201
|
Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 2018; 46:D708-D717. [PMID: 29040670 PMCID: PMC5753373 DOI: 10.1093/nar/gkx932] [Citation(s) in RCA: 624] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 11/13/2022] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.
Collapse
Affiliation(s)
- Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
202
|
García-López R. Construction of a Comprehensive Database from the Existing Viral Sequences Available from the International Nucleotide Sequence Database Collaboration. Methods Mol Biol 2018; 1838:231-243. [PMID: 30129000 DOI: 10.1007/978-1-4939-8682-8_16] [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: 06/08/2023]
Abstract
The progress in viromics research has led to the accumulation of a large number of sequences from different types of viruses obtained from different sources. Most databases are specific to different of species or types of viruses. However, raw sequences, as deposited in the reliable online collections, provide a valuable asset in the exploration of genomic and metagenomics datasets.The International Nucleotide Sequence Database Collaboration (INSDC) is the largest coordinated effort for compiling, sharing, and maintaining the most comprehensive collections of nucleic acids deposited throughout the most important public databases. The compendium includes different types of data such as complete genomes, genes, expressed sequence tags, and data generated by whole genome shotgun analyses spanning all domains of life, as well as the most complete collection of viral sequences available online.This chapter presents simplified computational methods for the automation of viral nucleotide sequence retrieval from online repositories of the INSDC databases, including all available sequences, except synthetic ones. The subsequent steps can be used for obtaining the taxonomy (including ranks: virus type, baltimore classification, order, family, subfamily, genus and species), and split the database into species subsets to dereplicate the sequences for other downstream applications. Only basic computational knowledge is required.
Collapse
Affiliation(s)
- Rodrigo García-López
- Department of Genomics and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (Fisabio), Valencia, Spain.
| |
Collapse
|
203
|
Abstract
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
Collapse
|
204
|
Abstract
The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need to be modified. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. In this chapter, we offer descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. We also provide comments and discussion on how viruses' unique features can affect standard analyses and how to overcome some of the major sources of problems. Topics include: (1) Clustering of related genomes, (2) Whole genome multiple sequence alignments for small RNA viruses, (3) Protein alignments for marker genes, (4) Analyses based on ortholog groups, and (5) Taxonomic identification and comparisons of viruses from environmental datasets.
Collapse
Affiliation(s)
- Deyvid Amgarten
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700, STN CSC, Victoria, BC, Canada, V8W 2Y2.
| |
Collapse
|
205
|
Johnson BA, Graham RL, Menachery VD. Viral metagenomics, protein structure, and reverse genetics: Key strategies for investigating coronaviruses. Virology 2017; 517:30-37. [PMID: 29279138 PMCID: PMC5869085 DOI: 10.1016/j.virol.2017.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022]
Abstract
Viral metagenomics, modeling of protein structure, and manipulation of viral genetics are key approaches that have laid the foundations of our understanding of coronavirus biology. In this review, we discuss the major advances each method has provided and discuss how future studies should leverage these strategies synergistically to answer novel questions.
Collapse
Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
206
|
Uprety S, Hong PY, Sadik N, Dangol B, Adhikari R, Jutla A, Shisler JL, Degnan P, Nguyen TH. The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal. Front Microbiol 2017; 8:2380. [PMID: 29270153 PMCID: PMC5724148 DOI: 10.3389/fmicb.2017.02380] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
We conducted a study to examine the effect of seasonal variations and the disruptive effects of the 2015 Nepal earthquake on microbial communities associated with drinking water sources. We first characterized the microbial communities of water samples in two Nepali regions (Kathmandu and Jhapa) to understand the stability of microbial communities in water samples collected in 2014. We analyzed additional water samples from the same sources collected from May to August 2015, allowing the comparison of samples from dry-to-dry season and from dry-to-monsoon seasons. Emphasis was placed on microbes responsible for maintaining the geobiochemical characteristics of water (e.g., ammonia-oxidizing and nitrite-oxidizing bacteria and archaea and sulfate-reducing bacteria) and opportunistic pathogens often found in water (Acinetobacter). When examining samples from Jhapa, we identified that most geobiochemical microbe populations remained similar. When examining samples from Kathmandu, the abundance of microbial genera responsible for maintaining the geobiochemical characteristics of water increased immediately after the earthquake and decreased 8 months later (December 2015). In addition, microbial source tracking was used to monitor human fecal contamination and revealed deteriorated water quality in some specific sampling sites in Kathmandu post-earthquake. This study highlights a disruption of the environmental microbiome after an earthquake and the restoration of these microbial communities as a function of time and sanitation practices.
Collapse
Affiliation(s)
- Sital Uprety
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nora Sadik
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Bipin Dangol
- Environment and Public Health Organization, Kathmandu, Nepal
| | | | - Antarpreet Jutla
- Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV, United States
| | - Joanna L. Shisler
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Patrick Degnan
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL, United States
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana Champaign, Urbana, IL, United States
| |
Collapse
|
207
|
Bigot D, Dalmon A, Roy B, Hou C, Germain M, Romary M, Deng S, Diao Q, Weinert LA, Cook JM, Herniou EA, Gayral P. The discovery of Halictivirus resolves the Sinaivirus phylogeny. J Gen Virol 2017; 98:2864-2875. [DOI: 10.1099/jgv.0.000957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Anne Dalmon
- INRA UR 406 Abeilles et environnement, Centre de recherche Provence-Alpes-Côte d'Azur, Site Agroparc, Domaine St Paul 228, Route de l'aérodrome CS40509 84914 Avignon, France
| | - Bronwen Roy
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Michèle Germain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Manon Romary
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Lucy A. Weinert
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| |
Collapse
|
208
|
Zhang Y, Kitajima M, Whittle AJ, Liu WT. Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. Front Microbiol 2017; 8:2036. [PMID: 29097994 PMCID: PMC5654357 DOI: 10.3389/fmicb.2017.02036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022] Open
Abstract
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs.
Collapse
Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Andrew J Whittle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
209
|
Jo Y, Choi H, Bae M, Kim SM, Kim SL, Lee BC, Cho WK, Kim KH. De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data. THE PLANT PATHOLOGY JOURNAL 2017; 33:478-487. [PMID: 29018311 PMCID: PMC5624490 DOI: 10.5423/ppj.oa.03.2017.0060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/07/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.
