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Tran NT, Le TBK. Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination. Nat Commun 2024; 15:4749. [PMID: 38834569 PMCID: PMC11150451 DOI: 10.1038/s41467-024-49114-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Gene Transfer Agents (GTAs) are phage-like particles that cannot self-multiply and be infectious. Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation, has recently been demonstrated to produce bona fide GTA particles (CcGTA). Since C. crescentus ultimately die to release GTA particles, the production of GTA particles must be tightly regulated and integrated with the host physiology to prevent a collapse in cell population. Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for complete CcGTA production. Here, we show that the CcGTA gene cluster is transcriptionally co-activated by GafY, integration host factor (IHF), and by GafZ-mediated transcription anti-termination. We present evidence that GafZ is a transcription anti-terminator that likely forms an anti-termination complex with RNA polymerase, NusA, NusG, and NusE to bypass transcription terminators within the 14 kb CcGTA cluster. Overall, we reveal a two-tier regulation that coordinates the synthesis of GTA particles in C. crescentus.
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Affiliation(s)
- Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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2
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Fogg PCM. Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution. Mol Microbiol 2024. [PMID: 38511257 DOI: 10.1111/mmi.15251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.
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3
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Guinet B, Leobold M, Herniou EA, Bloin P, Burlet N, Bredlau J, Navratil V, Ravallec M, Uzbekov R, Kester K, Gundersen Rindal D, Drezen JM, Varaldi J, Bézier A. A novel and diverse family of filamentous DNA viruses associated with parasitic wasps. Virus Evol 2024; 10:veae022. [PMID: 38617843 PMCID: PMC11013392 DOI: 10.1093/ve/veae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 04/16/2024] Open
Abstract
Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.
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Affiliation(s)
- Benjamin Guinet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Matthieu Leobold
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Pierrick Bloin
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Nelly Burlet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Justin Bredlau
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX 69622, France
- UMS 3601, Institut Français de Bioinformatique, IFB-Core, 2 rue Gaston Crémieu, Évry CEDEX 91057, France
- European Virus Bioinformatics Center, Leutragraben 1, Jena 07743, Germany
| | - Marc Ravallec
- Diversité, génomes et interactions microorganismes insectes (DGIMI), UMR 1333 INRA, Université de Montpellier 2, 2 Place Eugène Bataillon cc101, Montpellier CEDEX 5 34095, France
| | - Rustem Uzbekov
- Laboratory of Cell Biology and Electron Microscopy, Faculty of Medicine, Université de Tours, 10 bd Tonnelle, BP 3223, Tours CEDEX 37032, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskye Gory 73, Moscow 119992, Russia
| | - Karen Kester
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Dawn Gundersen Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Julien Varaldi
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
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4
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Simón D, Ramos N, Lamolle G, Musto H. Two decades ago, giant viruses were discovered: the fall of an old paradigm. Front Microbiol 2024; 15:1356711. [PMID: 38463488 PMCID: PMC10920292 DOI: 10.3389/fmicb.2024.1356711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024] Open
Affiliation(s)
- Diego Simón
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
- Laboratorio de Virología Molecular, Facultad de Ciencias, Centro de Investigaciones Nucleares, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología, Departamento de Biología Celular y Molecular, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Guillermo Lamolle
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
| | - Héctor Musto
- Laboratorio de Genómica Evolutiva, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Montevideo, Uruguay
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5
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Muzyukina P, Shkaruta A, Guzman NM, Andreani J, Borges AL, Bondy-Denomy J, Maikova A, Semenova E, Severinov K, Soutourina O. Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile. mSphere 2023; 8:e0040123. [PMID: 38009936 PMCID: PMC10732046 DOI: 10.1128/msphere.00401-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Clostridioides difficile is the widespread anaerobic spore-forming bacterium that is a major cause of potentially lethal nosocomial infections associated with antibiotic therapy worldwide. Due to the increase in severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments for C. difficile infections. In particular, phage therapy is regarded as a potential substitute for existing antimicrobial treatments. However, it faces challenges because C. difficile has highly active CRISPR-Cas immunity, which may be a specific adaptation to phage-rich and highly crowded gut environment. To overcome this defense, C. difficile phages must employ anti-CRISPR mechanisms. Here, we present the first anti-CRISPR protein that inhibits the CRISPR-Cas defense system in this pathogen. Our work offers insights into the interactions between C. difficile and its phages, paving the way for future CRISPR-based applications and development of effective phage therapy strategies combined with the engineering of virulent C. difficile infecting phages.
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Affiliation(s)
- Polina Muzyukina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anton Shkaruta
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Noemi M. Guzman
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Adair L. Borges
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Anna Maikova
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Konstantin Severinov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- Institute of Molecular Genetics, Kurchatov National Research Center, Moscow, Russia
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Institut Universitaire de France (IUF), Paris, France
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6
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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7
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Buivydaitė Ž, Aryal L, Corrêa FB, Chen T, Langlois V, Elberg CL, Netherway T, Wang R, Zhao T, Acharya B, Emerson JB, Hillary L, Khadka RB, Mason-Jones K, Sapkota R, Sutela S, Trubl G, White RA, Winding A, Carreira C. Meeting report: The first soil viral workshop 2022. Virus Res 2023; 331:199121. [PMID: 37086855 PMCID: PMC10457523 DOI: 10.1016/j.virusres.2023.199121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/20/2023] [Accepted: 04/20/2023] [Indexed: 04/24/2023]
Abstract
Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.
