Polymicrobial Periodontal Disease Triggers a Wide Radius of Effect and Unique Virome
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Gut Microbiota Beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD
International Journal of Molecular Sciences Review Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD Mario Matijaši´c 1,* , Tomislav Meštrovi´c 2, Hana Cipˇci´cPaljetakˇ 1, Mihaela Peri´c 1, Anja Bareši´c 3 and Donatella Verbanac 4 1 Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia; [email protected] (H.C.P.);ˇ [email protected] (M.P.) 2 University Centre Varaždin, University North, 42000 Varaždin, Croatia; [email protected] 3 Division of Electronics, Ruđer Boškovi´cInstitute, 10000 Zagreb, Croatia; [email protected] 4 Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia; [email protected] * Correspondence: [email protected]; Tel.: +385-01-4590-070 Received: 30 January 2020; Accepted: 7 April 2020; Published: 11 April 2020 Abstract: The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease. Keywords: gut microbiota; inflammatory bowel disease (IBD); mycobiome; virome; archaeome; eukaryotic parasites 1. Introduction Trillions of microbes colonize the human body, forming the microbial community collectively referred to as the human microbiota. -
Madarak Polyomavírusainak És CRESS DNS Vírusainak Összehasonlító Genomvizsgálata
Állatorvostudományi Egyetem Aujeszky Aladár Elméleti Állatorvostudományok Doktori Program Madarak polyomavírusainak és CRESS DNS vírusainak összehasonlító genomvizsgálata PhD értekezés Szabóné Kaszab Eszter 2021 Témavezető és témabizottsági tagok: ………………………………… dr. Fehér Enikő Állatorvostudományi Kutatóintézet Új kórokozók témacsoport témavezető Készült 8 példányban. Ez a …… sz. példány ………………………………….. Szabóné Kaszab Eszter 2 Tartalomjegyzék 1. Rövidítések jegyzéke ............................................................................................... 5 2. Összefoglalás .......................................................................................................... 7 3. Summary ................................................................................................................. 8 4. Bevezetés ................................................................................................................ 9 5. Irodalmi áttekintés...................................................................................................10 5.1. A Circoviridae család jellemzése ...................................................................10 5.1.1. A Circovirus nemzetség ........................................................................12 5.1.2. A Cyclovirus nemzetség ........................................................................18 5.2. A CRESS DNS vírusok jellemzése ................................................................19 5.3. A polyomavírusok jellemzése ........................................................................22 -
The Trans-Zoonotic Virome Interface: Measures to Balance, Control and Treat Epidemics
Review Article More Information *Address for Correspondence: Dr. Vinod Nikhra, MD, Hindu Rao Hospital & NDMC The Trans-zoonotic Virome interface: Medical College, New Delhi, India, Tel: +91- 9810874937; Measures to balance, control and Email: [email protected]; drvinodnikhra@rediff mail.com Submitted: 07 March 2020 treat epidemics Approved: 08 April 2020 Published: 09 April 2020 Vinod Nikhra* How to cite this article: Nikhra V. The Trans- zoonotic Virome interface: Measures to balance, MD, Hindu Rao Hospital & NDMC Medical College, New Delhi, India control and treat epidemics. Ann Biomed Sci Eng. 2020; 4: 020-027. Abstract DOI: 10.29328/journal.abse.1001009 ORCiD: orcid.org/0000-0003-0859-5232 The global virome: The viruses have a global distribution, phylogenetic diversity and host Copyright: © 2020 Nikhra V. This is an open specifi city. They are obligate intracellular parasites with single- or double-stranded DNA or RNA access article distributed under the Creative genomes, and affl ict bacteria, plants, animals and human population. The viral infection begins Commons Attribution License, which permits when surface proteins bind to receptor proteins on the host cell surface, followed by internalisation, unrestricted use, distribution, and reproduction replication and lysis. Further, trans-species interactions of viruses with bacteria, small eukaryotes in any medium, provided the original work is and host are associated with various zoonotic viral diseases and disease progression. properly cited. Keywords: Virome interface; Zoonotic viral Virome interface and transmission: The cross-species transmission from their natural transmission; Viral epidemics; COVID-19; MERS; reservoir, usually mammalian or avian, hosts to infect human-being is a rare probability, but occurs SARS; Nutraceuticals; Probiotics; Anti-viral leading to the zoonotic human viral infection. -
Machine Learning and Data-Parallel Processing for Viral Metagenomics
