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Bacteriophage of Enterococcus Species for Microbial Source Tracking
Bacteriophage of Enterococcus species for microbial source tracking Sarah Elizabeth Purnell A thesis submitted in partial fulfilment of the requirements of the University of Brighton for the degree of Doctor of Philosophy 2012 School of Environment and Technology University of Brighton United Kingdom Abstract Contamination of surface waters with faeces may lead to increased public risk of human exposure to pathogens through drinking water supply, aquaculture, and recreational activities. Determining the source(s) of contamination is important for assessing the degree of risk to public health, and for selecting appropriate mitigation measures. Phage-based microbial source tracking (MST) techniques have been promoted as effective, simple and low-cost. The intestinal enterococci are a faecal “indicator of choice” in many parts of the world for determining water quality, and recently, phages capable of infecting Enterococcus faecalis have been proposed as a potential alternative indicator of human faecal contamination. The primary aim of this study was to evaluate critically the suitability and efficacy of phages infecting host strains of Enterococcus species as a low-cost tool for MST. In total, 390 potential Enterococcus hosts were screened for their ability to detect phage in reference faecal samples. Development and implementation of a tiered screening approach allowed the initial large number of enterococcal hosts to be reduced rapidly to a smaller subgroup suitable for phage enumeration and MST. Twenty-nine hosts were further tested using additional faecal samples of human and non-human origin. Their specificity and sensitivity were found to vary, ranging from 44 to 100% and from 17 to 83%, respectively. Most notably, seven strains exhibited 100% specificity to cattle, human, or pig samples. -
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Hindawi Publishing Corporation Archaea Volume 2013, Article ID 372396, 18 pages http://dx.doi.org/10.1155/2013/372396 Review Article The Common Ancestor of Archaea and Eukarya Was Not an Archaeon Patrick Forterre1,2 1 Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France 2 Universite´ Paris-Sud, Institut de Gen´ etique´ et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France Correspondence should be addressed to Patrick Forterre; [email protected] Received 22 July 2013; Accepted 24 September 2013 Academic Editor: Gustavo Caetano-Anolles´ Copyright © 2013 Patrick Forterre. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. -
WO 2018/107129 Al O
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/107129 Al 14 June 2018 (14.06.2018) W !P O PCT (51) International Patent Classification: VARD COLLEGE [US/US]; 17 Quincy Street, Cam- C12N 15/09 (2006.01) C12N 15/11 (2006.01) bridge, MA 02138 (US). C12N 15/10 (2006.01) C12Q 1/68 (2006 .01) (72) Inventors: ABUDAYYEH, Omar; 77 Massachusetts Av (21) International Application Number: enue, Cambridge, MA 02139 (US). COLLINS, James PCT/US20 17/065477 Joseph; 77 Massachusetts Avenue, Cambridge, MA 02 139 (US). GOOTENBERG, Jonathan; 17 Quincy Street, (22) International Filing Date: Cambridge, MA 02138 (US). ZHANG, Feng; 415 Main 08 December 2017 (08.12.2017) Street, Cambridge, MA 02142 (US). LANDER, Eric, S.; (25) Filing Language: English 415 Main Street, Cambridge, MA 02142 (US). (26) Publication Language: English (74) Agent: NLX, F., Brent; Johnson, Marcou & Isaacs, LLC, 27 City Square, Suite 1, Hoschton, GA 30548 (US). (30) Priority Data: 62/432,553 09 December 20 16 (09. 12.20 16) US (81) Designated States (unless otherwise indicated, for every 62/456,645 08 February 2017 (08.02.2017) US kind of national protection available): AE, AG, AL, AM, 62/471,930 15 March 2017 (15.03.2017) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 62/484,869 12 April 2017 (12.04.2017) US CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 62/568,268 04 October 2017 (04.10.2017) US DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (71) Applicants: THE BROAD INSTITUTE, INC. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
On the Biological Success of Viruses
MI67CH25-Turner ARI 19 June 2013 8:14 V I E E W R S Review in Advance first posted online on June 28, 2013. (Changes may still occur before final publication E online and in print.) I N C N A D V A On the Biological Success of Viruses Brian R. Wasik and Paul E. Turner Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106; email: [email protected], [email protected] Annu. Rev. Microbiol. 2013. 67:519–41 Keywords The Annual Review of Microbiology is online at adaptation, biodiversity, environmental change, evolvability, extinction, micro.annualreviews.org robustness This article’s doi: 10.1146/annurev-micro-090110-102833 Abstract Copyright c 2013 by Annual Reviews. Are viruses more biologically successful than cellular life? Here we exam- All rights reserved ine many ways of gauging biological success, including numerical abun- dance, environmental tolerance, type biodiversity, reproductive potential, and widespread impact on other organisms. We especially focus on suc- cessful ability to evolutionarily adapt in the face of environmental change. Viruses are often challenged by dynamic environments, such as host immune function and evolved resistance as well as abiotic fluctuations in temperature, moisture, and other stressors that reduce virion stability. Despite these chal- lenges, our experimental evolution studies show that viruses can often readily adapt, and novel virus emergence in humans and other hosts is increasingly problematic. We additionally consider whether viruses are advantaged in evolvability—the capacity to evolve—and in avoidance of extinction. On the basis of these different ways of gauging biological success, we conclude that viruses are the most successful inhabitants of the biosphere. -
