201
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Fernández-Orth D, Miró E, Brown-Jaque M, Rodríguez-Rubio L, Espinal P, Rodriguez-Navarro J, González-López JJ, Muniesa M, Navarro F. Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment. J Antimicrob Chemother 2019; 74:854-864. [DOI: 10.1093/jac/dky540] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
| | - Judith Rodriguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan José González-López
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Pg Vall d’Hebron 119-129, Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Diagonal 643, Annex, Floor 0, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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202
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Taylor VL, Fitzpatrick AD, Islam Z, Maxwell KL. The Diverse Impacts of Phage Morons on Bacterial Fitness and Virulence. Adv Virus Res 2019; 103:1-31. [PMID: 30635074 DOI: 10.1016/bs.aivir.2018.08.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The viruses that infect bacteria, known as phages, are the most abundant biological entity on earth. They play critical roles in controlling bacterial populations through phage-mediated killing, as well as through formation of bacterial lysogens. In this form, the survival of the phage depends on the survival of the bacterial host in which it resides. Thus, it is advantageous for phages to encode genes that contribute to bacterial fitness and expand the environmental niche. In many cases, these fitness factors also make the bacteria better able to survive in human infections and are thereby considered pathogenesis or virulence factors. The genes that encode these fitness factors, known as "morons," have been shown to increase bacterial fitness through a wide range of mechanisms and play important roles in bacterial diseases. This review outlines the benefits provided by phage morons in various aspects of bacterial life, including phage and antibiotic resistance, motility, adhesion and quorum sensing.
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Affiliation(s)
| | | | - Zafrin Islam
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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203
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Van Belleghem JD, Dąbrowska K, Vaneechoutte M, Barr JJ, Bollyky PL. Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Viruses 2018; 11:E10. [PMID: 30585199 PMCID: PMC6356784 DOI: 10.3390/v11010010] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 02/07/2023] Open
Abstract
The human body is host to large numbers of bacteriophages (phages)⁻a diverse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the diverse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.
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Affiliation(s)
- Jonas D Van Belleghem
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland.
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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204
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Wahl A, Battesti A, Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol Microbiol 2018; 111:303-316. [PMID: 30466179 PMCID: PMC7380047 DOI: 10.1111/mmi.14167] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2018] [Indexed: 12/11/2022]
Abstract
Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site‐specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.
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Affiliation(s)
- Astrid Wahl
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Aurélia Battesti
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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205
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Botelho J, Roberts AP, León-Sampedro R, Grosso F, Peixe L. Carbapenemases on the move: it's good to be on ICEs. Mob DNA 2018; 9:37. [PMID: 30574213 PMCID: PMC6299553 DOI: 10.1186/s13100-018-0141-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons. Conclusions The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa. Electronic supplementary material The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Botelho
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Adam P Roberts
- 2Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,3Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ricardo León-Sampedro
- 4Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Filipa Grosso
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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206
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Keen EC, Dantas G. Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity. Trends Microbiol 2018; 26:943-954. [PMID: 29909042 PMCID: PMC6436384 DOI: 10.1016/j.tim.2018.05.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Recent years have witnessed an explosion of interest in the human microbiota. Although commensal bacteria have dominated research efforts to date, mounting evidence suggests that endogenous viral populations (the 'virome') play key roles in basic human physiology. The most numerous constituents of the human virome are not eukaryotic viruses but rather bacteriophages, viruses that infect bacteria. Here, we review phages' interactions with their immediate (prokaryotic) and extended (eukaryotic) hosts and with each other, with a particular emphasis on the temperate phages and prophages which dominate the human virome. We also discuss key outstanding questions in this emerging field and emphasize the urgent need for functional studies in animal models to complement previous in vitro work and current computational approaches.
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Affiliation(s)
- Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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207
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Kennedy EA, King KY, Baldridge MT. Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria. Front Physiol 2018; 9:1534. [PMID: 30429801 PMCID: PMC6220354 DOI: 10.3389/fphys.2018.01534] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/11/2018] [Indexed: 12/14/2022] Open
Abstract
As the intestinal microbiota has become better appreciated as necessary for maintenance of physiologic homeostasis and also as a modulator of disease processes, there has been a corresponding increase in manipulation of the microbiota in mouse models. While germ-free mouse models are generally considered to be the gold standard for studies of the microbiota, many investigators turn to antibiotics treatment models as a rapid, inexpensive, and accessible alternative. Here we describe and compare these two approaches, detailing advantages and disadvantages to both. Further, we detail what is known about the effects of antibiotics treatment on cell populations, cytokines, and organs, and clarify how this compares to germ-free models. Finally, we briefly describe recent findings regarding microbiota regulation of infectious diseases and other immunologic challenges by the microbiota, and highlight important future directions and considerations for the use of antibiotics treatment in manipulation of the microbiota.