From Department of Laboratory Medicine Karolinska Institutet, Stockholm, Sweden MACHINE LEARNING AND DATA-PARALLEL PROCESSING FOR VIRAL METAGENOMICS Zurab Bzhalava Stockholm 2020 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by Arkitektkopia AB, 2020 © Zurab Bzhalava, 2020 ISBN 978-91-7831-708-0 Machine Learning and Data-Parallel Processing for Viral Metagenomics THESIS FOR DOCTORAL DEGREE (Ph.D.) The thesis will be defended at Månen 9Q, Alfred Nobels allé 8 (Floor 9), Karolinska Institutet, Campus Fleminsberg, Huddinge. Friday, April 3, 2020, at 9:00 AM By Zurab Bzhalava Principal Supervisor: Opponent: Professor Joakim Dillner Ola Spjuth Karolinska Institutet Uppsala University Department of Laboratory Medicine Department of Pharmaceutical Biosciences Division of Pathology Examination Board: Co-supervisor(s): Panagiotis Papapetrou MD PhD Karin Sundström Stockholm University Karolinska Institutet Department of Computer and Department of Laboratory Medicine Systems Sciences Division of Pathology Tobias Allander Professor Piotr Bała Karolinska Institutet University of Warsaw Department of Microbiology, Tumor and Interdisciplinary Centre for Mathematical Cell Biology and Computational Modelling Jim Dowling KTH Royal Institute of Technology Division of Software and Computer Systems To my family and friends ABSTRACT More than 2 million cancer cases around the world each year are caused by viruses. In addition, there are epidemiological indications that other cancer-associated viruses may also exist. However, the identification of highly divergent and yet unknown viruses in human biospecimens is one of the biggest challenges in bio- informatics. Modern-day Next Generation Sequencing (NGS) technologies can be used to directly sequence biospecimens from clinical cohorts with unprecedented speed and depth. -
New Viral Facets in Oral Diseases: the EBV Paradox
International Journal of Molecular Sciences Review New Viral Facets in Oral Diseases: The EBV Paradox Lilit Tonoyan 1,*, Séverine Vincent-Bugnas 1,2 , Charles-Vivien Olivieri 1 and Alain Doglio 1,3,* 1 Faculté de Chirurgie Dentaire, Université Côte d’Azur, EA 7354 MICORALIS (Microbiologie Orale, Immunothérapie et Santé), 06357 Nice, France; [email protected] (S.V.-B.); [email protected] (C.-V.O.) 2 Pôle Odontologie, Centre Hospitalier Universitaire de Nice, 06001 Nice, France 3 Unité de Thérapie Cellulaire et Génique, Centre Hospitalier Universitaire de Nice, 06103 Nice, France * Correspondence: [email protected] (L.T.); [email protected] (A.D.) Received: 3 October 2019; Accepted: 20 November 2019; Published: 22 November 2019 Abstract: The oral cavity contributes to overall health, psychosocial well-being and quality of human life. Oral inflammatory diseases represent a major global health problem with significant social and economic impact. The development of effective therapies, therefore, requires deeper insights into the etiopathogenesis of oral diseases. Epstein–Barr virus (EBV) infection results in a life-long persistence of the virus in the host and has been associated with numerous oral inflammatory diseases including oral lichen planus (OLP), periodontal disease and Sjogren’s syndrome (SS). There is considerable evidence that the EBV infection is a strong risk factor for the development and progression of these conditions, but is EBV a true pathogen? This long-standing EBV paradox yet needs to be solved. This review discusses novel viral aspects of the etiopathogenesis of non-tumorigenic diseases in the oral cavity, in particular, the contribution of EBV in OLP, periodontitis and SS, the tropism of EBV infection, the major players involved in the etiopathogenic mechanisms and emerging contribution of EBV-pathogenic bacteria bidirectional interaction. -
Molecular Bases and Role of Viruses in the Human Microbiome
Review IMF YJMBI-64492; No. of pages: 15; 4C: 7 Molecular Bases and Role of Viruses in the Human Microbiome Shira R. Abeles 1 and David T. Pride 1,2 1 - Department of Medicine, University of California, San Diego, CA 92093, USA 2 - Department of Pathology, University of California, San Diego, CA 92093, USA Correspondence to David T. Pride: Department of Pathology, University of California, San Diego, CA 92093, USA. [email protected] http://dx.doi.org/10.1016/j.jmb.2014.07.002 Edited by J. L. Sonnenburg Abstract Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities (“viromes”) to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. -
Metatranscriptomics to Characterize Respiratory Virome, Microbiome, and Host Response Directly from Clinical Samples
Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples Seesandra Rajagopala ( [email protected] ) Vanderbilt University Medical Center Nicole Bakhoum Vanderbilt University Medical Center Suman Pakala Vanderbilt University Medical Center Meghan Shilts Vanderbilt University Medical Center Christian Rosas-Salazar Vanderbilt University Medical Center Annie Mai Vanderbilt University Medical Center Helen Boone Vanderbilt University Medical Center Rendie McHenry Vanderbilt University Medical Center Shibu Yooseph University of Central Florida https://orcid.org/0000-0001-5581-5002 Natasha Halasa Vanderbilt University Medical Center Suman Das Vanderbilt University Medical Center https://orcid.org/0000-0003-2496-9724 Article Keywords: Metatranscriptomics, Virome, Microbiome, Next-Generation