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Affiliation(s)
- Živilė Buivydaitė
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Laxman Aryal
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Felipe Borim Corrêa
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tingting Chen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, G1V 0A6 Québec, QC, Canada
| | - Christine Lorenzen Elberg
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
| | - Ruiqi Wang
- Department of Environmental Biology, Institute of Environmental Sciences (CML), Leiden University, Einsteinweg 2, 2333 CC Leiden, the Netherlands
| | - Tianci Zhao
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (Green), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747AG Groningen, the Netherlands
| | - Basistha Acharya
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA, USA
| | - Luke Hillary
- Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA, USA
| | - Ram B Khadka
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Suvi Sutela
- Forest Health and Biodiversity Group, Natural Resources Institute Finland, Helsinki, Finland
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Richard Allen White
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC, USA
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Cátia Carreira
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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8
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Yu L, Li T, Li H, Ma M, Li L, Lin S. In Situ Molecular Ecological Analyses Illuminate Distinct Factors Regulating Formation and Demise of a Harmful Dinoflagellate Bloom. Microbiol Spectr 2023; 11:e0515722. [PMID: 37074171 PMCID: PMC10269597 DOI: 10.1128/spectrum.05157-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 04/20/2023] Open
Abstract
The development and demise of a harmful algal bloom (HAB) are generally regulated by multiple processes; identifying specific critical drivers for a specific bloom is important yet challenging. Here, we conducted a whole-assemblage molecular ecological study on a dinoflagellate bloom to address the hypothesis that energy and nutrient acquisition, defense against grazing and microbial attacks, and sexual reproduction are critical to the rise and demise of the bloom. Microscopic and molecular analyses identified the bloom-causing species as Karenia longicanalis and showed that the ciliate Strombidinopsis sp. was dominant in a nonbloom plankton community, whereas the diatom Chaetoceros sp. dominated the after-bloom community, along with remarkable shifts in the community structure for both eukaryotes and prokaryotes. Metatranscriptomic analysis indicated that heightened energy and nutrient acquisition in K. longicanalis significantly contributed to bloom development. In contrast, active grazing by the ciliate Strombidinopsis sp. and attacks by algicidal bacteria (Rhodobacteracea, Cryomorphaceae, and Rhodobacteracea) and viruses prevented (at nonbloom stage) or collapsed the bloom (in after-bloom stage). Additionally, nutrition competition by the Chaetoceros diatoms plausibly contributed to bloom demise. The findings suggest the importance of energy and nutrients in promoting this K. longicanalis bloom and the failure of antimicrobial defense and competition of diatoms as the major bloom suppressor and terminator. This study provides novel insights into bloom-regulating mechanisms and the first transcriptomic data set of K. longicanalis, which will be a valuable resource and essential foundation for further elucidation of bloom regulators of this and related species of Kareniaceae in the future. IMPORTANCE HABs have increasingly occurred and impacted human health, aquatic ecosystems, and coastal economies. Despite great efforts, the factors that drive the development and termination of a bloom are poorly understood, largely due to inadequate in situ data about the physiology and metabolism of the causal species and the community. Using an integrative molecular ecological approach, we determined that heightened energy and nutrient acquisition promoted the bloom, while resource allocation in defense and failure to defend against grazing and microbial attacks likely prevented or terminated the bloom. Our findings reveal the differential roles of multiple abiotic and biotic environmental factors in driving the formation or demise of a toxic dinoflagellate bloom, suggesting the importance of a balanced biodiverse ecosystem in preventing a dinoflagellate bloom. The study also demonstrates the power of whole-assemblage metatranscriptomics coupled to DNA barcoding in illuminating plankton ecological processes and the underlying species and functional diversities.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Central Laboratory, Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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9
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Ettinger CL, Saunders M, Selbmann L, Delgado-Baquerizo M, Donati C, Albanese D, Roux S, Tringe S, Pennacchio C, Del Rio TG, Stajich JE, Coleine C. Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability. MICROBIOME 2023; 11:103. [PMID: 37158954 PMCID: PMC10165816 DOI: 10.1186/s40168-023-01554-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. RESULTS We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. CONCLUSION This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
| | - Morgan Saunders
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele All'Adige, 38098, Italy
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Susannah Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Christa Pennacchio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Tijana G Del Rio
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Claudia Coleine
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.
- Laboratorio de Biodiversidad Y Funcionamiento Ecosistémico, Instituto de Recursos Naturales Y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Seville, E-41012, Spain.
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10
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME COMMUNICATIONS 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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11
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Ibañez-Lligoña M, Colomer-Castell S, González-Sánchez A, Gregori J, Campos C, Garcia-Cehic D, Andrés C, Piñana M, Pumarola T, Rodríguez-Frias F, Antón A, Quer J. Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses. Viruses 2023; 15:v15020587. [PMID: 36851800 PMCID: PMC9965957 DOI: 10.3390/v15020587] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.