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Affiliation(s)
- Elizabeth A. Kennedy
- Division of Infectious Diseases, Department of Medicine, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Katherine Y. King
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
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208
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Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Dev Res 2018; 80:86-97. [PMID: 30370682 DOI: 10.1002/ddr.21466] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 12/28/2022]
Abstract
The exposure of the human gut to antibiotics can have a great impact on human health. Antibiotics pertain to the preservation of human health and are useful tools for fighting bacterial infections. They can be used for curing infections and can play a critical role in immunocompromised or chronic patients, or in fighting childhood severe malnutrition. Yet, the genomic and phylogenetic diversity of the human gut changes under antibiotic exposure. Antibiotics can also have severe side effects on human gut health, due to the spreading of potential antibiotic resistance genetic traits and to their correlation with virulence of some bacterial pathogens. They can shape, and even disrupt, the composition and functioning diversity of the human gut microbiome. Traditionally bacterial antibiotic resistances have been evaluated at clone or population level. However, the understanding of these two apparently disparate perspectives as both friends and foes may come from the study of microbiomes as a whole and from the evaluation of both positive and negative effects of antibiotics on microbial community dynamics and diversity. In this review we present some metagenomic tools and databases that enable the studying of antibiotic resistance in human gut metagenomes, promoting the development of personalized medicine strategies, new antimicrobial therapy protocols and patient follow-up.
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Affiliation(s)
- Teresa Nogueira
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro H C David
- cE3c - Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Muséum National d'Histoire naturelle, CNRS, EPHE, CP, Paris, France
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209
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Affiliation(s)
- Alan R Davidson
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, Canada.
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210
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Wang Q, Zeng X, Yang Q, Yang C. Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:617-623. [PMID: 29803035 DOI: 10.1016/j.scitotenv.2018.05.213] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Horizontal transfer of ARGs was generally considered to be mediated by three methods - transformation, conjugation and transduction through phages - during which the contribution of bacteriophages to gene transfer in the environment is unclear or even questioned. In this study, a multiple-antibiotic-resistant Escherichia coli strain and its phage (YZ1) were isolated from a municipal wastewater treatment system. The results of the morphological and genomic analyses of phage YZ1 showed that it is a member of the T7 viral genus in the subfamily Autographivirinae. Its genome is similar to that of the E. coli phage K1F in both organization and sequence and does not encode ARGs. However, 28 paired reads in the raw sequencing data aligned to ARGs, including those promoting β-lactam, aminoglycoside, and fluoroquinolone resistance, among others. Quantitative PCR showed that ARGs were present in bacteriophage DNA (approximately 103 copies/mL) and were also detected in the bacterial host DNA. The results suggested that while infrequent, some ARG-carrying transducing phages were presumably generated by erroneous packaging during infection of antibiotic-resistant bacteria, which may create the possibility of horizontal transfer of ARGs.
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Affiliation(s)
- Qiang Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China
| | - Xiangpeng Zeng
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Key Laboratory for Microorganisms and Functional Molecules (Henan Normal University), University of Henan Province, Xinxiang 453007, China.
| | - Chuanzhen Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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211
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The disparate effects of bacteriophages on antibiotic-resistant bacteria. Emerg Microbes Infect 2018; 7:168. [PMID: 30302018 PMCID: PMC6177407 DOI: 10.1038/s41426-018-0169-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/30/2018] [Accepted: 09/05/2018] [Indexed: 01/21/2023]
Abstract
Faced with the crisis of multidrug-resistant bacteria, bacteriophages, viruses that infect and replicate within bacteria, have been reported to have both beneficial and detrimental effects with respect to disease management. Bacteriophages (phages) have important ecological and evolutionary impacts on their bacterial hosts and have been associated with therapeutic use to kill bacterial pathogens, but can lead to the transmission of antibiotic resistance. Although the process known as transduction has been reported for many bacterial species by classic and modern genetic approaches, its contribution to the spread of antibiotic resistance in nature remains unclear. In addition, detailed molecular studies have identified phages residing in bacterial genomes, revealing unexpected interactions between phages and their bacterial hosts. Importantly, antibiotics can induce the production of phages and phage-encoded products, disseminating these viruses and virulence-related genes, which have dangerous consequences for disease severity. These unwanted side-effects of antibiotics cast doubt on the suitability of some antimicrobial treatments and may require new strategies to prevent and limit the selection for virulence. Foremost among these treatments is phage therapy, which could be used to treat many bacterial infectious diseases and confront the pressing problem of antibiotic resistance in pathogenic bacteria. This review discusses the interactions between bacteriophages, antibiotics, and bacteria and provides an integrated perspective that aims to inspire the development of successful antibacterial therapies.
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212
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Garin-Fernandez A, Pereira-Flores E, Glöckner FO, Wichels A. The North Sea goes viral: Occurrence and distribution of North Sea bacteriophages. Mar Genomics 2018; 41:31-41. [PMID: 29866485 DOI: 10.1016/j.margen.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 01/17/2023]
Abstract
Marine viruses are dominated by phages and have an enormous influence on microbial population dynamics, due to lysis and horizontal gene transfer. The aim of this study is to analyze the occurrence and diversity of phages in the North Sea, considering the virus-host interactions and biogeographic factors. The virus community of four sampling stations were described using virus metagenomics (viromes). The results show that the virus community was not evenly distributed throughout the North Sea. The dominant phage members were identified as unclassified phage group, followed by Caudovirales order. Myoviridae was the dominant phage family in the North Sea, which occurrence decreased from the coast to the open sea. In contrast, the occurrence of Podoviridae increased and the occurrence of Siphoviridae was low throughout the North Sea. The occurrence of other groups such as Phycodnaviridae decreased from the coast to the open sea. The coastal virus community was genetically more diverse than the open sea community. The influence of riverine inflow and currents, for instance the English Channel flow affects the genetic virus diversity with the community carrying genes from a variety of metabolic pathways and other functions. The present study offers the first insights in the virus community in the North Sea using viromes and shows the variation in virus diversity and the genetic information moved from coastal to open sea areas.