Collapse
Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Miah Bae
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365,
Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365,
Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365,
Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| |
Collapse
|
210
|
Nainu F, Shiratsuchi A, Nakanishi Y. Induction of Apoptosis and Subsequent Phagocytosis of Virus-Infected Cells As an Antiviral Mechanism. Front Immunol 2017; 8:1220. [PMID: 29033939 PMCID: PMC5624992 DOI: 10.3389/fimmu.2017.01220] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/14/2017] [Indexed: 01/14/2023] Open
Abstract
Viruses are infectious entities that hijack host replication machineries to produce their progeny, resulting, in most cases, in disease and, sometimes, in death in infected host organisms. Hosts are equipped with an array of defense mechanisms that span from innate to adaptive as well as from humoral to cellular immune responses. We previously demonstrated that mouse cells underwent apoptosis in response to influenza virus infection. These apoptotic, virus-infected cells were then targeted for engulfment by macrophages and neutrophils. We more recently reported similar findings in the fruit fly Drosophila melanogaster, which lacks adaptive immunity, after an infection with Drosophila C virus. In these experiments, the inhibition of phagocytosis led to severe influenza pathologies in mice and early death in Drosophila. Therefore, the induction of apoptosis and subsequent phagocytosis of virus-infected cells appear to be an antiviral innate immune mechanism that is conserved among multicellular organisms. We herein discuss the underlying mechanisms and significance of the apoptosis-dependent phagocytosis of virus-infected cells. Investigations on the molecular and cellular features responsible for this underrepresented virus–host interaction may provide a promising avenue for the discovery of novel substances that are targeted in medical treatments against virus-induced intractable diseases.
Collapse
Affiliation(s)
- Firzan Nainu
- Laboratory of Pharmacology and Toxicology, Faculty of Pharmacy, Hasanuddin University, Makassar, Indonesia.,Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Akiko Shiratsuchi
- Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yoshinobu Nakanishi
- Laboratory of Host Defense and Responses, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| |
Collapse
|
211
|
Herath D, Jayasundara D, Ackland D, Saeed I, Tang SL, Halgamuge S. Assessing Species Diversity Using Metavirome Data: Methods and Challenges. Comput Struct Biotechnol J 2017; 15:447-455. [PMID: 29085573 PMCID: PMC5650650 DOI: 10.1016/j.csbj.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 12/28/2022] Open
Abstract
Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.
Collapse
Affiliation(s)
- Damayanthi Herath
- Department of Mechanical Engineering, University of Melbourne, Parkville, 3010 Melbourne, Australia
- Department of Computer Engineering, University of Peradeniya, Prof. E. O. E. Pereira Mawatha, Peradeniya, 20400, Sri Lanka
| | - Duleepa Jayasundara
- School of Public Health and Community Medicine, University of New South Wales, Randwick, NSW 2052, Australia
| | - David Ackland
- Department of Biomedical Engineering, University of Melbourne, Parkville, 3010 Melbourne, Australia
| | - Isaam Saeed
- Department of Mechanical Engineering, University of Melbourne, Parkville, 3010 Melbourne, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan
| | - Saman Halgamuge
- Research School of Engineering, College of Engineering and Computer Science, The Australian National University, Canberra 2601, ACT, Australia
| |
Collapse
|
212
|
Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB. Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity. PeerJ 2017; 5:e3817. [PMID: 28948103 PMCID: PMC5610896 DOI: 10.7717/peerj.3817] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 08/26/2017] [Indexed: 12/20/2022] Open
Abstract
Background Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates. Results Tools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates. Conclusions These simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations.
Collapse
Affiliation(s)
- Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Joanne B Emerson
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Emiley A Eloe-Fadrosh
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, United States of America
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
213
|
Detection of a new species of torque teno mini virus from the gingival epithelium of patients with periodontitis. Virus Genes 2017; 53:823-830. [PMID: 28866831 DOI: 10.1007/s11262-017-1505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022]
Abstract
We describe a novel species of torque teno mini virus called TTMV-204, which was isolated from the gingival epithelium of patients with periodontitis and characterized using viral metagenomics. The sequence of the full genome is 2824 nt in length. Phylogenetic analysis and genetic analyses show classic Betatorquevirus species organization with less than 40% amino acid similarity in ORF1. The prevalence of TTMV-204 in the periodontitis patient population was 18.75% (15/80), which was higher than in periodontally healthy individuals (10.00%, 10/80). However, the difference of the TTMV-204 prevalence between two groups was not statistically significant (p = 0.115). Further investigation is required to determine whether this new virus is associated with inflammation.
Collapse
|
214
|
Montalvo-Proaño J, Buerger P, Weynberg KD, van Oppen MJH. A PCR-Based Assay Targeting the Major Capsid Protein Gene of a Dinorna-Like ssRNA Virus That Infects Coral Photosymbionts. Front Microbiol 2017; 8:1665. [PMID: 28919883 PMCID: PMC5585145 DOI: 10.3389/fmicb.2017.01665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/17/2017] [Indexed: 11/13/2022] Open
Abstract
The coral-Symbiodinium association is a critical component of coral reefs as it is the main primary producer and builds the reef's 3-dimensional structure. A breakdown of this endosymbiosis causes a loss of the dinoflagellate photosymbiont, Symbiodinium, and/or its photosynthetic pigments from the coral tissues (i.e., coral bleaching), and can lead to coral mortality. Coral bleaching has mostly been attributed to environmental stressors, and in some cases to bacterial infection. Viral lysis of Symbiodinium has been proposed as another possible cause of some instances of coral bleaching, but this hypothesis has not yet been experimentally confirmed. In this study, we used coral virome data to develop a novel PCR-based assay for examining the presence and diversity of a single-stranded RNA (ssRNA) virus by targeting its major capsid protein (MCP) gene. Illumina sequence analysis of amplicons obtained with novel primers showed 99.8% of the reads had the closest taxonomic affinity with the MCP gene of the virus, Heterocapsa circularisquama RNA virus (HcRNAV) known to infect dinoflagellates, indicating that dinorna-like viruses are commonly associated with corals on the Great Barrier Reef. A phylogenetic analysis of MCP gene sequences revealed strong coral species specificity of viral operational taxon units (OTUs). This assay allows a relatively easy and rapid evaluation of the presence and diversity of this particular viral group and will assist in enhancing our understanding of the role of viral lysis in coral bleaching.
