Nature Microbiology最新文献

Longitudinal phage–bacteria dynamics in the early life gut microbiome

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01906-4

Michael J. Tisza, Richard E. Lloyd, Kristi Hoffman, Daniel P. Smith, Marian Rewers, Sara J. Javornik Cregeen, Joseph F. Petrosino

{"title":"Longitudinal phage–bacteria dynamics in the early life gut microbiome","authors":"Michael J. Tisza, Richard E. Lloyd, Kristi Hoffman, Daniel P. Smith, Marian Rewers, Sara J. Javornik Cregeen, Joseph F. Petrosino","doi":"10.1038/s41564-024-01906-4","DOIUrl":"https://doi.org/10.1038/s41564-024-01906-4","url":null,"abstract":"Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage–bacteria interactions in the developing early life microbiome.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"1 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026713","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}

引用次数: 0

Explainable artificial intelligence evolves antimicrobial peptides

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01919-z

Jeremie Alexander, Gary Liu, Jonathan M. Stokes

引用次数: 0

A gut microorganism turns the dial on sugar intake

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01917-1

Clémence Fayt, Nuria Morales-Puerto, Amandine Everard

引用次数: 0

Predicting child health with gut microbiome development trajectories

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01920-6

Douglas E. Johnson, Roshonda B. Jones

引用次数: 0

T cell-mediated protection in absence of virus neutralizing antibodies 缺乏病毒中和抗体的T细胞介导的保护

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-23 DOI: 10.1038/s41564-024-01921-5

Yeranddy A. Alpizar, Kai Dallmeier

引用次数: 0

The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics 真核细胞器动力学中涉及的Arf家族gtp酶的阿斯加德古菌起源

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-23 DOI: 10.1038/s41564-024-01904-6

Romana Vargová, Roxanne Chevreau, Marine Alves, Camille Courbin, Kara Terry, Pierre Legrand, Marek Eliáš, Julie Ménétrey, Joel B. Dacks, Catherine L. Jackson

{"title":"The Asgard archaeal origins of Arf family GTPases involved in eukaryotic organelle dynamics","authors":"Romana Vargová, Roxanne Chevreau, Marine Alves, Camille Courbin, Kara Terry, Pierre Legrand, Marek Eliáš, Julie Ménétrey, Joel B. Dacks, Catherine L. Jackson","doi":"10.1038/s41564-024-01904-6","DOIUrl":"https://doi.org/10.1038/s41564-024-01904-6","url":null,"abstract":"The evolution of eukaryotes is a fundamental event in the history of life. The closest prokaryotic lineage to eukaryotes, the Asgardarchaeota, encode proteins previously found only in eukaryotes, providing insight into their archaeal ancestor. Eukaryotic cells are characterized by endomembrane organelles, and the Arf family GTPases regulate organelle dynamics by recruiting effector proteins to membranes upon activation. The Arf family is ubiquitous among eukaryotes, but its origins remain elusive. Here we report a group of prokaryotic GTPases, the ArfRs, which are widely present in Asgardarchaeota. Phylogenetic analyses reveal that eukaryotic Arf family proteins arose from the ArfR group. Expression of representative Asgardarchaeota ArfR proteins in yeast and X-ray crystallographic studies show that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results indicate that Arf family GTPases originated in the archaeal ancestor of eukaryotes, consistent with aspects of the endomembrane system evolving early in eukaryogenesis.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"32 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020842","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}

引用次数: 0

KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid 在多药耐药质粒中，KorB从dna滑动钳转换为抑制因子介导远程基因沉默

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-23 DOI: 10.1038/s41564-024-01915-3

Thomas C. McLean, Francisco Balaguer-Pérez, Joshua Chandanani, Christopher M. Thomas, Clara Aicart-Ramos, Sophia Burick, Paul Dominic B. Olinares, Giulia Gobbato, Julia E. A. Mundy, Brian T. Chait, David M. Lawson, Seth A. Darst, Elizabeth A. Campbell, Fernando Moreno-Herrero, Tung B. K. Le

{"title":"KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid","authors":"Thomas C. McLean, Francisco Balaguer-Pérez, Joshua Chandanani, Christopher M. Thomas, Clara Aicart-Ramos, Sophia Burick, Paul Dominic B. Olinares, Giulia Gobbato, Julia E. A. Mundy, Brian T. Chait, David M. Lawson, Seth A. Darst, Elizabeth A. Campbell, Fernando Moreno-Herrero, Tung B. K. Le","doi":"10.1038/s41564-024-01915-3","DOIUrl":"https://doi.org/10.1038/s41564-024-01915-3","url":null,"abstract":"Examples of long-range gene regulation in bacteria are rare and generally thought to involve DNA looping. Here, using a combination of biophysical approaches including X-ray crystallography and single-molecule analysis for the KorB–KorA system in Escherichia coli, we show that long-range gene silencing on the plasmid RK2, a source of multi-drug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We show that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters up to 1.5 kb away. We resolved the tripartite crystal structure of a KorB–KorA–DNA co-complex, revealing that KorA latches KorB into a closed clamp state. DNA-bound KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Together, our findings explain the mechanistic basis for KorB role switching from a DNA-sliding clamp to a co-repressor and provide an alternative mechanism for long-range regulation of gene expression in bacteria.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"81 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020619","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}

引用次数: 0

Microbiome science needs more microbiologists 微生物组学需要更多的微生物学家

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-22 DOI: 10.1038/s41564-024-01922-4

Lauren C. Radlinski, Andreas J. Bäumler

引用次数: 0

Author Correction: Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium 作者更正：tRNA基因表达的适应性丧失导致海洋藻蓝聚球菌的噬菌体抗性

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-20 DOI: 10.1038/s41564-025-01934-8

Sophia Zborowsky, Ran Tahan, Debbie Lindell

引用次数: 0

A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics 8,176 个蝙蝠 RNA 病毒元基因组简编揭示了生态驱动因素和循环动态

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-20 DOI: 10.1038/s41564-024-01884-7

Xiaomin Yan, Yang Liu, Tingsong Hu, Zhenglanyi Huang, Chenxi Li, Lei Guo, Yuhang Liu, Nan Li, Hailin Zhang, Yue Sun, Le Yi, Jianmin Wu, Jiang Feng, Fuqiang Zhang, Tinglei Jiang, Changchun Tu, Biao He

{"title":"A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics","authors":"Xiaomin Yan, Yang Liu, Tingsong Hu, Zhenglanyi Huang, Chenxi Li, Lei Guo, Yuhang Liu, Nan Li, Hailin Zhang, Yue Sun, Le Yi, Jianmin Wu, Jiang Feng, Fuqiang Zhang, Tinglei Jiang, Changchun Tu, Biao He","doi":"10.1038/s41564-024-01884-7","DOIUrl":"https://doi.org/10.1038/s41564-024-01884-7","url":null,"abstract":"Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"49 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989987","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}

引用次数: 0