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213
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Rands CM, Starikova EV, Brüssow H, Kriventseva EV, Govorun VM, Zdobnov EM. ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages. Environ Microbiol 2018; 20:2288-2300. [DOI: 10.1111/1462-2920.14276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Chris M. Rands
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
| | - Elizaveta V. Starikova
- Department of Molecular Biology and GeneticsFederal Research and Clinical Center of Physical‐Chemical Medicine Moscow, Russian Federation
| | - Harald Brüssow
- KU Leuven, Department of BiosystemsLaboratory of Gene Technology Leuven Belgium
| | - Evgenia V. Kriventseva
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
| | - Vadim M. Govorun
- Department of Molecular Biology and GeneticsFederal Research and Clinical Center of Physical‐Chemical Medicine Moscow, Russian Federation
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
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214
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Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol 2018; 3:1023-1031. [PMID: 30038310 PMCID: PMC6112176 DOI: 10.1038/s41564-018-0210-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/27/2018] [Indexed: 02/08/2023]
Abstract
The dysregulation of intestinal microbial communities is associated with inflammatory bowel diseases (IBD). Studies aimed at understanding the contribution of the microbiota to inflammatory diseases have primarily focused on bacteria, yet the intestine harbors a viral component dominated by prokaryotic viruses known as bacteriophages (phages). Phage numbers are elevated at the intestinal mucosal surface and phages increase in abundance during IBD, suggesting that phages play an unidentified role in IBD. We used a sequence independent approach for the selection of viral contigs and then applied quantitative metagenomics to study intestinal phages in a mouse model of colitis. We discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis. We identified phages specific to pathobiotic hosts associated with intestinal disease, whose abundances are significantly altered during colitis. Additionally, phage populations in healthy and diseased mice overlapped with phages from healthy humans and humans with IBD. Our findings indicate that intestinal phage communities are altered during inflammatory disease establishing a platform for investigating phage involvement in IBD.
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Affiliation(s)
- Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA.
| | | | - Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Brian Bushnell
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Brian Hassell
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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215
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Cadieux B, Colavecchio A, Jeukens J, Freschi L, Emond-Rheault JG, Kukavica-Ibrulj I, Levesque RC, Bekal S, Chandler JC, Coleman SM, Bisha B, Goodridge LD. Prophage induction reduces Shiga toxin producing Escherichia coli (STEC) and Salmonella enterica on tomatoes and spinach: A model study. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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216
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Yang Y, Shi W, Lu SY, Liu J, Liang H, Yang Y, Duan G, Li Y, Wang H, Zhang A. Prevalence of antibiotic resistance genes in bacteriophage DNA fraction from Funan River water in Sichuan, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:835-841. [PMID: 29396344 DOI: 10.1016/j.scitotenv.2018.01.148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 05/04/2023]
Abstract
To better understand the role that bacteriophages play in antibiotic resistance genes (ARGs) dissemination in the aquatic environment, 36 water samples were collected from the Funan River in Sichuan, China. The occurrence of 15 clinically relevant ARGs and one class 1 integron gene int1 in phage-particle DNA were evaluated by PCR. The abundance of ARGs (blaCTX-M, sul1, and aac-(6')-1b-cr) was determined by quantitative PCR (qPCR). High prevalence of the int1 gene (66.7%) was found in the phage-particle DNA of tested samples, followed by sul1 (41.7%), sul2 (33.3%), blaCTX-M (33.3%), aac-(6')-lb-cr (25%), aph(3')-IIIa (16.7%), and ermF (8.3%). The qPCR data showed higher gene copy (GC) numbers in samples collected near a hospital (site 7) and a wastewater treatment plant (WWTP) (site 10) (P < .05). Particularly the absolute abundance of aac-(6')-lb-cr gene was significantly higher than the blaCTX-M and sul1 genes with the gene copy (GC) numbers of 5.73 log10 copy/mL for site 7 and 4.99 log10 copy/mL for site 10. To our best knowledge, this is the first study to report the presence of sul2, aac-(6')-lb-cr, ermF and aph(3')-IIIa genes in bacteriophage DNA derived from aquatic environments. Our findings highlight the potential of ARGs to be transmitted via bacteriophages in the aquatic environment.
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Affiliation(s)
- Yanxian Yang
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Wenjin Shi
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Shao-Yeh Lu
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Jinxin Liu
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
| | - Huihui Liang
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Yifan Yang
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Guowei Duan
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Yunxia Li
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Hongning Wang
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China
| | - Anyun Zhang
- College of Life Sciences, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Chengdu, Sichuan, PR China.