Collapse
Affiliation(s)
- Jose Montalvo-Proaño
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- AIMS@JCU, James Cook UniversityTownsville, QLD, Australia
| | - Patrick Buerger
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- AIMS@JCU, James Cook UniversityTownsville, QLD, Australia
- College of Science and Engineering, Department of Marine Biology and Aquaculture, James Cook UniversityTownsville, QLD, Australia
| | | | - Madeleine J. H. van Oppen
- Australian Institute of Marine ScienceTownsville, QLD, Australia
- School of BioSciences, University of MelbourneParkville, VIC, Australia
| |
Collapse
|
215
|
Avni E, Snir S. Toxic genes present a unique phylogenetic signature. Mol Phylogenet Evol 2017; 116:141-148. [PMID: 28842276 DOI: 10.1016/j.ympev.2017.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/17/2017] [Accepted: 08/17/2017] [Indexed: 10/19/2022]
Abstract
Horizontal gene transfer (HGT) is a major part of the evolution of Archaea and Bacteria, to the extent that the validity of the Tree of Life concept for prokaryotes has been seriously questioned. The patterns and routes of HGT remain a subject of intense study and debate. It was discovered that while several genes exhibit rampant HGT across the whole prokaryotic tree of life, others are lethal to certain organisms and therefore cannot be successfully transferred to them. We distinguish between these two classes of genes and show analytically that genes found to be toxic to a specific species (E. coli) also resist HGT in general. Several tools we employ show evidence to support that claim. One of those tools is the quartet plurality distribution (QPD), a mathematical tool that measures tendency to HGT over a large set of genes and species. When aggregated over a collection of genes, it can reveal important properties of this collection. We conclude that evidence of toxicity of certain genes to a wide variety of prokaryotes are revealed using the new tool of quartet plurality distribution.
Collapse
Affiliation(s)
- Eliran Avni
- Dept. of Evolutionary Biology, University of Haifa, Haifa 31905, Israel.
| | - Sagi Snir
- Dept. of Evolutionary Biology, University of Haifa, Haifa 31905, Israel.
| |
Collapse
|
216
|
Corinaldesi C, Tangherlini M, Dell'Anno A. From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments. Sci Rep 2017; 7:8355. [PMID: 28827715 PMCID: PMC5566222 DOI: 10.1038/s41598-017-08783-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/13/2017] [Indexed: 11/09/2022] Open
Abstract
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.
Collapse
Affiliation(s)
- Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Michael Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| |
Collapse
|
217
|
Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
Collapse
Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| |
Collapse
|
218
|
Aswad A, Katzourakis A. A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data. Virus Evol 2017; 3:vex016. [PMID: 28798873 PMCID: PMC5544889 DOI: 10.1093/ve/vex016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.
Collapse
Affiliation(s)
- Amr Aswad
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
| |
Collapse
|
219
|
Lemay ML, Tremblay DM, Moineau S. Genome Engineering of Virulent Lactococcal Phages Using CRISPR-Cas9. ACS Synth Biol 2017; 6:1351-1358. [PMID: 28324650 DOI: 10.1021/acssynbio.6b00388] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phages are biological entities found in every ecosystem. Although much has been learned about them in past decades, significant knowledge gaps remain. Manipulating virulent phage genomes is challenging. To date, no efficient gene-editing tools exist for engineering virulent lactococcal phages. Lactococcus lactis is a bacterium extensively used as a starter culture in various milk fermentation processes, and its phage sensitivity poses a constant risk to the cheese industry. The lactococcal phage p2 is one of the best-studied models for these virulent phages. Despite its importance, almost half of its genes have no functional assignment. CRISPR-Cas9 genome editing technology, which is derived from a natural prokaryotic defense mechanism, offers new strategies for phage research. Here, the well-known Streptococcus pyogenes CRISPR-Cas9 was used in a heterologous host to modify the genome of a strictly lytic phage. Implementation of our adapted CRISPR-Cas9 tool in the prototype phage-sensitive host L. lactis MG1363 allowed us to modify the genome of phage p2. A simple, reproducible technique to generate precise mutations that allow the study of lytic phage genes and their encoded proteins in vivo is described.
Collapse
Affiliation(s)
- Marie-Laurence Lemay
- Département
de biochimie, de microbiologie, et de bioinformatique, Faculté
des sciences et de génie, Félix d’Hérelle
Reference Center for Bacterial Viruses, and Groupe de recherche en
écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec G1V 0A6, Canada
| | - Denise M. Tremblay
- Département
de biochimie, de microbiologie, et de bioinformatique, Faculté
des sciences et de génie, Félix d’Hérelle
Reference Center for Bacterial Viruses, and Groupe de recherche en
écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec G1V 0A6, Canada
| | - Sylvain Moineau
- Département
de biochimie, de microbiologie, et de bioinformatique, Faculté
des sciences et de génie, Félix d’Hérelle
Reference Center for Bacterial Viruses, and Groupe de recherche en
écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec G1V 0A6, Canada
| |
Collapse
|
220
|
Sidhu C, Vikram S, Pinnaka AK. Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies. Front Microbiol 2017; 8:1382. [PMID: 28769920 PMCID: PMC5515832 DOI: 10.3389/fmicb.2017.01382] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/07/2017] [Indexed: 01/06/2023] Open
Abstract
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.
Collapse
Affiliation(s)
- Chandni Sidhu
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
| | - Surendra Vikram
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of PretoriaPretoria, South Africa
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
| |
Collapse
|
221
|
Fahsbender E, Burns JM, Kim S, Kraberger S, Frankfurter G, Eilers AA, Shero MR, Beltran R, Kirkham A, McCorkell R, Berngartt RK, Male MF, Ballard G, Ainley DG, Breitbart M, Varsani A. Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica. Virus Evol 2017; 3:vex017. [PMID: 28744371 PMCID: PMC5518176 DOI: 10.1093/ve/vex017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.
