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Wu Z, Guo L, Wu Y, Yang M, Du S, Shao J, Zhang Z, Zhao Y. Novel phage infecting the Roseobacter CHUG lineage reveals a diverse and globally distributed phage family. mSphere 2024:e0045824. [PMID: 38926906 DOI: 10.1128/msphere.00458-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Bacteriophages play an essential role in shaping the diversity and metabolism of bacterial communities. Marine Roseobacter group is an abundant heterotrophic bacterial group that is involved in many major element cycles, especially carbon and sulfur. Members of the Roseobacter CHUG (Clade Hidden and Underappreciated Globally) lineage are globally distributed and are activated in pelagic marine environments. In this study, we isolated and characterized a phage, CRP-810, that infects the CHUG strain FZCC0198. The genome of CRP-810 was dissimilar to those of other known phages. Additionally, 251 uncultured viral genomes (UViGs) closely related to CRP-810 were obtained from the uncultivated marine viral contig databases. Comparative genomic and phylogenetic analyses revealed that CRP-810 and these related UViGs exhibited conserved genome synteny, representing a new phage family with at least eight subgroups. Most of the CRP-810-type phages contain an integrase gene, and CRP-810 can be integrated into the host genome. Further analysis revealed that three CRP-810-type members were prophages found in the genomes of marine SAR11, Poseidonocella, and Sphingomonadaceae. Finally, viromic read-mapping analysis showed that CRP-810-type phages were globally distributed and displayed distinct biogeographic patterns related to temperature and latitude. Many members with a lower G + C content were mainly distributed in the trade station, whereas members with a higher G + C content were mainly distributed in polar and westerlies station, indicating that the niche differentiation of phages was subject to host adaptation. Collectively, these findings identify a novel phage family and expand our understanding of phylogenetic diversity, evolution, and biogeography of marine phages. IMPORTANCE The Roseobacter CHUG lineage, affiliated with the Pelagic Roseobacter Cluster (PRC), is widely distributed in the global oceans and is active in oligotrophic seawater. However, knowledge of the bacteriophages that infect CHUG members is limited. In this study, a CHUG phage, CRP-810, that infects the CHUG strain FZCC0198, was isolated and shown to have a novel genomic architecture. In addition, 251 uncultured viral genomes closely related to CRP-810 were recovered and included in the analyses. Phylogenomic analyses revealed that the CRP-810-type phages represent a new phage family containing at least eight genus-level subgroups. Members of this family were predicted to infect various marine bacteria. We also demonstrated that the CRP-810-type phages are widely distributed in global oceans and display distinct biogeographic patterns related to latitude. Collectively, this study provides important insights into the genomic organization, diversity, and ecology of a novel phage family that infect ecologically important bacteria in the global ocean.
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Affiliation(s)
- Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Luyuan Guo
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiabing Shao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of JunCao Sciences and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Mao X, Larsen SB, Zachariassen LSF, Brunse A, Adamberg S, Mejia JLC, Larsen F, Adamberg K, Nielsen DS, Hansen AK, Hansen CHF, Rasmussen TS. Transfer of modified gut viromes improves symptoms associated with metabolic syndrome in obese male mice. Nat Commun 2024; 15:4704. [PMID: 38830845 PMCID: PMC11148109 DOI: 10.1038/s41467-024-49152-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/24/2024] [Indexed: 06/05/2024] Open
Abstract
Metabolic syndrome encompasses amongst other conditions like obesity and type-2 diabetes and is associated with gut microbiome (GM) dysbiosis. Fecal microbiota transplantation (FMT) has been explored to treat metabolic syndrome by restoring the GM; however, concerns on accidentally transferring pathogenic microbes remain. As a safer alternative, fecal virome transplantation (FVT, sterile-filtrated feces) has the advantage over FMT in that mainly bacteriophages are transferred. FVT from lean male donors have shown promise in alleviating the metabolic effects of high-fat diet in a preclinical mouse study. However, FVT still carries the risk of eukaryotic viral infections. To address this, recently developed methods are applied for removing or inactivating eukaryotic viruses in the viral component of FVT. Modified FVTs are compared with unmodified FVT and saline in a diet-induced obesity model on male C57BL/6 N mice. Contrasted with obese control, mice administered a modified FVT (nearly depleted for eukaryotic viruses) exhibits enhanced blood glucose clearance but not weight loss. The unmodified FVT improves liver pathology and reduces the proportions of immune cells in the adipose tissue with a non-uniform response. GM analysis suggests that bacteriophage-mediated GM modulation influences outcomes. Optimizing these approaches could lead to the development of safe bacteriophage-based therapies targeting metabolic syndrome through GM restoration.