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Starikova EV, Prianichnikov NA, Zdobnov E, Govorun VM. Bioinformatics Analysis of Antimicrobial Resistance Genes and Prophages Colocalized in Human Gut Metagenomes. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2018. [DOI: 10.1134/s1990750818020129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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218
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Elbehery AHA, Feichtmayer J, Singh D, Griebler C, Deng L. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. Front Microbiol 2018; 9:1110. [PMID: 29896176 PMCID: PMC5987705 DOI: 10.3389/fmicb.2018.01110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
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Affiliation(s)
- Ali H A Elbehery
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Dave Singh
- EvA Consortium, Manchester, United Kingdom.,Medicines Evaluation Unit, University Hospital of South Manchester Foundation Trust, University of Manchester, Manchester, United Kingdom
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
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219
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Gokulan K, Bekele AZ, Drake KL, Khare S. Responses of intestinal virome to silver nanoparticles: safety assessment by classical virology, whole-genome sequencing and bioinformatics approaches. Int J Nanomedicine 2018; 13:2857-2867. [PMID: 29844669 PMCID: PMC5961469 DOI: 10.2147/ijn.s161379] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Effects of silver nanoparticles (AgNP) on the intestinal virome/phage community are mostly unknown. The working hypothesis of this study was that the exposure of pharmaceutical/nanomedicine and other consumer-use material containing silver ions and nanoparticles to the gastrointestinal tract may result in disturbance of the beneficial gut viruses/phages. Methods This study assesses the impact of AgNP on the survival of individual bacteriophages using classical virology cultivation and electron microscopic techniques. Moreover, how the ingested AgNP may affect the intestinal virus/phages was investigated by conducting whole-genome sequencing (WGS). Results The viral cultivation methods showed minimal effect on selected viruses during short-term exposure (24 h) to 10 nm AgNP. However, long-term exposure (7 days) resulted in significant reduction in the viral/phage population. Data obtained from WGS were filtered and compared with a nonredundant viral database composed of the complete viral genomes from NCBI using KRAKEN (confidence scoring threshold of 0.5). To compare the relative differential changes, the sequence counts in each treatment group were normalized to account for differences in DNA sequencing library sizes. Bioinformatics techniques were developed to visualize the virome comparative changes in a phylogenic tree graph. The computed data revealed that AgNP had an impact on several intestinal bacteriophages that prey on bacterial genus Enterobacteria, Yersinia and Staphylococcus as host species. Moreover, there was an independent effect of nanoparticles and released ions. Conclusion Overall, this study reveals that the small-size AgNP could lead to perturbations of the gut microbial ecosystem, leading to the inactivation of resident phages that play an important role in influencing gastrointestinal health.
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Affiliation(s)
- Kuppan Gokulan
- Division of Microbiology, US Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
| | - Aschalew Z Bekele
- Division of Microbiology, US Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
| | | | - Sangeeta Khare
- Division of Microbiology, US Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
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220
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Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses 2018; 10:E256. [PMID: 29757994 PMCID: PMC5977249 DOI: 10.3390/v10050256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022] Open
Abstract
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.
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Affiliation(s)
- Bashar Ibrahim
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Utrecht University, 3508 TC Utrecht, The Netherlands.
| | - Arno C Andeweg
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Department of Viroscience, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands.
| | - Susana Posada-Céspedes
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France.
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, Brazil.
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Anne Kupczok
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Institute of General Microbiology, Kiel University, 24118 Kiel, Germany.
| | - Philippe Lemey
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Clinical and Epidemiological Virology, Rega Institute, KU Leuven, University of Leuven, 3000 Leuven, Belgium.
| | - Alice C McHardy
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.
| | - Dino P McMahon
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Institute of Biology, Free University Berlin, Schwendenerstr. 1, 14195 Berlin, Germany.
- Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany.
| | - Brett E Pickett
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- J. Craig Venter Institute, Rockville, MD 20850, USA.
| | - David L Robertson
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow G61 1QH, UK.
| | - Richard H Scheuermann
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- J. Craig Venter Institute, La Jolla, CA 92037, USA.
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, 9700 RB Groningen, The Netherlands.
| | - Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.
| | - Alexander Schönhuth
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Theoretical Biology and Bioinformatics, Utrecht University, 3508 TC Utrecht, The Netherlands.
- Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands.
| | - Bas E Dutilh
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Theoretical Biology and Bioinformatics, Utrecht University, 3508 TC Utrecht, The Netherlands.
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany.
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany.
- Leibniz Institute for Age Research-Fritz Lipmann Institute, 07745 Jena, Germany.
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Tan L, Li L, Ashbolt N, Wang X, Cui Y, Zhu X, Xu Y, Yang Y, Mao D, Luo Y. Arctic antibiotic resistance gene contamination, a result of anthropogenic activities and natural origin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:1176-1184. [PMID: 29070451 DOI: 10.1016/j.scitotenv.2017.10.110] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/10/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
The increasing global prevalence of antibiotic resistance genes (ARGs) in the environment is attributed to anthropogenic activities, particularly the misuse of antimicrobial drugs in human care and animal production. In the present study, we first examined Arctic/sub-Arctic (polar) sediments for the abundance and diversity of 30 ARGs against sulfonamide, tetracycline, aminoglycoside, quinolone, macrolide, and β-lactam antibiotics. Polar sediment ARGs were detected by qPCR at relatively low levels (10-9 to 10-5 copies/16S rRNA gene copies) compared to the reference sites, which were heavily impacted regions of China (the Haihe River, the Tianjin Water Park water and the Qilihai Wetland water, at 10-8 to 10-2 copies/16S rRNA gene copies). A human mitochondrial gene target, Hmt, was first used to aid in the identification of ARGs associated with anthropogenic activities, being relatively persistent, in high copy number and a human-specific molecular marker. Hmt was consistently present in easily quantifiable amounts in the polar sediment samples, indicating their relationship with human-impact, and it was also positively correlated with the relative abundance of ARGs and to the concentrations of modern-day antibiotics. Phylogenetic analyses of resistance sequences from both the Arctic marine sediments and a major database of human pathogens indicated that the ARGs in polar region were the result of a mix of human influence and natural origins. To our knowledge, this is the first study to show that ARGs in Arctic marine sediments appear to be a mixture of both natural origins and recent human influence. This study provides a significant reference regarding the global reach of antibiotic resistance, which is associated with anthropogenic activities.