Sequencing (NGS), RNA-Seq, Acute Respiratory Infection (ARI), Respiratory Syncytial Virus (RSV), Coronavirus (CoV) Posted Date: October 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-77157/v1 Page 1/31 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/31 Abstract We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low-biomass clinical samples. Using nasal swab samples, we have demonstrated that this method captures the comprehensive RNA virome with sucient sequencing depth required to assemble complete genomes. We nd a surprisingly high-frequency of Respiratory Syncytial Virus (RSV) and Coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-infections in children with symptomatic RSV. In addition, we have characterized commensal and pathogenic bacteria, and fungi at the species-level. Functional analysis of bacterial transcripts revealed H. -
Viral Diversity in Tree Species
Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Biologia Microbiana Doctoral Thesis Viral diversity in tree species FLÁVIA MILENE BARROS NERY Brasília - DF, 2020 FLÁVIA MILENE BARROS NERY Viral diversity in tree species Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Microbiology by the Post - Graduate Program in Microbiology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Fernando Lucas Melo BRASÍLIA, DF - BRAZIL FICHA CATALOGRÁFICA NERY, F.M.B Viral diversity in tree species Flávia Milene Barros Nery Brasília, 2025 Pages number: 126 Doctoral Thesis - Programa de Pós-Graduação em Biologia Microbiana, Universidade de Brasília, DF. I - Virus, tree species, metagenomics, High-throughput sequencing II - Universidade de Brasília, PPBM/ IB III - Viral diversity in tree species A minha mãe Ruth Ao meu noivo Neil Dedico Agradecimentos A Deus, gratidão por tudo e por ter me dado uma família e amigos que me amam e me apoiam em todas as minhas escolhas. Minha mãe Ruth e meu noivo Neil por todo o apoio e cuidado durante os momentos mais difíceis que enfrentei durante minha jornada. Aos meus irmãos André, Diego e meu sobrinho Bruno Kawai, gratidão. Aos meus amigos de longa data Rafaelle, Evanessa, Chênia, Tati, Leo, Suzi, Camilets, Ricardito, Jorgito e Diego, saudade da nossa amizade e dos bons tempos. Amo vocês com todo o meu coração! Minha orientadora e grande amiga Profa Rita de Cássia Pereira Carvalho, a quem escolhi e fui escolhida para amar e fazer parte da família. -
Viruses in Transplantation - Not Always Enemies
Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause -
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. -
Evolutionary Biology of the Virome and Impacts on Human Health and Disease: an Historical Perspective
Old Herborn University Seminar Monograph 31: Evolutionary biology of the virome, and impacts in human health and disease. Editors: Peter J. Heidt, Pearay L. Ogra, Mark S. Riddle and Volker Rusch. Old Herborn University Foundation, Herborn, Germany: 5-13 (2017). EVOLUTIONARY BIOLOGY OF THE VIROME AND IMPACTS ON HUMAN HEALTH AND DISEASE: AN HISTORICAL PERSPECTIVE PEARAY L. OGRA1 and MARK S. RIDDLE2 1Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA; 2Uniformed Services University of Health Sciences, Bethesda, MD, USA “THE SINGLE BIGGEST THREAT TO MAN’S CONTINUED DOMINANCE ON THE PLANET IS A VIRUS” (Joshua Lederberg) This quote opens the Hollywood movie “Outbreak” to introduce the epidemics of Haemorrhagic Virus fever in Zaire in 1967 and again in the mid 1990’s. The movie is a fascinating commentary on the contemporary perceptions of serious or fatal virus infections, and subsequent impact on human rights and the societal good versus evil. The perception of viruses as evil life forms has been part of human society for thousands of years, and the word “virus” has been used in Latin, Greek and Sanskrit languages for centuries to describe the venom of snake, a dangerous slimy liquid, a fatal poison, or a substance produced in the body as a result of disease, especially one that is capable of infecting others. Although numerous studies have at- viruses exist per ml of water in the tempted to explain the evolution of vi- oceans. It has been suggested that vi- ruses and their biologic ancestry, the ruses outnumber their hosts globally by precise origins of viruses continue to tenfold or more (Proctor, 1997). -
Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis Javanica)
viruses Article Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica) Ping Liu 1, Wu Chen 2 and Jin-Ping Chen 1,* 1 Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China; [email protected] 2 Guangzhou Zoo, Guangzhou 510230, China; [email protected] * Correspondence: [email protected]; Tel.: +020-8910-0920 Received: 30 September 2019; Accepted: 21 October 2019; Published: 24 October 2019 Abstract: Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones ( 300 nt) were related to viral sequences, of which 68 contigs ≥ had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals. Keywords: virome; Manis javanica; Sendai virus; Coronavirus; molecular epidemiology 1. Introduction The Malayan pangolin (Manis javanica), a representative mammal species of the order Pholidota, is one of the only eight pangolin species worldwide.