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Affiliation(s)
- Marta Ibañez-Lligoña
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frias
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Campus de la UAB, Plaça Cívica, 08193 Bellaterra, Spain
- Correspondence:
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12
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Cheng R, Li X, Jiang L, Gong L, Geslin C, Shao Z. Virus diversity and interactions with hosts in deep-sea hydrothermal vents. MICROBIOME 2022; 10:235. [PMID: 36566239 PMCID: PMC9789665 DOI: 10.1186/s40168-022-01441-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The deep sea harbors many viruses, yet their diversity and interactions with hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral composition, distribution, host preference, and metabolic potential in different habitats of global hydrothermal vents, including vent plumes, background seawater, diffuse fluids, and sediments. RESULTS From 34 samples collected at eight vent sites, a total of 4662 viral populations (vOTUs) were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages. Apart from the abundant unclassified viruses, tailed phages are most predominant across the global hydrothermal vents, while single-stranded DNA viruses, including Microviridae and small eukaryotic viruses, also constitute a significant part of the viromes. As revealed by protein-sharing network analysis, hydrothermal vent viruses formed many novel genus-level viral clusters and are highly endemic to specific vent sites and habitat types. Only 11% of the vOTUs can be linked to hosts, which are the key microbial taxa of hydrothermal habitats, such as Gammaproteobacteria and Campylobacterota. Intriguingly, vent viromes share some common metabolic features in that they encode auxiliary genes that are extensively involved in the metabolism of carbohydrates, amino acids, cofactors, and vitamins. Specifically, in plume viruses, various auxiliary genes related to methane, nitrogen, and sulfur metabolism were observed, indicating their contribution to host energy conservation. Moreover, the prevalence of sulfur-relay pathway genes indicated the significant role of vent viruses in stabilizing the tRNA structure, which promotes host adaptation to steep environmental gradients. CONCLUSIONS The deep-sea hydrothermal systems hold untapped viral diversity with novelty. They may affect both vent prokaryotic and eukaryotic communities and modulate host metabolism related to vent adaptability. More explorations are needed to depict global vent virus diversity and its roles in this unique ecosystem. Video Abstract.
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Affiliation(s)
- Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xiaofeng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Claire Geslin
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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13
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Kwok KTT, de Rooij MMT, Messink AB, Wouters IM, Smit LAM, Cotten M, Heederik DJJ, Koopmans MPG, Phan MVT. Establishing farm dust as a useful viral metagenomic surveillance matrix. Sci Rep 2022; 12:16308. [PMID: 36175536 PMCID: PMC9521564 DOI: 10.1038/s41598-022-20701-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
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Affiliation(s)
- Kirsty T T Kwok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Myrna M T de Rooij
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Aniek B Messink
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
- London School of Hygiene and Tropical Medicine, London, UK.
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14
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Manrubia S. The simple emergence of complex molecular function. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200422. [PMID: 35599566 DOI: 10.1098/rsta.2020.0422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Systems Biology Department, National Biotechnology Centre (CSIC), c/Darwin 3, 28049 Madrid, Spain
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15
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bin Umair M, Akusa FN, Kashif H, Seerat-e-Fatima, Butt F, Azhar M, Munir I, Ahmed M, Khalil W, Sharyar H, Rafique S, Shahid M, Afzal S. Viruses as tools in gene therapy, vaccine development, and cancer treatment. Arch Virol 2022; 167:1387-1404. [PMID: 35462594 PMCID: PMC9035288 DOI: 10.1007/s00705-022-05432-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022]
Abstract
Using viruses to our advantage has been a huge leap for humanity. Their ability to mediate horizontal gene transfer has made them useful tools for gene therapy, vaccine development, and cancer treatment. Adenoviruses, adeno-associated viruses, retroviruses, lentiviruses, alphaviruses, and herpesviruses are a few of the most common candidates for use as therapeutic agents or efficient gene delivery systems. Efforts are being made to improve and perfect viral-vector-based therapies to overcome potential or reported drawbacks. Some preclinical trials of viral vector vaccines have yielded positive results, indicating their potential as prophylactic or therapeutic vaccine candidates. Utilization of the oncolytic activity of viruses is the future of cancer therapy, as patients will then be free from the harmful effects of chemo- or radiotherapy. This review discusses in vitro and in vivo studies showing the brilliant therapeutic potential of viruses.
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Affiliation(s)
- Musab bin Umair
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fujimura Nao Akusa
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hadia Kashif
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Seerat-e-Fatima
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fatima Butt
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Marium Azhar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Iqra Munir
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Ahmed
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Wajeeha Khalil
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hafiz Sharyar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Shahid
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Samia Afzal
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
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16
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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17
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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18
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Dutilh BE, Varsani A, Tong Y, Simmonds P, Sabanadzovic S, Rubino L, Roux S, Muñoz AR, Lood C, Lefkowitz EJ, Kuhn JH, Krupovic M, Edwards RA, Brister JR, Adriaenssens EM, Sullivan MB. Perspective on taxonomic classification of uncultivated viruses. Curr Opin Virol 2021; 51:207-215. [PMID: 34781105 DOI: 10.1016/j.coviro.2021.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/19/2022]
Abstract
Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.
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Affiliation(s)
- Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Institute of Bioloversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany.
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa
| | - Yigang Tong
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS 39762, USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001, Leuven, Belgium; Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, F-75015, Paris, France
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
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19
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Moreno-Gallego JL, Reyes A. Informative Regions In Viral Genomes. Viruses 2021; 13:v13061164. [PMID: 34207030 PMCID: PMC8234400 DOI: 10.3390/v13061164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses, far from being just parasites affecting hosts' fitness, are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages, remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison with public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs (Eukaryotic Viruses and Phages Orthologous Groups). To do this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information, and used all annotated and predicted proteins to identify potential protein domains. The clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a random forest implementation to classify genomes into their taxonomy and found that the presence or absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1457 ViPhOGs that given their importance for the classification could be considered as markers or signatures for the different taxonomic groups defined by the ICTV at the order, family, and genus levels.