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Affiliation(s)
- Lu Tan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Linyun Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Nicholas Ashbolt
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China; School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Xiaolong Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yuxiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Xiao Zhu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yan Xu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yang Yang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, China.
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China.
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Shkoporov AN, Ryan FJ, Draper LA, Forde A, Stockdale SR, Daly KM, McDonnell SA, Nolan JA, Sutton TD, Dalmasso M, McCann A, Ross RP, Hill C. Reproducible protocols for metagenomic analysis of human faecal phageomes. MICROBIOME 2018; 6:68. [PMID: 29631623 PMCID: PMC5892011 DOI: 10.1186/s40168-018-0446-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/13/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Recent studies have demonstrated that the human gut is populated by complex, highly individual and stable communities of viruses, the majority of which are bacteriophages. While disease-specific alterations in the gut phageome have been observed in IBD, AIDS and acute malnutrition, the human gut phageome remains poorly characterised. One important obstacle in metagenomic studies of the human gut phageome is a high level of discrepancy between results obtained by different research groups. This is often due to the use of different protocols for enriching virus-like particles, nucleic acid purification and sequencing. The goal of the present study is to develop a relatively simple, reproducible and cost-efficient protocol for the extraction of viral nucleic acids from human faecal samples, suitable for high-throughput studies. We also analyse the effect of certain potential confounding factors, such as storage conditions, repeated freeze-thaw cycles, and operator bias on the resultant phageome profile. Additionally, spiking of faecal samples with an exogenous phage standard was employed to quantitatively analyse phageomes following metagenomic sequencing. Comparative analysis of phageome profiles to bacteriome profiles was also performed following 16S rRNA amplicon sequencing. RESULTS Faecal phageome profiles exhibit an overall greater individual specificity when compared to bacteriome profiles. The phageome and bacteriome both exhibited moderate change when stored at + 4 °C or room temperature. Phageome profiles were less impacted by multiple freeze-thaw cycles than bacteriome profiles, but there was a greater chance for operator effect in phageome processing. The successful spiking of faecal samples with exogenous bacteriophage demonstrated large variations in the total viral load between individual samples. CONCLUSIONS The faecal phageome sequencing protocol developed in this study provides a valuable additional view of the human gut microbiota that is complementary to 16S amplicon sequencing and/or metagenomic sequencing of total faecal DNA. The protocol was optimised for several confounding factors that are encountered while processing faecal samples, to reduce discrepancies observed within and between research groups studying the human gut phageome. Rapid storage, limited freeze-thaw cycling and spiking of faecal samples with an exogenous phage standard are recommended for optimum results.
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Affiliation(s)
| | - Feargal J. Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Amanda Forde
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Stephen R. Stockdale
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Karen M. Daly
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - James A. Nolan
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Marion Dalmasso
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, EA4651 ABTE, F-14032 Caen, France
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland
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Sun M, Ye M, Jiao W, Feng Y, Yu P, Liu M, Jiao J, He X, Liu K, Zhao Y, Wu J, Jiang X, Hu F. Changes in tetracycline partitioning and bacteria/phage-comediated ARGs in microplastic-contaminated greenhouse soil facilitated by sophorolipid. JOURNAL OF HAZARDOUS MATERIALS 2018; 345:131-139. [PMID: 29175125 DOI: 10.1016/j.jhazmat.2017.11.036] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 05/13/2023]
Abstract
The emerging mixed contamination of antibiotics and microplastics in greenhouse soil has made the control of antibiotic resistant gene (ARG) transmission a novel challenge. In this work, surfactant sophorolipid was applied to enhance the dissipation of tetracycline (TC) and tet genes in the presence of microplastics in greenhouse soil. During 49days of incubation, soil bacteria and phages were both found to be the crucial reservoirs of ARGs. Meanwhile, microplastic's presence significantly inhibited the dissipation of TC and ARGs in the soil. However, sophorolipid application was proved to outweigh the negative impact caused by microplastic existence, and lead to the highest dissipation of soil TC and ARGs. Significant positive correlation was detected between the dissipation rate of water-soluble and exchangeable TC content and bacteria/phage co-mediated ARG levels. This also held true between the two fractions of soil TC and the ratio of ARG level in the bacteria to that in the phages (BARGs/PARGs). The opposite impacts of microplastic presence and sophorolipid amendment on the TC/ARG dissipation found in this work provides new information for understanding ARG transmission between bacteria and phages in the mixed contaminated greenhouse soil.
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Affiliation(s)
- Mingming Sun
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wentao Jiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanfang Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, United States
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaguo Jiao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing 100038, China
| | - Kuan Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchao Zhao
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Wu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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224
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Reusing Treated Wastewater: Consideration of the Safety Aspects Associated with Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes. WATER 2018. [DOI: 10.3390/w10030244] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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225
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Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, Li A, Zeng Z, Zhang T. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. MICROBIOME 2018; 6:34. [PMID: 29439741 PMCID: PMC5811963 DOI: 10.1186/s40168-018-0419-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qinglin Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Andong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Forde A, Hill C. Phages of life - the path to pharma. Br J Pharmacol 2018; 175:412-418. [PMID: 29266197 PMCID: PMC5773946 DOI: 10.1111/bph.14106] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophage (phage) therapy has encountered both enthusiasm and scepticism in the past century. New antimicrobial strategies against lethal pathogens are now a top priority for the World Health Organization, and although compassionate use of phages recently met with significant success, regulated clinical interventions seem unlikely in the near future. The hundredth anniversary of their discovery seems an appropriate time for a revival of phage therapy, particularly as the dilemma of antibiotic resistance grows. Phages are ubiquitous in the environment, on our food and in and on our bodies. Their influence on human health is currently being evaluated, and in this mini-review, we examine data from recent metagenomic studies that propose a role for phages in the structure of the microbiome and in health and disease. We assess evidence for phages as vehicles for gene transfer in the context of antibiotic resistance and discuss challenges and opportunities along the critical path from phage discovery to a patient-focused pharmaceutical intervention.