A Systematic Review of Human Pathogens Carried by the Housefly
Khamesipour et al. BMC Public Health (2018) 18:1049 https://doi.org/10.1186/s12889-018-5934-3 REVIEWARTICLE Open Access A systematic review of human pathogens carried by the housefly (Musca domestica L.) Faham Khamesipour1,2* , Kamran Bagheri Lankarani1, Behnam Honarvar1 and Tebit Emmanuel Kwenti3,4 Abstract Background: The synanthropic house fly, Musca domestica (Diptera: Muscidae), is a mechanical vector of pathogens (bacteria, fungi, viruses, and parasites), some of which cause serious diseases in humans and domestic animals. In the present study, a systematic review was done on the types and prevalence of human pathogens carried by the house fly. Methods: Major health-related electronic databases including PubMed, PubMed Central, Google Scholar, and Science Direct were searched (Last update 31/11/2017) for relevant literature on pathogens that have been isolated from the house fly. Results: Of the 1718 titles produced by bibliographic search, 99 were included in the review. Among the titles included, 69, 15, 3, 4, 1 and 7 described bacterial, fungi, bacteria+fungi, parasites, parasite+bacteria, and viral pathogens, respectively. Most of the house flies were captured in/around human habitation and animal farms. Pathogens were frequently isolated from body surfaces of the flies. Over 130 pathogens, predominantly bacteria (including some serious and life-threatening species) were identified from the house flies. Numerous publications also reported antimicrobial resistant bacteria and fungi isolated from house flies. Conclusions: This review showed that house flies carry a large number of pathogens which can cause serious infections in humans and animals. More studies are needed to identify new pathogens carried by the house fly. -
Viruses of Hyperthermophilic Archaea: Entry and Egress from the Host Cell
Viruses of hyperthermophilic archaea : entry and egress from the host cell Emmanuelle Quemin To cite this version: Emmanuelle Quemin. Viruses of hyperthermophilic archaea : entry and egress from the host cell. Microbiology and Parasitology. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066329. tel-01374196 HAL Id: tel-01374196 https://tel.archives-ouvertes.fr/tel-01374196 Submitted on 30 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie – Paris VI Unité de Biologie Moléculaire du Gène chez les Extrêmophiles Ecole doctorale Complexité du Vivant ED515 Département de Microbiologie - Institut Pasteur 7, quai Saint-Bernard, case 32 25, rue du Dr. Roux 75252 Paris Cedex 05 75015 Paris THESE DE DOCTORAT DE L’UNIVERSITE PIERRE ET MARIE CURIE Spécialité : Microbiologie Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE PIERRE ET MARIE CURIE VIRUSES OF HYPERTHERMOPHILIC ARCHAEA: ENTRY INTO AND EGRESS FROM THE HOST CELL Présentée par M. Emmanuelle Quemin Soutenue le 28 Septembre 2015 devant le jury composé de : Prof. Guennadi Sezonov Président du jury Prof. Christa Schleper Rapporteur de thèse Dr. Paulo Tavares Rapporteur de thèse Dr. -
Sulfolobus As a Model Organism for the Study of Diverse
SULFOLOBUS AS A MODEL ORGANISM FOR THE STUDY OF DIVERSE BIOLOGICAL INTERESTS; FORAYS INTO THERMAL VIROLOGY AND OXIDATIVE STRESS by Blake Alan Wiedenheft A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana November 2006 © COPYRIGHT by Blake Alan Wiedenheft 2006 All Rights Reserved ii APPROVAL of a dissertation submitted by Blake Alan Wiedenheft This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education. Dr. Mark Young and Dr. Trevor Douglas Approved for the Department of Microbiology Dr.Tim Ford Approved for the Division of Graduate Education Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University – Bozeman, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to reproduce and distribute my dissertation in and from microfilm along with the non-exclusive right to reproduce and distribute my abstract in any format in whole or in part.” Blake Alan Wiedenheft November, 2006 iv DEDICATION This work was funded in part through grants from the National Aeronautics and Space Administration Program (NAG5-8807) in support of Montana State University’s Center for Life in Extreme Environments (MCB-0132156), and the National Institutes of Health (R01 EB00432 and DK57776). -
A Virus of Hyperthermophilic Archaea with a Unique Architecture Among DNA Viruses