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Affiliation(s)
- Xiaotian Mao
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Sabina Birgitte Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Line Sidsel Fisker Zachariassen
- Section of Preclinical Disease Biology, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Josue Leonardo Castro Mejia
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Frej Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Dennis Sandris Nielsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Axel Kornerup Hansen
- Section of Preclinical Disease Biology, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Camilla Hartmann Friis Hansen
- Section of Preclinical Disease Biology, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Torben Sølbeck Rasmussen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Frederiksberg, Denmark.
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3
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Gios E, Mosley OE, Hoggard M, Handley KM. High niche specificity and host genetic diversity of groundwater viruses. THE ISME JOURNAL 2024; 18:wrae035. [PMID: 38452204 PMCID: PMC10980836 DOI: 10.1093/ismejo/wrae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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4
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Yi Y, Liu S, Hao Y, Sun Q, Lei X, Wang Y, Wang J, Zhang M, Tang S, Tang Q, Zhang Y, Liu X, Wang Y, Xiao X, Jian H. A systematic analysis of marine lysogens and proviruses. Nat Commun 2023; 14:6013. [PMID: 37758717 PMCID: PMC10533544 DOI: 10.1038/s41467-023-41699-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
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Affiliation(s)
- Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Lei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yecheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingxue Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xipeng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
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5
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Huang Y, Sun H, Wei S, Cai L, Liu L, Jiang Y, Xin J, Chen Z, Que Y, Kong Z, Li T, Yu H, Zhang J, Gu Y, Zheng Q, Li S, Zhang R, Xia N. Structure and proposed DNA delivery mechanism of a marine roseophage. Nat Commun 2023; 14:3609. [PMID: 37330604 PMCID: PMC10276861 DOI: 10.1038/s41467-023-39220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
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Affiliation(s)
- Yang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Liqin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yanan Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jiabao Xin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhenqin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yuqiong Que
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhibo Kong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, 361102, China.
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6
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Graham EH, Tom WA, Neujahr AC, Adamowicz MS, Clarke JL, Herr JR, Fernando SC. The persistence and stabilization of auxiliary genes in the human skin virome. Virol J 2023; 20:49. [PMID: 36949545 PMCID: PMC10031188 DOI: 10.1186/s12985-023-02012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/16/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood. RESULTS Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions. CONCLUSIONS This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.
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Grants
- 2017-IJ-CX-0025, 2019-75-CX-0075, and 2019-R2-CX-0048 U.S. Department of Justice
- 2017-IJ-CX-0025, 2019-75-CX-0075, and 2019-R2-CX-0048 U.S. Department of Justice
- 2017-IJ-CX-0025, 2019-75-CX-0075, and 2019-R2-CX-0048 U.S. Department of Justice
- 2017-IJ-CX-0025, 2019-75-CX-0075, and 2019-R2-CX-0048 U.S. Department of Justice
- 2017-IJ-CX-0025, 2019-75-CX-0075, and 2019-R2-CX-0048 U.S. Department of Justice
- 2018-67015-27496 and 2018-68003-27545 National Institute of Food and Agriculture
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Affiliation(s)
- Ema H Graham
- PhD Program in Complex Biosystems, University of Nebraska, 3940 Fair St, C220K, Lincoln, NE, 68583, USA
| | - Wesley A Tom
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Alison C Neujahr
- PhD Program in Complex Biosystems, University of Nebraska, 3940 Fair St, C220K, Lincoln, NE, 68583, USA
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA
| | - Michael S Adamowicz
- College of Agricultural Sciences and Natural Resources, University of Nebraska, Lincoln, NE, 68583, USA
| | - Jennifer L Clarke
- PhD Program in Complex Biosystems, University of Nebraska, 3940 Fair St, C220K, Lincoln, NE, 68583, USA
- Department of Statistics, University of Nebraska, Lincoln, NE, 68588, USA
- Food Science and Technology Department, University of Nebraska, Lincoln, NE, 68588, USA
| | - Joshua R Herr
- PhD Program in Complex Biosystems, University of Nebraska, 3940 Fair St, C220K, Lincoln, NE, 68583, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, 68503, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68503, USA
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583, USA
| | - Samodha C Fernando
- PhD Program in Complex Biosystems, University of Nebraska, 3940 Fair St, C220K, Lincoln, NE, 68583, USA.