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Affiliation(s)
- Amanda Forde
- APC Microbiome InstituteUniversity College CorkCorkIreland
| | - Colin Hill
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome InstituteUniversity College CorkCorkIreland
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Zhou W, Liu L, Feng Y, Zong Z. A P7 Phage-Like Plasmid Carrying mcr-1 in an ST15 Klebsiella pneumoniae Clinical Isolate. Front Microbiol 2018; 9:11. [PMID: 29403463 PMCID: PMC5786510 DOI: 10.3389/fmicb.2018.00011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/05/2018] [Indexed: 02/05/2023] Open
Abstract
A Klebsiella pneumoniae clinical strain, named SCKP83, was isolated and found to be resistant to colistin thanks to the presence plasmid-borne colistin resistant gene mcr-1. The strain was subjected to whole genome sequencing and conjugation experiments. The subsequent analysis indicated that the strain belongs to ST15 and the capsular type K41. In SCKP83, mcr-1 was carried by a 97.4-kb non-self-transmissible plasmid, a 90.9-kb region of which was predicted as an intact phage. This phage was 47.79% GC content, encoded 105 proteins and contained three tRNAs. mcr-1 was located downstream of two copies of the insertion sequence ISApl1 (one complete and one truncated) and was inserted in the ant1 gene, which encodes a putative antirepressor for antagonizing C1 repression, in this phage. The phage is highly similar to phage P7 (77% coverage and 98% identity) from Escherichia coli. Several similar mcr-1-carrying plasmids have been found in E. coli at various locations in China, suggesting that these phage-like plasmids have circulated in China. The findings in this study suggest that the P7 phage-like plasmids are not restricted to E. coli and may represent new vehicles to mediate the inter-species spread of mcr-1.
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Affiliation(s)
- Weilong Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Lu Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
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228
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Rodríguez-Rubio L, Jofre J, Muniesa M. Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy? Antibiotics (Basel) 2017; 6:antibiotics6040032. [PMID: 29206153 PMCID: PMC5745475 DOI: 10.3390/antibiotics6040032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/15/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
The emergence of multi-drug resistant bacteria has undermined our capacity to control bacterial infectious diseases. Measures needed to tackle this problem include controlling the spread of antibiotic resistance, designing new antibiotics, and encouraging the use of alternative therapies. Phage therapy seems to be a feasible alternative to antibiotics, although there are still some concerns and legal issues to overcome before it can be implemented on a large scale. Here we highlight some of those concerns, especially those related to the ability of bacteriophages to transport bacterial DNA and, in particular, antibiotic resistance genes.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Joan Jofre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
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229
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The human gut virome: form and function. Emerg Top Life Sci 2017; 1:351-362. [PMID: 33525769 DOI: 10.1042/etls20170039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/18/2017] [Accepted: 10/20/2017] [Indexed: 01/15/2023]
Abstract
Advances in next-generation sequencing technologies and the application of metagenomic approaches have fuelled an exponential increase in our understanding of the human gut microbiome. These approaches are now also illuminating features of the diverse and abundant collection of viruses (termed the virome) subsisting with the microbial ecosystems residing within the human holobiont. Here, we focus on the current and emerging knowledge of the human gut virome, in particular on viruses infecting bacteria (bacteriophage or phage), which are a dominant component of this viral community. We summarise current insights regarding the form and function of this 'human gut phageome' and highlight promising avenues for future research. In doing so, we discuss the potential for phage to drive ecological functioning and evolutionary change within this important microbial ecosystem, their contribution to modulation of host-microbiome interactions and stability of the community as a whole, as well as the potential role of the phageome in human health and disease. We also consider the emerging concepts of a 'core healthy gut phageome' and the putative existence of 'viral enterotypes' and 'viral dysbiosis'.
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230
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Abstract
Bacteriophages are numerically the most abundant DNA-containing entities in the oligotrophic ocean, yet how specific phage populations vary over time and space remains to be fully explored. Here, we conducted a metagenomic time-series survey of double-stranded DNA phages throughout the water column in the North Pacific Subtropical Gyre, encompassing 1.5 years from depths of 25 to 1,000 m. Viral gene sequences were identified in assembled metagenomic samples, yielding an estimated 172,385 different viral gene families. Viral marker gene distributions suggested that lysogeny was more prevalent at mesopelagic depths than in surface waters, consistent with prior prophage induction studies using mitomycin C. A total of 129 ALOHA viral genomes and genome fragments from 20 to 108 kbp were selected for further study, which represented the most abundant phages in the water column. Phage genotypes displayed discrete population structures. Most phages persisted throughout the time-series and displayed a strong depth structure that mirrored the stratified depth distributions of co-occurring bacterial taxa in the water column. Mesopelagic phages were distinct from surface water phages with respect to diversity, gene content, putative life histories, and temporal persistence, reflecting depth-dependent differences in host genomic architectures and phage reproductive strategies. The spatiotemporal distributions of the most abundant open-ocean bacteriophages that we report here provide new insight into viral temporal persistence, life history, and virus-host-environment interactions throughout the open-ocean water column. The North Pacific Subtropical Gyre represents one of the largest biomes on the planet, where microbial communities are central mediators of ecosystem dynamics and global biogeochemical cycles. Critical members of these communities are the viruses of marine bacteria, which can alter microbial metabolism and significantly influence their survival and productivity. To better understand these viral assemblages, we conducted genomic analyses of planktonic viruses over a seasonal cycle to ocean depths of 1,000 m. We identified 172,385 different viral gene families and 129 unique virus genotypes in this open-ocean setting. The spatiotemporal distributions of the most abundant open-ocean viruses that we report here provide new insights into viral temporal variability, life history, and virus-host-environment interactions throughout the water column.