Collapse
Affiliation(s)
- Elizabeth Fahsbender
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Stacy Kim
- Moss Landing Marine Laboratories, Moss Landing, CA 95039, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Greg Frankfurter
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | | | - Michelle R Shero
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Roxanne Beltran
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK 99775, USA
| | - Amy Kirkham
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Rd, Juneau, Alaska 99801, USA
| | - Robert McCorkell
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Grant Ballard
- Point Blue Conservation Science, Petaluma, CA 94954, USA
| | | | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| |
Collapse
|
222
|
Clark IC, Abate AR. Finding a helix in a haystack: nucleic acid cytometry with droplet microfluidics. LAB ON A CHIP 2017; 17:2032-2045. [PMID: 28540956 PMCID: PMC6005652 DOI: 10.1039/c7lc00241f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nucleic acids encode the information of life, programming cellular functions and dictating many biological outcomes. Differentiating between cells based on their nucleic acid programs is, thus, a powerful way to unravel the genetic bases of many phenotypes. This is especially important considering that most cells exist in heterogeneous populations, requiring them to be isolated before they can be studied. Existing flow cytometry techniques, however, are unable to reliably recover specific cells based on nucleic acid content. Nucleic acid cytometry is a new field built on droplet microfluidics that allows robust identification, sorting, and sequencing of cells based on specific nucleic acid biomarkers. This review highlights applications that immediately benefit from the approach, biological questions that can be addressed for the first time with it, and considerations for building successful workflows.
Collapse
Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | | |
Collapse
|
223
|
Hayes S, Mahony J, Nauta A, van Sinderen D. Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Viruses 2017; 9:v9060127. [PMID: 28538703 PMCID: PMC5490804 DOI: 10.3390/v9060127] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral ‘dark matter’ of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.
Collapse
Affiliation(s)
- Stephen Hayes
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
| | - Arjen Nauta
- Friesland Campina, Amersfoort 3800 BN, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
| |
Collapse
|
224
|
Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 2017; 5:e3243. [PMID: 28480138 PMCID: PMC5419219 DOI: 10.7717/peerj.3243] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
Collapse
Affiliation(s)
- Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Ho Bin Jang
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Guilhem Doulcier
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, PSL Research University, Paris, France
- ESPCI, PSL Research University, Paris, France
| | - Zhi-Qiang You
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States
| | - Simon Roux
- Department of Microbiology, Ohio State University, Columbus, OH, United States
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States
| |
Collapse
|
225
|
Yu P, Mathieu J, Yang Y, Alvarez PJJ. Suppression of Enteric Bacteria by Bacteriophages: Importance of Phage Polyvalence in the Presence of Soil Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5270-5278. [PMID: 28414441 DOI: 10.1021/acs.est.7b00529] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168). Although T4 was more effective than PEf1 in infecting E. coli K-12 in pure cultures, PEf1 was 20-fold more effective in suppressing E. coli under simulated multispecies biofilm conditions because polyvalence enhanced PEf1 propagation in P. putida. In contrast, soil bacteria do not propagate coliphages and hindered T4 diffusion through the biofilm. Similar tests were also conducted under planktonic conditions to discern how interspecies competition contributes to E. coli suppression without the confounding effects of restricted phage diffusion. Significant synergistic suppression was observed by the combined effects of phages plus competing bacteria. T4 was slightly more effective in suppressing E. coli in these planktonic mixed cultures, even though PEf1 reached higher concentrations by reproducing also in P. putida (7.2 ± 0.4 vs 6.0 ± 1.0 log10PFU/mL). Apparently, enhanced suppression by higher PEf1 propagation was offset by P. putida lysis, which decreased stress from interspecies competition relative to incubations with T4. In similar planktonic tests with more competing soil bacteria species, P. putida lysis was less critical in mitigating interspecies competition and PEf1 eliminated E. coli faster than T4 (36 vs 42 h). Overall, this study shows that polyvalent phages can propagate in soil bacteria and significantly enhance suppression of co-occurring enteric species.
Collapse
Affiliation(s)
- Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas 77005, United States
| |
Collapse
|
226
|
Parmar KM, Gaikwad SL, Dhakephalkar PK, Kothari R, Singh RP. Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics. Front Microbiol 2017; 8:559. [PMID: 28439260 PMCID: PMC5383658 DOI: 10.3389/fmicb.2017.00559] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/16/2017] [Indexed: 01/09/2023] Open
Abstract
Innovations in next-generation sequencing technology have introduced new avenues in microbial studies through “omics” approaches. This technology has considerably augmented the knowledge of the microbial world without isolation prior to their identification. With an enormous volume of bacterial “omics” data, considerable attempts have been recently invested to improve an insight into virosphere. The interplay between bacteriophages and their host has created a significant influence on the biogeochemical cycles, microbial diversity, and bacterial population regulation. This review highlights various concepts such as genomics, transcriptomics, proteomics, and metabolomics to infer the phylogenetic affiliation and function of bacteriophages and their impact on diverse microbial communities. Omics technologies illuminate the role of bacteriophage in an environment, the influences of phage proteins on the bacterial host and provide information about the genes important for interaction with bacteria. These investigations will reveal some of bio-molecules and biomarkers of the novel phage which demand to be unveiled.
Collapse
Affiliation(s)
| | | | | | - Ramesh Kothari
- Department of Biosciences, Saurashtra UniversityRajkot, India
| | | |
Collapse
|
227
|
Modelling plankton ecosystems in the meta-omics era. Are we ready? Mar Genomics 2017; 32:1-17. [DOI: 10.1016/j.margen.2017.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/30/2022]
|
228
|
Munang'andu HM, Mugimba KK, Byarugaba DK, Mutoloki S, Evensen Ø. Current Advances on Virus Discovery and Diagnostic Role of Viral Metagenomics in Aquatic Organisms. Front Microbiol 2017; 8:406. [PMID: 28382024 PMCID: PMC5360701 DOI: 10.3389/fmicb.2017.00406] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
The global expansion of the aquaculture industry has brought with it a corresponding increase of novel viruses infecting different aquatic organisms. These emerging viral pathogens have proved to be a challenge to the use of traditional cell-cultures and immunoassays for identification of new viruses especially in situations where the novel viruses are unculturable and no antibodies exist for their identification. Viral metagenomics has the potential to identify novel viruses without prior knowledge of their genomic sequence data and may provide a solution for the study of unculturable viruses. This review provides a synopsis on the contribution of viral metagenomics to the discovery of viruses infecting different aquatic organisms as well as its potential role in viral diagnostics. High throughput Next Generation sequencing (NGS) and library construction used in metagenomic projects have simplified the task of generating complete viral genomes unlike the challenge faced in traditional methods that use multiple primers targeted at different segments and VPs to generate the entire genome of a novel virus. In terms of diagnostics, studies carried out this far show that viral metagenomics has the potential to serve as a multifaceted tool able to study and identify etiological agents of single infections, co-infections, tissue tropism, profiling viral infections of different aquatic organisms, epidemiological monitoring of disease prevalence, evolutionary phylogenetic analyses, and the study of genomic diversity in quasispecies viruses. With sequencing technologies and bioinformatics analytical tools becoming cheaper and easier, we anticipate that metagenomics will soon become a routine tool for the discovery, study, and identification of novel pathogens including viruses to enable timely disease control for emerging diseases in aquaculture.