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Affiliation(s)
- Jaime Leonardo Moreno-Gallego
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
- Correspondence:
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20
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Agnati LF, Anderlini D, Guidolin D, Marcoli M, Maura G. Man is a "Rope" Stretched Between Virosphere and Humanoid Robots: On the Urgent Need of an Ethical Code for Ecosystem Survival. FOUNDATIONS OF SCIENCE 2021; 27:311-325. [PMID: 34177285 PMCID: PMC8210962 DOI: 10.1007/s10699-021-09796-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/21/2021] [Indexed: 06/13/2023]
Abstract
In this paper we compare the strategies applied by two successful biological components of the ecosystem, the viruses and the human beings, to interact with the environment. Viruses have had and still exert deep and vast actions on the ecosystem especially at the genome level of most of its biotic components. We discuss on the importance of the human being as contraptions maker in particular of robots, hence of machines capable of automatically carrying out complex series of actions. Beside the relevance of designing and assembling these contraptions, it is of basic importance the goal for which they are assembled and future scenarios of their possible impact on the ecosystem. We can't procrastinate the development and implementation of a highly inspired and stringent "ethical code" for human beings and humanoid robots because it will be a crucial aspect for the wellbeing of the mankind and of the entire ecosystem.
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Affiliation(s)
- Luigi F. Agnati
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Deanna Anderlini
- Centre for Sensorimotor Performance, The University of Queensland, Brisbane, Australia
| | - Diego Guidolin
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, GENOVA, Italy
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, GENOVA, Italy
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21
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Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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22
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Analysis of Different Size Fractions Provides a More Complete Perspective of Viral Diversity in a Freshwater Embayment. Appl Environ Microbiol 2021; 87:AEM.00197-21. [PMID: 33741611 DOI: 10.1128/aem.00197-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/11/2021] [Indexed: 11/20/2022] Open
Abstract
Inspired by recent discoveries of the prevalence of large viruses in the environment, we reassessed the longstanding approach of filtering water through small-pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 data sets derived from <0.45-μm- and >0.45-μm-size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family, we observed highly diverse and distinct virus communities in the >0.45-μm-size fractions, whereas the <0.45-μm-size fractions were composed primarily of Caudovirales The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions, with higher relative abundances of cyanophages in the >0.45-μm-size fractions, potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, were detected exclusively in the often-disregarded >0.45-μm-size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions, suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of double-stranded DNA (dsDNA) viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing.IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller-size "free-virus" fraction. Our study demonstrates that analysis of virus communities using only the smaller-size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger->0.45-μm-size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data show that examining only the smaller-size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.
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Steczkiewicz K, Prestel E, Bidnenko E, Szczepankowska AK. Expanding Diversity of Firmicutes Single-Strand Annealing Proteins: A Putative Role of Bacteriophage-Host Arms Race. Front Microbiol 2021; 12:644622. [PMID: 33959107 PMCID: PMC8093625 DOI: 10.3389/fmicb.2021.644622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/25/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage-encoded single strand annealing proteins (SSAPs) are recombinases which can substitute the classical, bacterial RecA and manage the DNA metabolism at different steps of phage propagation. SSAPs have been shown to efficiently promote recombination between short and rather divergent DNA sequences and were exploited for in vivo genetic engineering mainly in Gram-negative bacteria. In opposition to the conserved and almost universal bacterial RecA protein, SSAPs display great sequence diversity. The importance for SSAPs in phage biology and phage-bacteria evolution is underlined by their role as key players in events of horizontal gene transfer (HGT). All of the above provoke a constant interest for the identification and study of new phage recombinase proteins in vivo, in vitro as well as in silico. Despite this, a huge body of putative ssap genes escapes conventional classification, as they are not properly annotated. In this work, we performed a wide-scale identification, classification and analysis of SSAPs encoded by the Firmicutes bacteria and their phages. By using sequence similarity network and gene context analyses, we created a new high quality dataset of phage-related SSAPs, substantially increasing the number of annotated SSAPs. We classified the identified SSAPs into seven distinct families, namely RecA, Gp2.5, RecT/Redβ, Erf, Rad52/22, Sak3, and Sak4, organized into three superfamilies. Analysis of the relationships between the revealed protein clusters led us to recognize Sak3-like proteins as a new distinct SSAP family. Our analysis showed an irregular phylogenetic distribution of ssap genes among different bacterial phyla and specific phages, which can be explained by the high rates of ssap HGT. We propose that the evolution of phage recombinases could be tightly linked to the dissemination of bacterial phage-resistance mechanisms (e.g., abortive infection and CRISPR/Cas systems) targeting ssap genes and be a part of the constant phage-bacteria arms race.
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Affiliation(s)
| | - Eric Prestel
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Elena Bidnenko
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Ciuffreda L, Rodríguez-Pérez H, Flores C. Nanopore sequencing and its application to the study of microbial communities. Comput Struct Biotechnol J 2021; 19:1497-1511. [PMID: 33815688 PMCID: PMC7985215 DOI: 10.1016/j.csbj.2021.02.020] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022] Open
Abstract
Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable technologies. The use of long reads has allowed to address several previously unsolved issues in the field, such as the resolution of complex genomic structures, and facilitated the access to metagenome assembled genomes (MAGs). Furthermore, the low cost and portability of platforms together with the development of rapid protocols and analysis pipelines have featured nanopore technology as an attractive and ever-growing tool for real-time in-field sequencing for environmental microbial analysis. This review provides an up-to-date summary of the experimental protocols and bioinformatic tools for the study of microbial communities using nanopore sequencing, highlighting the most important and recent research in the field with a major focus on infectious diseases. An overview of the main approaches including targeted and shotgun approaches, metatranscriptomics, epigenomics, and epitranscriptomics is provided, together with an outlook to the major challenges and perspectives over the use of this technology for microbial studies.