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- College of Agricultural Sciences and Natural Resources, University of Nebraska, Lincoln, NE, 68583, USA.
- Food Science and Technology Department, University of Nebraska, Lincoln, NE, 68588, USA.
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583, USA.
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7
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Yu H, Xiong L, Li Y, Wei Y, Zhang Q, Li H, Chen W, Ji X. Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland. Sci Rep 2023; 13:3250. [PMID: 36828854 PMCID: PMC9958192 DOI: 10.1038/s41598-023-28488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/19/2023] [Indexed: 02/26/2023] Open
Abstract
Viruses play important roles in ecosystems by interfering with the central metabolic pathways of the host during infection via the expression of auxiliary metabolic genes (AMGs), altering the productivity of ecosystems and thus affecting geochemical cycling. In this study, the genetic diversity of phosphorus metabolism AMGs phoH, phoU and pstS was investigated by phylogenetic analysis, PCoA analysis, and alpha diversity analysis based on metagenomic data. It was found that the majority of the sequences were unique to Napahai plateau wetland. It was shown that the genetic diversity of phoH, phoU and pstS genes was independent of both habitats and host origins. In addition, the metabolic pathway of AMGs associated with the phosphorus cycling was identified based on metagenomic data. When phosphorus is deficient, virus utilizes AMGs to affect the metabolic pathway, contributing to higher phosphorus levels in the host and facilitating virus survival, replication, and propagation in the host cell.
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Affiliation(s)
- Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China
| | - Wei Chen
- Medical School, Kunming University of Science and Technology, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
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8
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Li Y, Xiong L, Yu H, Xiang Y, Wei Y, Zhang Q, Ji X. Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:44430-44438. [PMID: 36692711 DOI: 10.1007/s11356-023-25408-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/15/2023] [Indexed: 01/25/2023]
Abstract
Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.
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Affiliation(s)
- Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yingying Xiang
- Department of Stomatology, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650031, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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9
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Wang S, Gao B, Chen A, Zhang Z, Wang S, Lv L, Zhao G, Li J. Structural analysis of the housecleaning nucleoside triphosphate pyrophosphohydrolase MazG from Mycobacterium tuberculosis. Front Microbiol 2023; 14:1137279. [PMID: 36937295 PMCID: PMC10014863 DOI: 10.3389/fmicb.2023.1137279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
The housecleaning enzyme of Mycobacterium tuberculosis (Mtb), MazG, is a nucleoside triphosphate pyrophosphohydrolase (NTP-PPase) and can hydrolyze all canonical or non-canonical NTPs into NMPs and pyrophosphate. The Mycobacterium tuberculosis MazG (Mtb-MazG) contributes to antibiotic resistance in response to oxidative or nitrosative stress under dormancy, making it a promising target for treating TB in latent infection patients. However, the structural basis of Mtb-MazG is not clear. Here we describe the crystal structure of Mtb-MazG (1-185) at 2.7 Å resolution, composed of two similar folded spherical domains in tandem. Unlike other all-α NTP pyrophosphatases, Mtb-MazG has an N-terminal extra region composed of three α-helices and five β-strands. The second domain is global, with five α-helices located in the N-terminal domain. Gel-filtration assay and SAXS analysis show that Mtb-MazG forms an enzyme-active dimer in solution. In addition, the metal ion Mg2+ is bound with four negative-charged residues Glu119, Glu122, Glu138, and Asp141. Different truncations and site-directed mutagenesis revealed that the full-length dimeric form and the metal ion Mg2+ are indispensable for the catalytic activity of Mtb-MazG. Thus, our work provides new insights into understanding the molecular basis of Mtb-MazG.