Collapse
Affiliation(s)
- Hetron M. Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Kizito K. Mugimba
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Denis K. Byarugaba
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere UniversityKampala, Uganda
| | - Stephen Mutoloki
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| | - Øystein Evensen
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life SciencesOslo, Norway
| |
Collapse
|
229
|
Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. Prediction of virus-host infectious association by supervised learning methods. BMC Bioinformatics 2017; 18:60. [PMID: 28361670 PMCID: PMC5374558 DOI: 10.1186/s12859-017-1473-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background The study of virus-host infectious association is important for understanding the functions and dynamics of microbial communities. Both cellular and fractionated viral metagenomic data generate a large number of viral contigs with missing host information. Although relative simple methods based on the similarity between the word frequency vectors of viruses and bacterial hosts have been developed to study virus-host associations, the problem is significantly understudied. We hypothesize that machine learning methods based on word frequencies can be efficiently used to study virus-host infectious associations. Methods We investigate four different representations of word frequencies of viral sequences including the relative word frequency and three normalized word frequencies by subtracting the number of expected from the observed word counts. We also study five machine learning methods including logistic regression, support vector machine, random forest, Gaussian naive Bayes and Bernoulli naive Bayes for separating infectious from non-infectious viruses for nine bacterial host genera with at least 45 infecting viruses. Area under the receiver operating characteristic curve (AUC) is used to compare the performance of different machine learning method and feature combinations. We then evaluate the performance of the best method for the identification of the hosts of contigs in metagenomic studies. We also develop a maximum likelihood method to estimate the fraction of true infectious viruses for a given host in viral tagging experiments. Results Based on nine bacterial host genera with at least 45 infectious viruses, we show that random forest together with the relative word frequency vector performs the best in identifying viruses infecting particular hosts. For all the nine host genera, the AUC is over 0.85 and for five of them, the AUC is higher than 0.98 when the word size is 6 indicating the high accuracy of using machine learning approaches for identifying viruses infecting particular hosts. We also show that our method can predict the hosts of viral contigs of length at least 1kbps in metagenomic studies with high accuracy. The random forest together with word frequency vector outperforms current available methods based on Manhattan and \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$d_{2}^{*}$\end{document}d2∗ dissimilarity measures. Based on word frequencies, we estimate that about 95% of the identified T4-like viruses in viral tagging experiment infect Synechococcus, while only about 29% of the identified non-T4-like viruses and 30% of the contigs in the study potentially infect Synechococcus. Conclusions The random forest machine learning method together with the relative word frequencies as features of viruses can be used to predict viruses and viral contigs for specific bacterial hosts. The maximum likelihood approach can be used to estimate the fraction of true infectious associated viruses in viral tagging experiments. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1473-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mengge Zhang
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Lianping Yang
- College of Sciences, Northeastern University, Shenyang, China
| | - Jie Ren
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA
| | - Nathan A Ahlgren
- Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA.,Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Jed A Fuhrman
- Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA. .,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanhai, China.
| |
Collapse
|
230
|
Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| |
Collapse
|
231
|
Thannesberger J, Hellinger HJ, Klymiuk I, Kastner MT, Rieder FJJ, Schneider M, Fister S, Lion T, Kosulin K, Laengle J, Bergmann M, Rattei T, Steininger C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples. FASEB J 2017; 31:1987-2000. [PMID: 28179422 DOI: 10.1096/fj.201601168r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023]
Abstract
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter). Unknown phages also predominated in the oropharynx and urine of healthy individuals and patients infected with cytomegalovirus despite demonstration of active cytomegalovirus replication. The novelty of viral sequences correlated primarily with the individual evaluated, whereas relative abundance of encoded protein functions was associated with the ecologic niches probed. Together, these observations demonstrate the extensive presence of viral dark matter in human and artificial ecosystems.-Thannesberger, J., Hellinger, H.-J., Klymiuk, I., Kastner, M.-T., Rieder, F. J. J., Schneider, M., Fister, S., Lion, T., Kosulin, K., Laengle, J., Bergmann, M., Rattei, T., Steininger, C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
Collapse
Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Hans-Joerg Hellinger
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Franz J J Rieder
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Martina Schneider
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Vienna, Austria
| | - Karin Kosulin
- Children's Cancer Research Institute, Vienna, Austria
| | - Johannes Laengle
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Michael Bergmann
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria;
| |
Collapse
|
232
|
Snir S. Ordered orthology as a tool in prokaryotic evolutionary inference. Mob Genet Elements 2017; 6:e1120576. [PMID: 28090377 DOI: 10.1080/2159256x.2015.1120576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022] Open
Abstract
Molecular data is accumulated at exponentially increasing pace. This deluge of information should have brought us closer to resolving one of the most fundamental issues in biology - deciphering the history of life on Earth. So far, however, this abundance of data only seems to blur our understanding of the problem. This is largely due to horizontal gene transfer (HGT), the transfer of genetic material between evolutionarily unrelated organisms that transforms the prokaryotic tree into a network of relationships. Recently, we developed a method to infer evolutionary relationships among closely related species where the conventional evolutionary markers do not provide a strong enough signal. The method relies on the loss of synteny, gene order conservation among species that provides a stronger signal, sufficient to classify even strains of a given species. Here we elaborate on this method and suggest further uses of it in the context of detecting HGT events and genome architecture.