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Affiliation(s)
- Laura Ciuffreda
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, 38010 Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, 38010 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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Viral speciation through subcellular genetic isolation and virogenesis incompatibility. Nat Commun 2021; 12:342. [PMID: 33436625 PMCID: PMC7804931 DOI: 10.1038/s41467-020-20575-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding how biological species arise is critical for understanding the evolution of life on Earth. Bioinformatic analyses have recently revealed that viruses, like multicellular life, form reproductively isolated biological species. Viruses are known to share high rates of genetic exchange, so how do they evolve genetic isolation? Here, we evaluate two related bacteriophages and describe three factors that limit genetic exchange between them: 1) A nucleus-like compartment that physically separates replicating phage genomes, thereby limiting inter-phage recombination during co-infection; 2) A tubulin-based spindle that orchestrates phage replication and forms nonfunctional hybrid polymers; and 3) A nuclear incompatibility factor that reduces phage fitness. Together, these traits maintain species differences through Subcellular Genetic Isolation where viral genomes are physically separated during co-infection, and Virogenesis Incompatibility in which the interaction of cross-species components interferes with viral production. Virus speciation cannot be fully explained by the evolution of different host specificities. Here, Chaikeeratisak et al. identify ways viruses can remain genetically isolated despite co-infecting the same cell, providing insight into how new virus species evolve.
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Metagenomic Approach with the NetoVIR Enrichment Protocol Reveals Virus Diversity within Ethiopian Honey Bees ( Apis mellifera simensis). Viruses 2020; 12:v12111218. [PMID: 33121140 PMCID: PMC7692050 DOI: 10.3390/v12111218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomics studies have accelerated the discovery of novel or divergent viruses of the honey bee. However, most of these studies predominantly focused on RNA viruses, and many suffer from the relatively low abundance of viral nucleic acids in the samples (i.e., compared to that of the host). Here, we explored the virome of the Ethiopian honey bee, Apis mellifera simensis, using an unbiased metagenomic approach in which the next-generation sequencing step was preceded by an enrichment protocol for viral particles. Our study revealed five well-known bee viruses and 25 atypical virus species, most of which have never been found in A. mellifera before. The viruses belong to Iflaviridae, Dicistroviridae, Secoviridae, Partitiviridae, Parvoviridae, Potyviridae, and taxonomically unclassified families. Fifteen of these atypical viruses were most likely plant-specific, and the remaining ten were presumed to be insect-specific. Apis mellifera filamentous virus (AmFV) was found in one sampling site out of 10. Two samples contained high read counts of a virus similar to Diatraea saccharales densovirus (DsDNV), which is a virus that causes high mortality in the sugarcane borer. AmFV and the DsDNV-like virus were the only DNA viruses found. Three viruses that primarily infect Drosophila spp. were also discovered: La Jolla virus (LJV), Kilifi virus (KiV), and Thika virus. Our study suggests that phoretic varroa mites are involved in the transmission of LJV and KiV and that both viruses replicate in mites and adult bees. We also found an overwhelming dominance of the deformed wing virus type B variant, which fits well with the apparently harmless infestation by Varroa destructor. It was suggested that Ethiopian bees have developed tolerance against virus infections as the result of natural selection.
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Chelkha N, Levasseur A, La Scola B, Colson P. Host-virus interactions and defense mechanisms for giant viruses. Ann N Y Acad Sci 2020; 1486:39-57. [PMID: 33090482 DOI: 10.1111/nyas.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/28/2020] [Accepted: 07/26/2020] [Indexed: 12/26/2022]
Abstract
Giant viruses, with virions larger than 200 nm and genomes larger than 340 kilobase pairs, modified the now outdated perception of the virosphere. With virions now reported reaching up to 1.5 μm in size and genomes of up to 2.5 Mb encoding components shared with cellular life forms, giant viruses exhibit a complexity similar to microbes, such as bacteria and archaea. Here, we review interactions of giant viruses with their hosts and defense strategies of giant viruses against their hosts and coinfecting microorganisms or virophages. We also searched by comparative genomics for homologies with proteins described or suspected to be involved in defense mechanisms. Our search reveals that natural immunity and apoptosis seem to be crucial components of the host defense against giant virus infection. Conversely, giant viruses possess methods of hijacking host functions to counteract cellular antiviral responses. In addition, giant viruses may encode other unique and complex pathways to manipulate the host machinery and eliminate other competing microorganisms. Notably, giant viruses have evolved defense mechanisms against their virophages and they might trigger defense systems against other viruses through sequence integration. We anticipate that comparative genomics may help identifying genes involved in defense strategies of both giant viruses and their hosts.
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Affiliation(s)
- Nisrine Chelkha
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems4020023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.
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Birnberg L, Temmam S, Aranda C, Correa-Fiz F, Talavera S, Bigot T, Eloit M, Busquets N. Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes. Viruses 2020; 12:E274. [PMID: 32121402 PMCID: PMC7150749 DOI: 10.3390/v12030274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 01/10/2023] Open
Abstract
Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral diseases surveillance, and for the detection of new viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at the Llobregat River Delta (Catalonia, Spain). Next generation sequencing (NGS) metagenomics analysis was applied on honey-baited FTA cards, which had been exposed to field-captured mosquitoes to characterize their associated virome. Arthropod- and plant-infecting viruses governed the virome profile on FTA cards. Twelve near-complete viral genomes were successfully obtained, suggesting good quality preservation of viral RNAs. Mosquito pools linked to the FTA cards were screened for the detection of mosquito-associated viruses by specific RT-PCRs to confirm the presence of these viruses. The circulation of viruses related to Alphamesonivirus, Quaranjavirus and unclassified Bunyavirales was detected in mosquitoes, and phylogenetic analyses revealed their similarities to viruses previously reported in other continents. To the best our knowledge, our findings constitute the first distribution record of these viruses in European mosquitoes and the first hint of insect-specific viruses in mosquitoes' saliva in field conditions, demonstrating the feasibility of this approach to monitor the transmissible fraction of the mosquitoes' virome. In conclusion, this pilot viromics study on honey-baited FTA cards was shown to be a valid approach for the detection of viruses circulating in mosquitoes, thereby setting up an alternative tool for arbovirus surveillance and control programs.