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Affiliation(s)
- Sen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Baocai Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Anke Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Zhifei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai, China
| | - Liangdong Lv
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Guoping Zhao,
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Huashan Hospital, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jixi Li,
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10
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Sun M, Chen F. Distribution of rare N4-like viruses in temperate estuaries unveiled by viromics. Environ Microbiol 2022; 24:6100-6111. [PMID: 36054739 DOI: 10.1111/1462-2920.16172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2022] [Indexed: 01/12/2023]
Abstract
The relative abundance of N4-like viruses in two temperate estuaries was assessed using four different methods, read mapping to known N4-like virus isolates, read mapping to native viral contigs, reciprocal blast search based on core genes, and read taxonomy classification using Kaiju. Overall, N4-like viruses were found to be of low abundance in the estuarine viromes. When mapping reads to only known N4-like virus genomes, high occurrences of N4-like viruses infecting Roseobacter were found, with their diversity consisting mostly of locally isolated Roseobacter N4-like virus species. Both contig-based methods and Kaiju classification showed similar seasonal patterns for N4-like viruses, and redundancy analysis revealed a negative correlation between N4-like viruses and temperature, suggesting that N4-like viruses may be more abundant in colder water. The discrepancy of relative abundance estimates using different methods indicates that N4-like viruses are best represented by native viral sequences. Our study indicates that N4-like viruses are rare in the marine environment and also provide insight into the importance of including local viral sequences in reference databases.
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Affiliation(s)
- Mengqi Sun
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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11
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Brown TL, Charity OJ, Adriaenssens EM. Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut. Curr Opin Microbiol 2022; 70:102229. [PMID: 36347213 DOI: 10.1016/j.mib.2022.102229] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/22/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022]
Abstract
While they are the most abundant biological entities on the planet, the role of bacteriophages (phages) in the microbiome remains enigmatic and understudied. With a rise in the number of metagenomics studies and the publication of highly efficient phage mining programmes, we now have extensive data on the genomic and taxonomic diversity of (mainly) DNA bacteriophages in a wide range of environments. In addition, the higher throughput and quality of sequencing is allowing for strain-level reconstructions of phage genomes from metagenomes. These factors will ultimately help us to understand the role these phages play as part of specific microbial communities, enabling the tracking of individual virus genomes through space and time. Using lessons learned from the latest metagenomic studies, we focus on two explicit aspects of the role bacteriophages play within the microbiome, their ecological role in structuring bacterial populations, and their contribution to microbiome functioning by encoding auxiliary metabolism genes.
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Affiliation(s)
- Teagan L Brown
- Quadram Institute Bioscience, Norwich NR4 7UQ, United Kingdom
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12
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Karaynir A, Salih H, Bozdoğan B, Güçlü Ö, Keskin D. Isolation and characterization of Brochothrix phage ADU4. Virus Res 2022; 321:198902. [PMID: 36064042 DOI: 10.1016/j.virusres.2022.198902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
B. thermosphacta is a psychrotrophic bacterium that often forms the predominant part of the spoilage microflora of aerobically and anaerobically stored meats. Bacteriophages are natural enemies of bacteria and their potential for use in environmentally friendly biocontrol of specific pathogens in food is being intensively studied. In this study, we reported the isolation and characterization of the newly isolated lytic Brochothrix phage ADU4, which is capable of infecting the B. thermosphacta bacterium. For the characterization of Brochothrix phage ADU4; host range, multiplicity of infection values (MOI), phage growth parameters (latent period and burst size), stability at various temperatures and pH, reduction growth of bacteria, effect on biofilm, and molecular characterization were investigated. The spot-test analysis showed positivity with B. thermosphacta strains, while no infection was observed in any other species and genera of bacteria tested. The optimal MOI value of the phage was determined