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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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Cook R, Telatin A, Hsieh SY, Newberry F, Tariq MA, Baker DJ, Carding SR, Adriaenssens EM. Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microb Genom 2024; 10. [PMID: 38683195 DOI: 10.1099/mgen.0.001236] [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] [Indexed: 05/01/2024] Open
Abstract
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | | | | | - Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Mohammad A Tariq
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
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3
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Ma R, Chen X, Li Y, Jiao N, Zhang R. Diversity, evolution and life strategies of CbK-like phages. Environ Microbiol 2023. [PMID: 36807729 DOI: 10.1111/1462-2920.16354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Caulobacter phage CbK has been extensively studied as a model system in virology and bacteriology. Lysogeny-related genes have been found in each CbK-like isolate, suggesting a life strategy of both lytic and lysogenic cycles. However, whether CbK-related phages can enter lysogeny is still undetermined. This study identified new CbK-like sequences and expanded the collection of CbK-related phages. A common ancestry with a temperate lifestyle was predicted for the group, however, which subsequently evolved into two clades of different genome sizes and host associations. Through the examination of phage recombinase genes, alignment of attachment sites on the phage and bacterial genomes (attP-attB pairing), and the experimental validation, different lifestyles were found among the different members. A majority of clade II members retain a lysogenic lifestyle, whereas all clade I members have evolved into an obligate lytic lifestyle via a loss of the gene encoding Cre-like recombinase and the coupled attP fragment. We postulated that the loss of lysogeny may be a by-product of the increase in phage genome size, and vice versa. Clade I is likely to overcome the costs through maintaining more auxiliary metabolic genes (AMGs), particularly for those involved in protein metabolism, to strengthen host takeover and further benefit virion production.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yingying Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 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, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol 2023; 168:74. [PMID: 36683075 PMCID: PMC9868039 DOI: 10.1007/s00705-022-05694-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, BS16 1QY UK
| | - Andrey N. Shkoporov
- Department of Medicine and APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Cédric Lood
- Department of Biosystems, Faculty of Bioscience Engineering, KU, Leuven, Belgium
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH The Netherlands
| | | | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, 7535 Bellville, Cape Town, South Africa
| | - Ramy K. Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
- Egypt/ and Children’s Cancer Hospital, 57357, 11617 Cairo, Egypt
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Andrew M. Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Nina Chanisvili
- The Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia
| | - Rob A. Edwards
- Flinders Accelerator for Microbiome Exploration, Adelaide, Australia
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Croix du Sud 2, L7.05.12, 1348 Louvain-la-Neuve, Belgium
| | - Petar Knezevic
- PK Lab, Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, Novi Sad, Serbia
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, 75015 France
| | - Ipek Kurtböke
- School of Science, Technology and Engineering, University of the Sunshine Coast, 4558 Maroochydore, BC, QLD Australia
| | - Alla Kushkina
- Department of Bacteriophage molecular genetics, D.K.Zabolotny Institute of microbiology and virology, NAS of Ukraine, 154 Acad. Zabolotnoho str, 03143 Kyiv, Ukraine
- Department of Bacterial molecular genetics, Faculty of biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Rob Lavigne
- Department of Biosystems, Faculty of Bioscience Engineering, KU, Leuven, Belgium
| | - Susan Lehman
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD USA
| | - Malgorzata Lobocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrea Moreno Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Jesca Nakavuma
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, 111711 Bogotá, Colombia
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, 1067 Riga, Latvia
| | - BL Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210 USA
| | - Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 7008530 Japan
| | - Johannes Wittmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Tong Yigang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 China
| | - Evelien M. Adriaenssens
- Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ UK
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5
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Zhang Z, Wu Z, Liu H, Yang M, Wang R, Zhao Y, Chen F. Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus. Front Microbiol 2023; 14:1164101. [PMID: 37138617 PMCID: PMC10149686 DOI: 10.3389/fmicb.2023.1164101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world's oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters.
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Affiliation(s)
- Zefeng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zuqing Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyu Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yanlin Zhao,
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
- Feng Chen,
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6
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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7
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Uchiyama J, Takemura-Uchiyama I, Gotoh K, Kato SI, Sakaguchi Y, Murakami H, Fukuyama T, Kaneki M, Matsushita O, Matsuzaki S. Phylogenic analysis of new viral cluster of large phages with unusual DNA genomes containing uracil in place of thymine in gene-sharing network, using phages S6 and PBS1 and relevant uncultured phages derived from sewage metagenomics. Virus Res 2022; 319:198881. [PMID: 35934259 DOI: 10.1016/j.virusres.2022.198881] [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: 03/29/2022] [Revised: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022]
Abstract
Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan.
| | - Iyo Takemura-Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Kazuyoshi Gotoh
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi 783-0093, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Tomoki Fukuyama
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Mao Kaneki
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Osamu Matsushita
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shigenobu Matsuzaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi 780-0955, Japan
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8
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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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9
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Shen A, Millard A. Phage Genome Annotation: Where to Begin and End. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:183-193. [PMID: 36159890 PMCID: PMC9041514 DOI: 10.1089/phage.2021.0015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.
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Affiliation(s)
- Anastasiya Shen
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom.,Address correspondence to: Andrew Millard, BSc, PhD, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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10
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Arava YS, Béjà O. Phage biology: Stuck with dU. Curr Biol 2021; 31:R898-R900. [PMID: 34314715 DOI: 10.1016/j.cub.2021.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A new environmental study has discovered marine phages containing deoxyuridine instead of deoxythymidine in their DNA. The newly isolated viruses are phylogenetically distinct from any currently known double-stranded DNA phages.
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Affiliation(s)
- Yoav S Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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Šimoliūnienė M, Žukauskienė E, Truncaitė L, Cui L, Hutinet G, Kazlauskas D, Kaupinis A, Skapas M, de Crécy-Lagard V, Dedon PC, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA. Int J Mol Sci 2021; 22:7333. [PMID: 34298953 PMCID: PMC8306585 DOI: 10.3390/ijms22147333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Emilija Žukauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
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