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Affiliation(s)
- Lotty Birnberg
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Sarah Temmam
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
| | - Carles Aranda
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
- Servei de Control de Mosquits del Consell Comarcal del Baix Llobregat, 08820 Barcelona, Spain
| | - Florencia Correa-Fiz
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Sandra Talavera
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
| | - Thomas Bigot
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
- Institut Pasteur – Bioinformatics and Biostatistics Hub—Computational Biology department, Institut Pasteur, USR 3756 CNRS—75015 Paris, France
| | - Marc Eloit
- Institut Pasteur, Pathogen Discovery Laboratory, 75015 Paris, France; (S.T.); (T.B.); (M.E.)
- National Veterinary School of Alfort, Paris-Est University, 94704 CEDEX, Maisons-Alfort, France
| | - Núria Busquets
- Centre de Recerca en Sanitat Animal (CReSA), Institut de recerca en Tecnologies Agroalimentaries (IRTA), 08193 Barcelona, Spain; (L.B.); (C.A.); (F.C.-F.); (S.T.)
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Koonin EV, Yutin N. The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome. Trends Microbiol 2020; 28:349-359. [PMID: 32298613 DOI: 10.1016/j.tim.2020.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 02/07/2023]
Abstract
Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were predicted, including unusual ones such as giant RNA polymerase polyproteins. The host range of the crAss-like phages consists of various members of the bacterial phylum Bacteroidetes as demonstrated by CRISPR spacer analysis and by analysis of genes acquired by phages from the hosts. New metagenomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancient association with primates. The first members of the crAss-like group was recently isolated and shown to infect the bacterium Bacteroides intestinales. Characterization of this phage validated the predicted podovirus-like virion structure and the identity of the major capsid protein and other predicted virion proteins, including three RNA polymerase subunits.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 2019; 22:178-193. [PMID: 31848574 PMCID: PMC7820839 DOI: 10.1093/bib/bbz155] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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Affiliation(s)
- Richa Bharti
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
| | - Dominik G Grimm
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
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Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MDR, Peralta R, Hernández-Mendoza A, Dobson ADW, Gonzalez RA, Pastor N, Batista-García RA. A Review on Viral Metagenomics in Extreme Environments. Front Microbiol 2019; 10:2403. [PMID: 31749771 PMCID: PMC6842933 DOI: 10.3389/fmicb.2019.02403] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.
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Affiliation(s)
- Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hugo G Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | | | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Ramón A Gonzalez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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Douglas GM, Langille MGI. Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. Genome Biol Evol 2019; 11:2750-2766. [PMID: 31504488 PMCID: PMC6777429 DOI: 10.1093/gbe/evz184] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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Ecological Factors of Transmission, Persistence and Circulation of Pathogens In Bat Populations. FOLIA VETERINARIA 2019. [DOI: 10.2478/fv-2019-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
The existence of bats is crucial for all ecosystem units as they fulfil numerous ecological roles. However, they are also considered to be natural reservoirs of a wide range of zoonotic microorganisms, especially viruses. In this review article we briefly summarize current knowledge about various ecological factors that facilitate bat pathogen dispersal and about the current approaches to monitoring viral communities present within bat populations. On the basis of the cited papers, we suggest that the increased focus on complex viral populations in bats and their interactions with other populations and the environment is necessary to fully comprehend the relationship between emerging infectious diseases, the environment and their toll on human health.
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Machine Learning Models for Error Detection in Metagenomics and Polyploid Sequencing Data. INFORMATION 2019. [DOI: 10.3390/info10030110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Metagenomics studies, as well as genomics studies of polyploid species such as wheat, deal with the analysis of high variation data. Such data contain sequences from similar, but distinct genetic chains. This fact presents an obstacle to analysis and research. In particular, the detection of instrumentation errors during the digitalization of the sequences may be hindered, as they can be indistinguishable from the real biological variation inside the digital data. This can prevent the determination of the correct sequences, while at the same time make variant studies significantly more difficult. This paper details a collection of ML-based models used to distinguish a real variant from an erroneous one. The focus is on using this model directly, but experiments are also done in combination with other predictors that isolate a pool of error candidates.
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Fogg PCM. Identification and characterization of a direct activator of a gene transfer agent. Nat Commun 2019; 10:595. [PMID: 30723210 PMCID: PMC6363796 DOI: 10.1038/s41467-019-08526-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/15/2019] [Indexed: 11/10/2022] Open
Abstract
Gene transfer agents (GTAs) are thought to be ancient bacteriophages that have been co-opted into serving their host and can now transfer any gene between bacteria. Production of GTAs is controlled by several global regulators through unclear mechanisms. In Rhodobacter capsulatus, gene rcc01865 encodes a putative regulatory protein that is essential for GTA production. Here, I show that rcc01865 (hereafter gafA) encodes a transcriptional regulator that binds to the GTA promoter to initiate production of structural and DNA packaging components. Expression of gafA is in turn controlled by the pleiotropic regulator protein CtrA and the quorum-sensing regulator GtaR. GafA and CtrA work together to promote GTA maturation and eventual release through cell lysis. Identification of GafA as a direct GTA regulator allows the first integrated regulatory model to be proposed and paves the way for discovery of GTAs in other species that possess gafA homologues.