as 0.1. The phage latent period and burst sizes were 40-50 min and 311 PFU/ml per infected host cell, respectively by one-step growth curve analysis. Brochothrix phage ADU4 reduced bacteria immediately after infection, which is shown by optical density (OD) measurement and colony counting (<10 CFU/ml) for 3 days. The degradation of B. thermosphacta in biofilm by Brochothrix phage ADU4 was analyzed and it was found that high titer phage breakdown the existing biofilm and also persistently inhibited biofilm formation. Brochothrix phage ADU4 genome was found to be 127,819 bp, and GC content 41.65%. The genome contains 217 putative open reading frames (ORFs), 4 tRNAs, and additionally, no known virulence and antibiotic resistance genes (AMR) were identified. Brochothrix phage ADU4 showed a high identity (96.09%) to the A9 phage that belongs to the Herelleviridae family. Nevertheless, the assembly module and its around appeared less conserved, and some DNA fragments in Brochothrix phage ADU4 genome were not found in A9 genome and vice versa. A9 contains TnpB, a transposase accessory protein involved in lysogenicity which is absent in Brochothrix phage ADU4. In contrary Brochothrix phage ADU4 had auxiliary metabolic genes (AMG) mostly carried by lytic phages. All these results showed that the Brochothrix phage ADU4 has excellent properties such as strong antibacterial activity, short latent period, high burst size, stability in different conditions, inhibition of biofilms, and absence of virulence and AMR genes. Based on all these features, this newly isolated phage is promising to control B. thermosphacta contamination in meat and meat products, and has the potential to be used alone or in combination with phage cocktails.
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Affiliation(s)
- Abdulkerim Karaynir
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey
| | - Hanife Salih
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey
| | - Bülent Bozdoğan
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Medicine Faculty, Department of Medical Microbiology, Aydın Adnan Menderes University, Turkey
| | - Özgür Güçlü
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Sultanhisar Vocational School, Aydın Adnan Menderes University, Köşk- AYDIN, Turkey
| | - Dilek Keskin
- Recombinant DNA and Recombinant Protein Research Center (REDPROM), Aydın Adnan Menderes University, Turkey; Köşk Vocational School, Aydın Adnan Menderes University, Köşk- AYDIN, Turkey.
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13
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Yu Z, Ma Y, Guan Y, Zhu Y, Wang K, Wang Y, Liu P, Chen J, Yu Y. Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar. Foods 2022; 11:3296. [PMCID: PMC9602057 DOI: 10.3390/foods11203296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Traditional Chinese vinegar offers an exceptional flavor and rich nutrients due to its unique solid-state fermentation process, which is a multiple microbial fermentation system including various bacteria, fungi and viruses. However, few studies on the virus diversities in traditional Chinese vinegar have been reported. In this paper, using Zhenjiang aromatic vinegar as a model system, we systemically explored the viral communities in the solid-state brewing process of traditional Chinese vinegar using bacterial and viral metagenomes. Results showed that the viral diversity in vinegar Pei was extensive and the virus communities varied along with the fermentation process. In addition, there existed some interactions between viral and bacterial communities. Moreover, abundant antibiotic resistance genes were found in viromes, indicating that viruses might protect fermentation bacteria strains from the stress of antibiotics in the fermentation environment. Remarkably, we identified abundant auxiliary carbohydrate metabolic genes (including alcohol oxidases, the key enzymes for acetic acid synthesis) from viromes, implying that viruses might participate in the acetic acid synthesis progress of the host through auxiliary metabolic genes. Taken together, our results indicated the potential roles of viruses in the vinegar brewing process and provided a new perspective for studying the fermentation mechanisms of traditional Chinese vinegar.
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Affiliation(s)
- Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yan Ma
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yingfen Guan
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Juan Chen
- College of Food Science and Engineering, Moutai Institute, Renhuai 564501, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Correspondence: ; Tel.: +86-0511-84400686
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14
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Hegarty B, Dai Z, Raskin L, Pinto A, Wigginton K, Duhaime M. A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use. WATER RESEARCH 2022; 218:118484. [PMID: 35504157 DOI: 10.1016/j.watres.2022.118484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/19/2022] [Indexed: 05/22/2023]
Abstract
Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.
