel A. Frank, Anat A. Herskovits","doi":"10.1038/s41564-024-01793-9","DOIUrl":"10.1038/s41564-024-01793-9","url":null,"abstract":"Tailocins are phage tail-like bacteriocins produced by various bacterial species to kill kin competitors. Given that tailocin release is dependent upon cell lysis, regulation of tailocin production at the single-cell and population level remains unclear. Here we used flow cytometry, competition assays and structural characterization of tailocin production in a human bacterial pathogen, Listeria monocytogenes. We revealed that a specialized subpopulation, constituting less than 1% of the total bacterial population, differentiates to produce, assemble and store thousands of tailocin particles. Tailocins are packed in a highly ordered manner, clustered in a liquid crystalline phase that occupies a substantial volume of the cell. Tailocin production confers a competitive growth advantage for the rest of the population. This study provides molecular insights into tailocin production as a form of altruism, showing how cell specialization within bacterial populations can confer competitive advantages at the population level. Specialized Listeria monocytogenes subpopulations produce high quantities of densely packed tailocins to confer a population-level advantage against kin competitors.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2727-2737"},"PeriodicalIF":20.5,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245304","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":"Cell envelope diversity and evolution across the bacterial tree of life","authors":"Ameena Hashimi, Elitza I. Tocheva","doi":"10.1038/s41564-024-01812-9","DOIUrl":"10.1038/s41564-024-01812-9","url":null,"abstract":"The bacterial cell envelope is a complex multilayered structure conserved across all bacterial phyla. It is categorized into two main types based on the number of membranes surrounding the cell. Monoderm bacteria are enclosed by a single membrane, whereas diderm cells are distinguished by the presence of a second, outer membrane (OM). An ancient divide in the bacterial domain has resulted in two major clades: the Gracilicutes, consisting strictly of diderm phyla; and the Terrabacteria, encompassing monoderm and diderm species with diverse cell envelope architectures. Recent structural and phylogenetic advancements have improved our understanding of the diversity and evolution of the OM across the bacterial tree of life. Here we discuss cell envelope variability within major bacterial phyla and focus on conserved features found in diderm lineages. Characterizing the mechanisms of OM biogenesis and the evolutionary gains and losses of the OM provides insights into the primordial cell and the last universal common ancestor from which all living organisms subsequently evolved. This Review discusses the diversity of cell envelope architectures across major bacterial phyla and highlights conserved features found in diderm lineages.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2475-2487"},"PeriodicalIF":20.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236289","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":"Bismuth-based drugs sensitize Pseudomonas aeruginosa to multiple antibiotics by disrupting iron homeostasis","authors":"Yushan Xia, Xueying Wei, Peng Gao, Chenyuan Wang, Anne de Jong, Jonathan Hon Kwan Chen, María José Rodríguez-Sánchez, Alba Rodríguez-Nogales, Patricia Diez-Echave, Julio Gálvez, Federico García, Weihui Wu, Richard Yi-Tsun Kao, Hongyan Li, Rubén Cebrián, Oscar P. Kuipers, Hongzhe Sun","doi":"10.1038/s41564-024-01807-6","DOIUrl":"10.1038/s41564-024-01807-6","url":null,"abstract":"Pseudomonas aeruginosa infections are difficult to treat due to rapid development of antibiotic drug resistance. The synergistic combination of already-in-use drugs is an alternative to developing new antibiotics to combat antibiotic-resistant bacteria. Here we demonstrate that bismuth-based drugs (bismuth subsalicylate, colloidal bismuth subcitrate) in combination with different classes of antibiotics (tetracyclines, macrolides, quinolones, rifamycins and so on) can eliminate multidrug-resistant P. aeruginosa and do not induce development of antibiotic resistance. Bismuth disrupts iron homeostasis by binding to P. aeruginosa siderophores. Inside cells, bismuth inhibits the electron transport chain, dissipates the proton motive force and impairs efflux pump activity by disrupting iron–sulfur cluster-containing enzymes, including respiration complexes. As a result, bismuth facilitates antibiotic accumulation inside bacteria, enhancing their efficacy. The combination therapy shows potent antibacterial efficacy and low toxicity in an ex vivo bacteraemia model and increases the survival rate of mice in in vivo mouse lung-infection models. Our findings highlight the potential of bismuth-based drugs to be repurposed to combat P. aeruginosa infections in combination with clinically used antibiotics. Bismuth-based drugs combined with antibiotics enhance efficacy against multidrug-resistant Pseudomonas aeruginosa by disrupting bacterial iron homeostasis and electron transport.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2600-2613"},"PeriodicalIF":20.