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Affiliation(s)
- Paul C M Fogg
- Biology Department, University of York, Wentworth Way, York, YO10 5DD, UK.
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Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5' region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
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Hwang J, Park SY, Lee S, Lee TK. High diversity and potential translocation of DNA viruses in ballast water. MARINE POLLUTION BULLETIN 2018; 137:449-455. [PMID: 30503454 DOI: 10.1016/j.marpolbul.2018.10.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 09/07/2018] [Accepted: 10/24/2018] [Indexed: 05/22/2023]
Abstract
Ballast water is a common vector for the transport of invasive species to new marine and aquatic environments. We used a metagenomics approach to examine the composition and diversity of viral communities in ballast water from ships originating in Mexico, Saudi Arabia, New York, and Panama, and in water from the port of their destination in Busan, Korea. Myoviridae was the most abundant virus family in ballast water, followed Podoviridae and Siphoviridae. We also identified viruses that infect invertebrates, amoebas, and algae in ballast water and in the Busan port water. Interestingly, there were several viruses that infect humans or other animals (Swinepox virus, Raccoonpox virus, Suid herpesvirus, and Human endogenous retrovirus) in the samples from New York and Panama. In addition, there were giant viruses in all the ballast water samples, especially, identified Megavirus chilensis in New York and Panama, and Pandoravirus salinus in Mexico and Saudi Arabia. These results provide detailed descriptions of the characteristics of the viruses present in ballast water, document significant viral diversity, and indicate the potential translocation of viruses via ballast water.
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Affiliation(s)
- Jinik Hwang
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea; Marine Ecology and Resource Convergence Center, AICT, Suwon, 16229, Republic of Korea
| | - So Yun Park
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Taek-Kyun Lee
- South Sea Environment Research Department, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea.
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Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India. Sci Rep 2018; 8:16036. [PMID: 30375431 PMCID: PMC6207776 DOI: 10.1038/s41598-018-34332-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/04/2018] [Indexed: 11/08/2022] Open
Abstract
The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.
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Guajardo-Leiva S, Pedrós-Alió C, Salgado O, Pinto F, Díez B. Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs. Front Microbiol 2018; 9:2039. [PMID: 30233525 PMCID: PMC6129581 DOI: 10.3389/fmicb.2018.02039] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2018] [Indexed: 01/16/2023] Open
Abstract
Cyanophages are viruses with a wide distribution in aquatic ecosystems, that specifically infect Cyanobacteria. These viruses can be readily isolated from marine and fresh waters environments; however, their presence in cosmopolitan thermophilic phototrophic mats remains largely unknown. This study investigates the morphological diversity (TEM), taxonomic composition (metagenomics), and active infectivity (metatranscriptomics) of viral communities over a thermal gradient in hot spring phototrophic mats from Northern Patagonia (Chile). The mats were dominated (up to 53%) by cosmopolitan thermophilic filamentous true-branching cyanobacteria from the genus Mastigocladus, the associated viral community was predominantly composed of Caudovirales (70%), with most of the active infections driven by cyanophages (up to 90% of Caudovirales transcripts). Metagenomic assembly lead to the first full genome description of a T7-like Thermophilic Cyanophage recovered from a hot spring (Porcelana Hot Spring, Chile), with a temperature of 58°C (TC-CHP58). This could potentially represent a world-wide thermophilic lineage of podoviruses that infect cyanobacteria. In the hot spring, TC-CHP58 was active over a temperature gradient from 48 to 66°C, showing a high population variability represented by 1979 single nucleotide variants (SNVs). TC-CHP58 was associated to the Mastigocladus spp. by CRISPR spacers. Marked differences in metagenomic CRISPR loci number and spacers diversity, as well as SNVs, in the TC-CHP58 proto-spacers at different temperatures, reinforce the theory of co-evolution between natural virus populations and cyanobacterial hosts. Considering the importance of cyanobacteria in hot spring biogeochemical cycles, the description of this new cyanopodovirus lineage may have global implications for the functioning of these extreme ecosystems.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fabián Pinto
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.,Center for Climate and Resilience Research, Santiago, Chile
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Hily JM, Candresse T, Garcia S, Vigne E, Tannière M, Komar V, Barnabé G, Alliaume A, Gilg S, Hommay G, Beuve M, Marais A, Lemaire O. High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member. Front Microbiol 2018; 9:1782. [PMID: 30210456 PMCID: PMC6123372 DOI: 10.3389/fmicb.2018.01782] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
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Affiliation(s)
- Jean-Michel Hily
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Shahinez Garcia
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Emmanuelle Vigne
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Mélanie Tannière
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Véronique Komar
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Guillaume Barnabé
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Antoine Alliaume
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Sophie Gilg
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Gérard Hommay
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Monique Beuve
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Olivier Lemaire
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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Lopez-Zavala AA, Guevara-Hernandez E, Vazquez-Lujan LH, Sanchez-Paz A, Garcia-Orozco KD, Contreras-Vergara CA, Lopez-Leal G, Arvizu-Flores AA, Ochoa-Leyva A, Sotelo-Mundo RR. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites. PeerJ 2018; 6:e5023. [PMID: 29922516 PMCID: PMC6005164 DOI: 10.7717/peerj.5023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.,Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Eduardo Guevara-Hernandez
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Luz H Vazquez-Lujan
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Arturo Sanchez-Paz
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biologicas del Noroeste, Hermosillo, Sonora, Mexico
| | - Karina D Garcia-Orozco
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Carmen A Contreras-Vergara
- Laboratorio de Genetica de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Gamaliel Lopez-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