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Affiliation(s)
- Bridget Hegarty
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA
| | - Zihan Dai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Georgia
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, Environmental and Water Resources Engineering Building, University of Michigan, 1351 Beal Ave. 181, Ann Arbor, MI 48109-2125, USA.
| | - Melissa Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105N University Ave., 4068 Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
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15
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Isolation and Characterization of a Novel Cyanophage Encoding Multiple Auxiliary Metabolic Genes. Viruses 2022; 14:v14050887. [PMID: 35632629 PMCID: PMC9146016 DOI: 10.3390/v14050887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 02/04/2023] Open
Abstract
As significant drivers of cyanobacteria mortality, cyanophages have been known to regulate the population dynamics, metabolic activities, and community structure of this most important marine autotrophic picoplankton and, therefore, influence the global primary production and biogeochemical cycle in aquatic ecosystems. In the present study, a lytic Synechococcus phage, namely S-SZBM1, was isolated and identified. Cyanophage S-SZBM1 has a double-stranded DNA genome of 177,834 bp with a G+C content of 43.31% and contains a total of 218 predicted ORFs and six tRNA genes. Phylogenetic analysis and nucleotide-based intergenomic similarity suggested that cyanophage S-SZBM1 belongs to a new genus under the family Kyanoviridae. A variety of auxiliary metabolic genes (AMGs) that have been proved or speculated to relate to photosynthesis, carbon metabolism, nucleotide synthesis and metabolism, cell protection, and other cell metabolism were identified in cyanophage S-SZBM1 genome and may affect host processes during infection. In addition, 24 of 32 predicted structural proteins were identified by a high-throughput proteome analysis which were potentially involved in the assembly processes of virion. The genomic and proteomic analysis features of cyanophage S-SZBM1 offer a valuable insight into the interactions between cyanophages and their hosts during infection.
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16
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Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean. Adv Virus Res 2022. [DOI: 10.1016/bs.aivir.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Genomic Characterization of Two Novel RCA Phages Reveals New Insights into the Diversity and Evolution of Marine Viruses. Microbiol Spectr 2021; 9:e0123921. [PMID: 34668749 PMCID: PMC8528129 DOI: 10.1128/spectrum.01239-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Viruses are the most abundant living entities in marine ecosystems, playing critical roles in altering the structure and function of microbial communities and driving ocean biogeochemistry. Phages that infect Roseobacter clade-affiliated (RCA) cluster strains are an important component of marine viral communities. Here, we characterize the genome sequences of two new RCA phages, CRP-9 and CRP-13, which infect RCA strain FZCC0023. Genomic analysis reveals that CRP-9 and CRP-13 represent a novel evolutionary lineage of marine phages. They both have a DNA replication module most similar to those in Cobavirus group phages. In contrast, their morphogenesis and packaging modules are distinct from those in cobaviruses but homologous to those in HMO-2011-type phages. The genomic architecture of CRP-9 and CRP-13 suggests a genomic recombination event between distinct phage groups. Metagenomic data sets were examined for metagenome-assembled viral genomes (MAVGs) with similar recombinant genome architectures. Fifteen CRP-9-type MAVGs were identified from marine viromes. Additionally, 158 MAVGs were identified containing HMO-2011-type morphogenesis and packaging modules with other types of DNA replication genes, providing more evidence that recombination between different phage groups is a major driver of phage evolution. Altogether, this study significantly expands the understanding of diversity and evolution of marine roseophages. Meanwhile, the analysis of these novel RCA phages and MAVGs highlights the critical role of recombination in shaping phage diversity. These phage sequences are valuable resources for inferring the evolutionary connection of distinct phage groups. IMPORTANCE Diversity and evolution of phages that infect the relatively slow-growing but dominant Roseobacter lineages are largely unknown. In this study, RCA phages CRP-9 and CRP-13 have been isolated on a Roseobacter RCA strain and shown to have a unique genomic architecture, which appears to be the result of a recombination event. CRP-9 and CRP-13 have a DNA replication module most similar to those in Cobavirus group phages and morphogenesis and packaging modules most similar to those in HMO-2011-type phages. HMO-2011-type morphogenesis and packaging modules are found in combination with distinct types of DNA replication genes, suggesting compatibility with various DNA replication modules. Altogether, this study contributes toward a better understanding of marine viral diversity and evolution.
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18
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Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
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Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
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