A virus of hyperthermophilic archaea with a unique architecture among DNA viruses Elena Ilka Rensena,1, Tomohiro Mochizukia,b,1, Emmanuelle Quemina, Stefan Schoutenc, Mart Krupovica,2, and David Prangishvilia,2 aDepartment of Microbiology, Institut Pasteur, 75015 Paris, France; bEarth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan; and cDepartment of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research, 1790 AB Den Burg, The Netherlands Edited by James L. Van Etten, University of Nebraska-Lincoln, Lincoln, NE, and approved January 19, 2016 (received for review September 23, 2015) Viruses package their genetic material in diverse ways. Most known shell consisting of two protein layers and an external envelope. strategies include encapsulation of nucleic acids into spherical or Our results provide new insights into the diversity of architec- filamentous virions with icosahedral or helical symmetry, respec- tural solutions used by filamentous viruses. tively. Filamentous viruses with dsDNA genomes are currently as- sociated exclusively with Archaea. Here, we describe a filamentous Results hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 Virus and Host Isolation. From the environmental sample collected (PFV1), with a type of virion organization not previously observed at the Pozzuoli Solfatara, Italy, enrichment cultures were estab- in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an lished in conditions known to favor the growth of aerobic mem- envelope and an inner core consisting of two structural units: a rod- bers of the archaeal genus Pyrobaculum (14). The virus-like particles shaped helical nucleocapsid formed of two 14-kDa major virion pro- (VLPs) were detected in the enrichment culture by transmission teins and a nucleocapsid-encompassing protein sheath composed electron microscopy (TEM). -
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. -
Diversity of Large DNA Viruses of Invertebrates ⇑ Trevor Williams A, Max Bergoin B, Monique M
Journal of Invertebrate Pathology 147 (2017) 4–22 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity of large DNA viruses of invertebrates ⇑ Trevor Williams a, Max Bergoin b, Monique M. van Oers c, a Instituto de Ecología AC, Xalapa, Veracruz 91070, Mexico b Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France c Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands article info abstract Article history: In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for Received 22 June 2016 invertebrates. We present their taxonomical classification and describe the evolutionary relationships Revised 3 August 2016 among various groups of invertebrate-infecting viruses. We also indicate the relationships of the Accepted 4 August 2016 invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of Available online 31 August 2016 the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of Keywords: the most important viruses in these families and indicate, which orders of invertebrates are susceptible to Entomopoxvirus these pathogens. Iridovirus Ó Ascovirus 2016 Elsevier Inc. All rights reserved. Nudivirus Hytrosavirus Filamentous viruses of hymenopterans Mollusk-infecting herpesviruses 1. Introduction in the cytoplasm. This group comprises viruses in the families Poxviridae (subfamily Entomopoxvirinae) and Iridoviridae. The Invertebrate DNA viruses span several virus families, some of viruses in the family Ascoviridae are also discussed as part of which also include members that infect vertebrates, whereas other this group as their replication starts in the nucleus, which families are restricted to invertebrates. -
Survey of High-Resolution Archaeal Virus Structures
Available online at www.sciencedirect.com ScienceDirect Survey of high-resolution archaeal virus structures 1 2 3,4 Ross Hartman , Jacob Munson-McGee , Mark J Young and 1,4 Charles Martin Lawrence Archaeal viruses exhibit diverse morphologies whose folds [5]. Of these, only 20 folds are known for the major structures are just beginning to be explored at high-resolution. capsid proteins (MCPs) of viruses [6,7]. Despite the genetic In this review, we update recent findings on archaeal structural diversity of viruses, their structural proteins, and especially proteins and virion architectures and place them in the their MCPs, fit within a limited number of groups. This biological context in which these viruses replicate. We limited number of common structural themes unite viruses conclude that many of the unusual structural features and across all three domains of life (Eukarya, Bacteria, and dynamics of archaeal viruses aid their replication and survival in Archaea) and evolutionary history [8]. Virion structure also the chemically harsh environments, in which they replicate. allows for insights into viral assembly, release, attachment, Furthermore, we should expect to find more novel features and entry by comparing well-characterized members of a from examining the high-resolution structures of additional structural lineage with less characterized members [9–11]. archaeal viruses. Our understanding of viruses that infect Archaea Addresses (archaeal viruses), lags far behind those infecting Bacte- 1 Department of Chemistry and Biochemistry, Montana State University, ria and Eukaryotes and we refer the reader to several Bozeman, MT, USA 2 excellent reviews on archaeal viruses [12–14]. Many Department of Microbiology and Immunology, Montana State archaeal viruses have unique morphologies [12,15–18].