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Breitbart M, Bonnain C, Malki K, Sawaya NA. Phage puppet masters of the marine microbial realm. Nat Microbiol 2018; 3:754-766. [PMID: 29867096 DOI: 10.1038/s41564-018-0166-y] [Citation(s) in RCA: 313] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Viruses numerically dominate our oceans; however, we have only just begun to document the diversity, host range and infection dynamics of marine viruses, as well as the subsequent effects of infection on both host cell metabolism and oceanic biogeochemistry. Bacteriophages (that is, phages: viruses that infect bacteria) are highly abundant and are known to play critical roles in bacterial mortality, biogeochemical cycling and horizontal gene transfer. This Review Article summarizes current knowledge of marine viral ecology and highlights the importance of phage particles to the dissolved organic matter pool, as well as the complex interactions between phages and their bacterial hosts. We emphasize the newly recognized roles of phages as puppet masters of their bacterial hosts, where phages are capable of altering the metabolism of infected bacteria through the expression of auxiliary metabolic genes and the redirection of host gene expression patterns. Finally, we propose the 'royal family model' as a hypothesis to describe successional patterns of bacteria and phages over time in marine systems, where despite high richness and significant seasonal differences, only a small number of phages appear to continually dominate a given marine ecosystem. Although further testing is required, this model provides a framework for assessing the specificity and ecological consequences of phage-host dynamics.
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Affiliation(s)
- Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA.
| | - Chelsea Bonnain
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kema Malki
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Natalie A Sawaya
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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Forterre P. Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life. Clin Infect Dis 2018; 65:S74-S79. [PMID: 28859344 DOI: 10.1093/cid/cix349] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The curiosity-driven discovery of giant DNA viruses infecting amoebas has triggered an intense debate about the origin, nature, and definition of viruses. This discovery was delayed by the current paradigm confusing viruses with small virions. Several new definitions and concepts have been proposed either to reconcile the unique features of giant viruses with previous paradigms or to propose a completely new vision of the living world. I briefly review here how several other lines of research in virology converged during the last 2 decades with the discovery of giant viruses to change our traditional perception of the viral world. This story emphasizes the power of multidisciplinary curiosity-driven research, from the hospital to the field and the laboratory. Notably, some philosophers have now also joined biologists in their quest to make sense of the abundance and diversity of viruses and related capsidless mobile elements in the biosphere.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, Département de Microbiologie, Paris; and Institut Intégré de Biologie Cellulaire, Département de Microbiologie, Centre National de la Recherche Scientifique, Université Paris-Saclay, France
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Mahmoudabadi G, Phillips R. A comprehensive and quantitative exploration of thousands of viral genomes. eLife 2018; 7:31955. [PMID: 29624169 PMCID: PMC5908442 DOI: 10.7554/elife.31955] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/30/2018] [Indexed: 01/27/2023] Open
Abstract
The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends.
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Affiliation(s)
- Gita Mahmoudabadi
- Department of Bioengineering, California Institute of Technology, Pasadena, United States
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, United States.,Department of Applied Physics, California Institute of Technology, Pasadena, United States
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48
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Yutin N, Bäckström D, Ettema TJG, Krupovic M, Koonin EV. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis. Virol J 2018; 15:67. [PMID: 29636073 PMCID: PMC5894146 DOI: 10.1186/s12985-018-0974-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/28/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. RESULTS We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes. CONCLUSIONS The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA
| | - Disa Bäckström
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, -75123, Uppsala, SE, Sweden
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD, 20894, USA.
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Grybchuk D, Kostygov AY, Macedo DH, d'Avila-Levy CM, Yurchenko V. RNA viruses in trypanosomatid parasites: a historical overview. Mem Inst Oswaldo Cruz 2018. [PMID: 29513877 PMCID: PMC5851034 DOI: 10.1590/0074-02760170487] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Viruses of trypanosomatids are now being extensively studied because of their diversity and the roles they play in flagellates' biology. Among the most prominent examples are leishmaniaviruses implicated in pathogenesis of Leishmania parasites. Here, we present a historical overview of this field, starting with early reports of virus-like particles on electron microphotographs, and culminating in detailed molecular descriptions of viruses obtained using modern next generation sequencing-based techniques. Because of their diversity, different life cycle strategies and host specificity, we believe that trypanosomatids are a fertile ground for further explorations to better understand viral evolution, routes of transitions, and molecular mechanisms of adaptation to different hosts.
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Affiliation(s)
- Danyil Grybchuk
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Alexei Y Kostygov
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Diego H Macedo
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
| | - Claudia M d'Avila-Levy
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Estudos Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Vyacheslav Yurchenko
- University of Ostrava, Faculty of Science, Life Science Research Centre, Ostrava, Czech Republic
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50
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Gutiérrez-Aguirre I, Kutnjak D, Rački N, Rupar M, Ravnikar M. Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples. Methods Mol Biol 2018; 1746:63-75. [PMID: 29492887 DOI: 10.1007/978-1-4939-7683-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.
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Affiliation(s)
- Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Rački
- Lek Pharmaceuticals d.d., Menges, Slovenia
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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