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231
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Brown-Jaque M, Calero-Cáceres W, Espinal P, Rodríguez-Navarro J, Miró E, González-López JJ, Cornejo T, Hurtado JC, Navarro F, Muniesa M. Antibiotic resistance genes in phage particles isolated from human faeces and induced from clinical bacterial isolates. Int J Antimicrob Agents 2017; 51:434-442. [PMID: 29180282 DOI: 10.1016/j.ijantimicag.2017.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 11/07/2017] [Accepted: 11/18/2017] [Indexed: 12/31/2022]
Abstract
Phage particles have emerged as elements with the potential to mobilise antibiotic resistance genes (ARGs) in different environments, including the intestinal habitat. This study aimed to determine the occurrence of ARGs in phage particles present in faecal matter and induced from strains isolated from faeces. Nine ARGs (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, blaOXA-48, qnrA, qnrS, mecA, sul1 and armA) were quantified by qPCR in the phage DNA fractions of 150 faecal samples obtained from healthy individuals who had not received antibiotic treatment or travelled abroad in the 3 months prior to sample collection. On the suspicion that the detected particles originated from bacterial flora, 82 Escherichia coli and Klebsiella pneumoniae isolates possessing at least one identified ARG (blaTEM, blaCTX-M-1 group, blaCTX-M-9 group, armA, qnrA, qnrS and sul1) were isolated and their capacity to produce phage particles carrying these ARGs following induction was evaluated. Of 150 samples, 72.7% were positive for at least one ARG, with blaTEM and blaCTX-M-9 group being the most prevalent and abundant. Of the 82 isolates, 51 (62%) showed an increase in the number of copies of the respective ARG in the phage fraction following induction, with blaTEM, blaCTX-M-1 group, blaCTX-M-9 group and sul1 being the most abundant. Phages induced from the isolates were further purified and visualised using microscopy and their DNA showed ARG levels of up to 1010 gene copies/mL. This study highlights the abundance of phage particles harbouring ARGs and indicates that bacterial strains in the intestinal habitat could be source of these particles.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Paula Espinal
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Judith Rodríguez-Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elisenda Miró
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain
| | - Juan José González-López
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Thais Cornejo
- Department of Clinical Microbiology, Hospital Vall d'Hebron, Vall d'Hebron Institut de Recerca, Barcelona, Spain
| | - Juan Carlos Hurtado
- ISGlobal, Barcelona Centre for International Health Research, Department of Microbiology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ferran Navarro
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Institut d'Investigació Biomèdica Sant Pau, Sant Quintí 89, 08041 Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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232
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Phage Therapy Approaches to Reducing Pathogen Persistence and Transmission in Animal Production Environments: Opportunities and Challenges. Microbiol Spectr 2017; 5. [PMID: 28664828 DOI: 10.1128/microbiolspec.pfs-0017-2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The era of genomics has allowed for characterization of phages for use as antimicrobials to treat animal infections with a level of precision never before realized. As more research in phage therapy has been conducted, several advantages of phage therapy have been realized, including the ubiquitous nature, specificity, prevalence in the biosphere, and low inherent toxicity of phages, which makes them a safe and sustainable technology for control of animal diseases. These unique qualities of phages have led to several opportunities with respect to emerging trends in infectious disease treatment. However, the opportunities are tempered by several challenges to the successful implementation of phage therapy, such as the fact that an individual phage can only infect one or a few bacterial strains, meaning that large numbers of different phages will likely be needed to treat infections caused by multiple species of bacteria. In addition, phages are only effective if enough of them can reach the site of bacterial colonization, but clearance by the immune system upon introduction to the animal is a reality that must be overcome. Finally, bacterial resistance to the phages may develop, resulting in treatment failure. Even a successful phage infection and lysis of its host has consequences, because large amounts of endotoxin are released upon lysis of Gram-negative bacteria, which can lead to local and systemic complications. Overcoming these challenges will require careful design and development of phage cocktails, including comprehensive characterization of phage host range and assessment of immunological risks associated with phage treatment.
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233
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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234
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Balcázar JL. How do bacteriophages promote antibiotic resistance in the environment? Clin Microbiol Infect 2017; 24:447-449. [PMID: 29066402 DOI: 10.1016/j.cmi.2017.10.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/05/2017] [Accepted: 10/14/2017] [Indexed: 11/25/2022]
Affiliation(s)
- J L Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
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235
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Aggarwala V, Liang G, Bushman FD. Viral communities of the human gut: metagenomic analysis of composition and dynamics. Mob DNA 2017; 8:12. [PMID: 29026445 PMCID: PMC5627405 DOI: 10.1186/s13100-017-0095-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/24/2017] [Indexed: 01/17/2023] Open
Abstract
Background The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. Main body Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal. Short conclusion Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning.