Collapse
Affiliation(s)
- Sagi Snir
- Department of Evolutionary Biology, University of Haifa , Haifa, Israel
| |
Collapse
|
233
|
Thurber RV, Payet JP, Thurber AR, Correa AMS. Virus-host interactions and their roles in coral reef health and disease. Nat Rev Microbiol 2017; 15:205-216. [PMID: 28090075 DOI: 10.1038/nrmicro.2016.176] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest that the influence of viruses on reef function is an essential component of these globally important environments.
Collapse
Affiliation(s)
- Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jérôme P Payet
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.,College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Andrew R Thurber
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA.,College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, Oregon 97331, USA
| | - Adrienne M S Correa
- BioSciences Department, Rice University, 6100 Main Street, Houston, Texas 77005, USA
| |
Collapse
|
234
|
Khalil JYB, Langlois T, Andreani J, Sorraing JM, Raoult D, Camoin L, La Scola B. Flow Cytometry Sorting to Separate Viable Giant Viruses from Amoeba Co-culture Supernatants. Front Cell Infect Microbiol 2017; 6:202. [PMID: 28111619 PMCID: PMC5216029 DOI: 10.3389/fcimb.2016.00202] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/15/2016] [Indexed: 12/03/2022] Open
Abstract
Flow cytometry has contributed to virology but has faced many drawbacks concerning detection limits, due to the small size of viral particles. Nonetheless, giant viruses changed many concepts in the world of viruses, as a result of their size and hence opened up the possibility of using flow cytometry to study them. Recently, we developed a high throughput isolation of viruses using flow cytometry and protozoa co-culture. Consequently, isolating a viral mixture in the same sample became more common. Nevertheless, when one virus multiplies faster than others in the mixture, it is impossible to obtain a pure culture of the minority population. Here, we describe a robust sorting system, which can separate viable giant virus mixtures from supernatants. We tested three flow cytometry sorters by sorting artificial mixtures. Purity control was assessed by electron microscopy and molecular biology. As proof of concept, we applied the sorting system to a co-culture supernatant taken from a sample containing a viral mixture that we couldn't separate using end point dilution. In addition to isolating the quick-growing Mimivirus, we sorted and re-cultured a new, slow-growing virus, which we named “Cedratvirus.” The sorting assay presented in this paper is a powerful and versatile tool for separating viral populations from amoeba co-cultures and adding value to the new field of flow virometry.
Collapse
Affiliation(s)
- Jacques Y B Khalil
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 Centre national de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Facultés de Médecine et de PharmacieMarseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de MarseilleMarseille, France
| | - Thierry Langlois
- Becton Dickinson (Life Sciences-Biosciences) 94523 Rungis Cedex, France
| | - Julien Andreani
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 Centre national de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Facultés de Médecine et de PharmacieMarseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de MarseilleMarseille, France
| | | | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 Centre national de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Facultés de Médecine et de PharmacieMarseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de MarseilleMarseille, France
| | - Laurence Camoin
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 Centre national de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Facultés de Médecine et de PharmacieMarseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de MarseilleMarseille, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 Centre national de la Recherche Scientifique 7278 IRD 198 Institut National de la Santé et de la Recherche Médicale U1095, Facultés de Médecine et de PharmacieMarseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de MarseilleMarseille, France
| |
Collapse
|
235
|
Abstract
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.
Collapse
|
236
|
Munang'andu HM. Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control. Front Microbiol 2016; 7:1986. [PMID: 28018317 PMCID: PMC5155513 DOI: 10.3389/fmicb.2016.01986] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 11/17/2022] Open
Abstract
Studies on the epidemiology of viral diseases in aquaculture have for a long time depended on isolation of viruses from infected aquatic organisms. The role of aquatic environments in the epidemiology of viral diseases in aquaculture has not been extensively expounded mainly because of the lack of appropriate tools for environmental studies on aquatic viruses. However, the upcoming of metagenomics analyses opens great avenues in which environmental samples can be used to study the epidemiology of viral diseases outside their host species. Hence, in this review I have shown that epidemiological factors that influence the composition of viruses in different aquatic environments include ecological factors, anthropogenic activities and stocking densities of cultured organisms based on environmental metagenomics studies carried out this far. Ballast water transportation and global trade of aquatic organisms are the most common virus dispersal process identified this far. In terms of disease control for outdoor aquaculture systems, baseline data on viruses found in different environments intended for aquaculture use can be obtained to enable the design of effective disease control strategies. And as such, high-risk areas having a high specter of pathogenic viruses can be identified as an early warning system. As for the control of viral diseases for indoor recirculation aquaculture systems (RAS), the most effective disinfection methods able to eliminate pathogenic viruses from water used in RAS can be identified. Overall, the synopsis I have put forth in this review shows that environmental samples can be used to study the epidemiology of viral diseases in aquaculture using viral metagenomics analysis as an overture for the design of rational disease control strategies.
Collapse
Affiliation(s)
- Hetron M Munang'andu
- Section of Aquatic Medicine and Nutrition, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences Oslo, Norway
| |
Collapse
|
237
|
Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB. Towards quantitative viromics for both double-stranded and single-stranded DNA viruses. PeerJ 2016; 4:e2777. [PMID: 28003936 PMCID: PMC5168678 DOI: 10.7717/peerj.2777] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/08/2016] [Indexed: 01/06/2023] Open
Abstract
Background Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation). Methods Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses. Results Mock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the Microviridae family, can be among the most abundant viral genomes in a sample. Discussion Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.
Collapse
Affiliation(s)
- Simon Roux
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University , Columbus , OH , United States
| | - Vinh T Dang
- Department of Microbiology, Ha Long University , Uong Bi , Quang Ninh , Vietnam
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona , Tucson , AZ , United States
| | - Dawn B Goldsmith
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago , Chicago , IL , United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida , St. Petersburg , FL , United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
238
|
Lance ST, Sukovich DJ, Stedman KM, Abate AR. Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry. Virol J 2016; 13:201. [PMID: 27906039 PMCID: PMC5131442 DOI: 10.1186/s12985-016-0655-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 11/21/2022] Open
Abstract
Background Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts of viruses. Methods PAVS enables specific sorting of viruses with flow cytometry. A sample containing a virus population is processed through a microfluidic device to encapsulate it into droplets, such that the droplets contain different viruses from the sample. TaqMan PCR reagents are also included targeting specific virus species such that, upon thermal cycling, droplets containing the species become fluorescent. The target viruses are then recovered via droplet sorting. The recovered virus genomes can then be analyzed with qPCR and next generation sequencing. Results and Conclusions We describe the PAVS workflow and demonstrate its specificity for identifying target viruses in a heterogeneous population. In addition, we demonstrate recovery of the target viruses via droplet sorting and analysis of their nucleic acids with qPCR. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0655-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shea T Lance
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA.,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - David J Sukovich
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA
| | - Kenneth M Stedman
- Center for Life in Extreme Environments, Biology Department, Portland State University, Portland, Oregon, USA
| | - Adam R Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA. .,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA. .,UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.