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236274","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":"Taurolithocholic acid protects against viral haemorrhagic fever via inhibition of ferroptosis","authors":"Xiaojie Zheng, Yunfa Zhang, Lingyu Zhang, Tong Yang, Faxue Zhang, Xi Wang, Shu Jeffrey Zhu, Ning Cui, Hongdi Lv, Xiaoai Zhang, Hao Li, Wei Liu","doi":"10.1038/s41564-024-01801-y","DOIUrl":"10.1038/s41564-024-01801-y","url":null,"abstract":"Bile acids are microbial metabolites that can impact infection of enteric and hepatitis viruses, but their functions during systemic viral infection remain unclear. Here we show that elevated levels of the secondary bile acid taurolithocholic acid (TLCA) are associated with reduced fatality rates and suppressed viraemia in patients infected with severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging tick-borne haemorrhagic fever virus. TLCA inhibits viral replication and mitigates host inflammation during SFTSV infection in vitro, and indirectly suppresses SFTSV-mediated induction of ferroptosis by upregulating fatty acid desaturase 2 via the TGR5–PI3K/AKT–SREBP2 axis. High iron and ferritin serum levels during early infection were correlated with decreased TLCA levels and fatal outcomes in SFTSV-infected patients, indicating potential biomarkers. Furthermore, treatment with either ferroptosis inhibitors or TLCA protected mice from lethal SFTSV infection. Our findings highlight the therapeutic potential of bile acids to treat haemorrhagic fever viral infection. A microbially derived bile acid, taurolithocholic acid, limits viral replication, host inflammation and ferroptosis during infection with severe fever with thrombocytopenia syndrome virus, an emerging tick-borne haemorrhagic fever virus.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2583-2599"},"PeriodicalIF":20.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236277","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":"The host–parasite–virus triad","authors":"Elodie Ghedin, Megan R. Hockman","doi":"10.1038/s41564-024-01817-4","DOIUrl":"10.1038/s41564-024-01817-4","url":null,"abstract":"Sequencing data reveal highly diverse viromes associated with clinically important parasitic nematodes. Serological data suggest that this ongoing relationship could impact disease.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2473-2474"},"PeriodicalIF":20.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236273","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":"Protein interactions in human pathogens revealed through deep learning","authors":"Ian R. Humphreys, Jing Zhang, Minkyung Baek, Yaxi Wang, Aditya Krishnakumar, Jimin Pei, Ivan Anishchenko, Catherine A. Tower, Blake A. Jackson, Thulasi Warrier, Deborah T. Hung, S. Brook Peterson, Joseph D. Mougous, Qian Cong, David Baker","doi":"10.1038/s41564-024-01791-x","DOIUrl":"10.1038/s41564-024-01791-x","url":null,"abstract":"Identification of bacterial protein–protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue–residue coevolution and protein structure prediction to systematically identify and structurally characterize protein–protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them. RoseTTAFold2-Lite uses residue–residue coevolution and protein structure prediction to identify and structurally characterize protein–protein interactions in bacterial pathogens.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2642-2652"},"PeriodicalIF":20.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01791-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236275","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":"Silencing the transcriptionally active HIV reservoir to improve treatment outcomes","authors":"Julia Prigann, Rubens Tavora, Robert L. Furler O’Brien, Ursula Schulze-Gahmen, Daniela Boehm, Nadia R. Roan, Douglas F. Nixon, Lishomwa C. Ndhlovu, Susana Valente, Melanie Ott","doi":"10.1038/s41564-024-01816-5","DOIUrl":"10.1038/s41564-024-01816-5","url":null,"abstract":"Persistence of the transcriptionally active HIV reservoir has important implications for people living with HIV, including chronic immune activation and inflammation. Supplementing antiretroviral therapy with transcriptional inhibitors could overcome this by silencing the transcriptionally active HIV reservoir.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2470-2472"},"PeriodicalIF":20.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235100","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":"Lessons from a data scientist during COVID-19","authors":"Julie Chih-yu Chen","doi":"10.1038/s41564-024-01815-6","DOIUrl":"10.1038/s41564-024-01815-6","url":null,"abstract":"Julie Chih-yu Chen is the head of Data Sciences at the National Microbiology Laboratory, Public Health Agency of Canada, and an Assistant Professor at the University of Manitoba, Canada. She develops and applies statistical and machine learning techniques to diverse omics data related to infectious disease.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"9 10","pages":"2466-2467"},"PeriodicalIF":20.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235099","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}