| |
Collapse
|
239
|
Gambelli L, Cremers G, Mesman R, Guerrero S, Dutilh BE, Jetten MSM, Op den Camp HJM, van Niftrik L. Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture. Front Microbiol 2016; 7:1740. [PMID: 27877158 PMCID: PMC5099504 DOI: 10.3389/fmicb.2016.01740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/18/2016] [Indexed: 01/21/2023] Open
Abstract
With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study.
Collapse
Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Simon Guerrero
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrecht, Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical CentreNijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| |
Collapse
|
240
|
Karimi M, Mirshekari H, Moosavi Basri SM, Bahrami S, Moghoofei M, Hamblin MR. Bacteriophages and phage-inspired nanocarriers for targeted delivery of therapeutic cargos. Adv Drug Deliv Rev 2016; 106:45-62. [PMID: 26994592 PMCID: PMC5026880 DOI: 10.1016/j.addr.2016.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 02/08/2023]
Abstract
The main goal of drug delivery systems is to target therapeutic cargoes to desired cells and to ensure their efficient uptake. Recently a number of studies have focused on designing bio-inspired nanocarriers, such as bacteriophages, and synthetic carriers based on the bacteriophage structure. Bacteriophages are viruses that specifically recognize their bacterial hosts. They can replicate only inside their host cell and can act as natural gene carriers. Each type of phage has a particular shape, a different capacity for loading cargo, a specific production time, and their own mechanisms of supramolecular assembly, that have enabled them to act as tunable carriers. New phage-based technologies have led to the construction of different peptide libraries, and recognition abilities provided by novel targeting ligands. Phage hybridization with non-organic compounds introduces new properties to phages and could be a suitable strategy for construction of bio-inorganic carriers. In this review we try to cover the major phage species that have been used in drug and gene delivery systems, and the biological application of phages as novel targeting ligands and targeted therapeutics.
Collapse
Affiliation(s)
- Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamed Mirshekari
- Advanced Nanobiotechnology & Nanomedicine Research Group [ANNRG], Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran; Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - Sajad Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran
| | - Mohsen Moghoofei
- Student Research Committee, Iran University of Medical Sciences, Tehran, IR, Iran; Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
241
|
Abstract
Self-replicating genetic material presumably provided the architecture necessary for generating the last universal ancestor of all nucleic-acid-based life. As biological complexity increased in the billions of years that followed, the same genetic material also morphed into a wide spectrum of viruses and other parasitic genetic elements. The resulting struggle for existence drove the evolution of host defenses, giving rise to a perpetual arms race. This Perspective summarizes the antiviral mechanisms evident across the tree of life, discussing each in their evolutionary context to postulate how the coevolution of host and pathogen shaped the cellular antiviral defenses we know today.
Collapse
|
242
|
Dirk BS, Van Nynatten LR, Dikeakos JD. Where in the Cell Are You? Probing HIV-1 Host Interactions through Advanced Imaging Techniques. Viruses 2016; 8:v8100288. [PMID: 27775563 PMCID: PMC5086620 DOI: 10.3390/v8100288] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/06/2016] [Accepted: 10/10/2016] [Indexed: 12/19/2022] Open
Abstract
Viruses must continuously evolve to hijack the host cell machinery in order to successfully replicate and orchestrate key interactions that support their persistence. The type-1 human immunodeficiency virus (HIV-1) is a prime example of viral persistence within the host, having plagued the human population for decades. In recent years, advances in cellular imaging and molecular biology have aided the elucidation of key steps mediating the HIV-1 lifecycle and viral pathogenesis. Super-resolution imaging techniques such as stimulated emission depletion (STED) and photoactivation and localization microscopy (PALM) have been instrumental in studying viral assembly and release through both cell-cell transmission and cell-free viral transmission. Moreover, powerful methods such as Forster resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) have shed light on the protein-protein interactions HIV-1 engages within the host to hijack the cellular machinery. Specific advancements in live cell imaging in combination with the use of multicolor viral particles have become indispensable to unravelling the dynamic nature of these virus-host interactions. In the current review, we outline novel imaging methods that have been used to study the HIV-1 lifecycle and highlight advancements in the cell culture models developed to enhance our understanding of the HIV-1 lifecycle.
Collapse
Affiliation(s)
- Brennan S Dirk
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Logan R Van Nynatten
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada.
| |
Collapse
|
243
|
Rosani U, Gerdol M. A bioinformatics approach reveals seven nearly-complete RNA-virus genomes in bivalve RNA-seq data. Virus Res 2016; 239:33-42. [PMID: 27769778 DOI: 10.1016/j.virusres.2016.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/17/2023]
Abstract
Viral metagenomics (viromics) can provide a great contribution in expanding the knowledge of viruses and the relationship with their hosts. Viromic studies on marine organisms are still at a very early stage and only little efforts have been spent in the identification of viruses associated to marine invertebrates to date, leaving the complexity of marine viromes associated to bivalve hosts almost completely unexplored. However, the potential use of viromic approaches in the management of viral diseases affecting aquacultured species has been recently evidenced by the flourishing of studies on the Ostreid herpesvirus type-1, which has been associated with bivalve mortality events. Herein we discuss an effective pipeline to retrieve and reconstruct nearly complete and previously unreported viral genomes from existing host RNA-seq data. As a case study, we report the identification of seven RNA-virus genomes within the frame of a highly diversified viral community that characterizes both Crassostrea gigas and Mytilus galloprovincialis samples collected from the lagoon of Goro (Italy).
Collapse
Affiliation(s)
- Umberto Rosani
- Dept. of Biology, University of Padua, Via U. Bassi 58/B, 35121 Padova Italy.
| | - Marco Gerdol
- Dept. of Life Sciences, University of Trieste, Via L. Giorgieri 5, 34127 Trieste Italy
| |
Collapse
|
244
|
Eukaryotic association module in phage WO genomes from Wolbachia. Nat Commun 2016; 7:13155. [PMID: 27727237 PMCID: PMC5062602 DOI: 10.1038/ncomms13155] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/08/2016] [Indexed: 01/13/2023] Open
Abstract
Viruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbour bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report a metagenomic analysis of purified bacteriophage WO particles of Wolbachia and uncover a eukaryotic association module in the complete WO genome. It harbours predicted domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). To the best of our knowledge, these eukaryotic-like domains have never before been reported in packaged bacteriophages and their phylogeny, distribution and sequence diversity imply lateral transfers between bacteriophage/prophage and animal genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation of Wolbachia. Viruses commonly exchange genetic material with their hosts, but not with species from other domains of life. Here, the authors find that the bacteriophage WO of Wolbachia contains eukaryotic-like genes, implicating lateral genetic transfer between eukaryotes and viruses infecting bacteria.
Collapse
|
245
|
Davison M, Treangen TJ, Koren S, Pop M, Bhaya D. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. PLoS One 2016; 11:e0160574. [PMID: 27611571 PMCID: PMC5017753 DOI: 10.1371/journal.pone.0160574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/21/2016] [Indexed: 12/13/2022] Open
Abstract
The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2–13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics.
Collapse
Affiliation(s)
- Michelle Davison
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America
- Stanford University, Department of Biology, Stanford, CA, 94305, United States of America
- * E-mail: (MD); (DB)
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
| | - Sergey Koren
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, Biomolecular Sciences Building, College Park, MD, 20742, United States of America
- Department of Computer Science, University of Maryland, College Park, MD, 20742, United States of America
| | - Devaki Bhaya
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America
- Stanford University, Department of Biology, Stanford, CA, 94305, United States of America
- * E-mail: (MD); (DB)
| |
Collapse
|
246
|
|
247
|
Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS Comput Biol 2016; 12:e1005071. [PMID: 27532298 PMCID: PMC4988722 DOI: 10.1371/journal.pcbi.1005071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 07/20/2016] [Indexed: 12/30/2022] Open
Abstract
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.
Collapse
|
248
|
Dann LM, Rosales S, McKerral J, Paterson JS, Smith RJ, Jeffries TC, Oliver RL, Mitchell JG. Marine and giant viruses as indicators of a marine microbial community in a riverine system. Microbiologyopen 2016; 5:1071-1084. [PMID: 27506856 PMCID: PMC5221468 DOI: 10.1002/mbo3.392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9-38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas-Becking hypothesis "everything is everywhere, but, the environment selects." We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.
Collapse
Affiliation(s)
- Lisa M Dann
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Stephanie Rosales
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Jody McKerral
- School of Computer Science, Engineering and Mathematics, Flinders University, Adelaide, Australia
| | - James S Paterson
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Renee J Smith
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Rod L Oliver
- Land and Water Research Division at the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Adelaide, South Australia, Australia
| | - James G Mitchell
- School of Biological Sciences at Flinders University, Adelaide, South Australia, Australia
| |
Collapse
|
249
|
Abstract
UNLABELLED Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes. Such a network can be partitioned into modules that combine nodes from both classes. The bipartite network of dsDNA viruses includes 19 modules that form 5 major and 3 minor supermodules. Of these modules, 11 include tailed bacteriophages, reflecting the diversity of this largest group of viruses. The module analysis quantitatively validates and refines previously proposed nontrivial evolutionary relationships. An expansive supermodule combines the large and giant viruses of the putative order "Megavirales" with diverse moderate-sized viruses and related mobile elements. All viruses in this supermodule share a distinct morphogenetic tool kit with a double jelly roll major capsid protein. Herpesviruses and tailed bacteriophages comprise another supermodule, held together by a distinct set of morphogenetic proteins centered on the HK97-like major capsid protein. Together, these two supermodules cover the great majority of currently known dsDNA viruses. We formally identify a set of 14 viral hallmark genes that comprise the hubs of the network and account for most of the intermodule connections. IMPORTANCE Viruses and related mobile genetic elements are the dominant biological entities on earth, but their evolution is not sufficiently understood and their classification is not adequately developed. The key reason is the characteristic high rate of virus evolution that involves not only sequence change but also extensive gene loss, gain, and exchange. Therefore, in the study of virus evolution on a large scale, traditional phylogenetic approaches have limited applicability and have to be complemented by gene and genome network analyses. We applied state-of-the art methods of such analysis to reveal robust hierarchical modularity in the genomes of double-stranded DNA viruses. Some of the identified modules combine highly diverse viruses infecting bacteria, archaea, and eukaryotes, in support of previous hypotheses on direct evolutionary relationships between viruses from the three domains of cellular life. We formally identify a set of 14 viral hallmark genes that hold together the genomic network.
Collapse
|
250
|
MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies. PLoS One 2016; 11:e0160334. [PMID: 27479078 PMCID: PMC4968819 DOI: 10.1371/journal.pone.0160334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
Metagenomics, the sequence characterization of all genomes within a sample, is widely used as a virus discovery tool as well as a tool to study viral diversity of animals. Metagenomics can be considered to have three main steps; sample collection and preparation, sequencing and finally bioinformatics. Bioinformatic analysis of metagenomic datasets is in itself a complex process, involving few standardized methodologies, thereby hampering comparison of metagenomics studies between research groups. In this publication the new bioinformatics framework MetLab is presented, aimed at providing scientists with an integrated tool for experimental design and analysis of viral metagenomes. MetLab provides support in designing the metagenomics experiment by estimating the sequencing depth needed for the complete coverage of a species. This is achieved by applying a methodology to calculate the probability of coverage using an adaptation of Stevens’ theorem. It also provides scientists with several pipelines aimed at simplifying the analysis of viral metagenomes, including; quality control, assembly and taxonomic binning. We also implement a tool for simulating metagenomics datasets from several sequencing platforms. The overall aim is to provide virologists with an easy to use tool for designing, simulating and analyzing viral metagenomes. The results presented here include a benchmark towards other existing software, with emphasis on detection of viruses as well as speed of applications. This is packaged, as comprehensive software, readily available for Linux and OSX users at https://github.com/norling/metlab.
Collapse
|