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Affiliation(s)
- Varun Aggarwala
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4319 USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 USA
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236
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Abstract
Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration. FDA regulations on agricultural antibiotic use have focused on antibiotics that are important for human medicine. Carbadox is an antibiotic not used in humans but frequently used on U.S. pig farms. It is important to study possible side effects of carbadox use because it has been shown to promote bacterial evolution, which could indirectly impact antibiotic resistance in bacteria of clinical importance. Interestingly, the present study shows greater prophage gene expression in feces from carbadox-fed animals than in feces from nonmedicated animals 2 days after the initiation of in-feed carbadox treatment. Importantly, the phage genetic material isolated in this study contained genes that could provide resistance to antibiotics that are important in human medicine, indicating that human-relevant antibiotic resistance genes are mobile between bacteria via phages. This study highlights the collateral effects of antibiotics and demonstrates the need to consider diverse antibiotic effects whenever antibiotics are being used or new regulations are considered.
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237
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Kim Y, Van Bonn W, Aw TG, Rose JB. Aquarium Viromes: Viromes of Human-Managed Aquatic Systems. Front Microbiol 2017; 8:1231. [PMID: 28713358 PMCID: PMC5492393 DOI: 10.3389/fmicb.2017.01231] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.
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Affiliation(s)
- Yiseul Kim
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,National Institute of Agricultural Sciences, Rural Development AdministrationWanju, South Korea
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States.,A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, ChicagoIL, United States
| | - Tiong G Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New OrleansLA, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East LansingMI, United States
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238
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Colavecchio A, Cadieux B, Lo A, Goodridge LD. Bacteriophages Contribute to the Spread of Antibiotic Resistance Genes among Foodborne Pathogens of the Enterobacteriaceae Family - A Review. Front Microbiol 2017; 8:1108. [PMID: 28676794 PMCID: PMC5476706 DOI: 10.3389/fmicb.2017.01108] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 05/31/2017] [Indexed: 01/21/2023] Open
Abstract
Foodborne illnesses continue to have an economic impact on global health care systems. There is a growing concern regarding the increasing frequency of antibiotic resistance in foodborne bacterial pathogens and how such resistance may affect treatment outcomes. In an effort to better understand how to reduce the spread of resistance, many research studies have been conducted regarding the methods by which antibiotic resistance genes are mobilized and spread between bacteria. Transduction by bacteriophages (phages) is one of many horizontal gene transfer mechanisms, and recent findings have shown phage-mediated transduction to be a significant contributor to dissemination of antibiotic resistance genes. Here, we review the viability of transduction as a contributing factor to the dissemination of antibiotic resistance genes in foodborne pathogens of the Enterobacteriaceae family, including non-typhoidal Salmonella and Shiga toxin-producing Escherichia coli, as well as environmental factors that increase transduction of antibiotic resistance genes.
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Affiliation(s)
- Anna Colavecchio
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-BellevueQC, Canada
| | - Brigitte Cadieux
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-BellevueQC, Canada
| | - Amanda Lo
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-BellevueQC, Canada
| | - Lawrence D Goodridge
- Food Safety and Quality Program, Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-BellevueQC, Canada
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239
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Touchon M, Moura de Sousa JA, Rocha EP. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr Opin Microbiol 2017; 38:66-73. [PMID: 28527384 DOI: 10.1016/j.mib.2017.04.010] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/21/2023]
Abstract
Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition. The characteristics of transduction and lysogenic conversion complement those of other mechanisms of transfer, and could play a key role in the spread of adaptive genes between communities.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France
| | - Jorge A Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France
| | - Eduardo Pc Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France.
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240
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Ménage à trois in the human gut: interactions between host, bacteria and phages. Nat Rev Microbiol 2017; 15:397-408. [DOI: 10.1038/nrmicro.2017.30] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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241
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Hesse U, van Heusden P, Kirby BM, Olonade I, van Zyl LJ, Trindade M. Virome Assembly and Annotation: A Surprise in the Namib Desert. Front Microbiol 2017; 8:13. [PMID: 28167933 PMCID: PMC5253355 DOI: 10.3389/fmicb.2017.00013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/03/2017] [Indexed: 11/13/2022] Open
Abstract
Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from a copper rich site in the Namib Desert. We found that scaffold network analysis and cluster-specific read reassembly improved reconstruction of sequences with excessive read coverage, and that strict data filtering for non-viral sequences prior to downstream analyses was essential. In this study we describe novel viral genomes identified in the Namib Desert copper site virome. Taxonomic affiliations of diverse proteins in the dataset and phylogenetic analyses of circovirus-like proteins indicated links to the marine habitat. Considering additional evidence from this dataset we hypothesize that viruses may have been carried from the Atlantic Ocean into the Namib Desert by fog and wind, highlighting the impact of the extended environment on an investigated niche in metagenome studies.
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Affiliation(s)
- Uljana Hesse
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Peter van Heusden
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Bronwyn M. Kirby
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Israel Olonade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
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242
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Shigatoxin encoding Bacteriophage ϕ24 B modulates bacterial metabolism to raise antimicrobial tolerance. Sci Rep 2017; 7:40424. [PMID: 28106081 PMCID: PMC5247750 DOI: 10.1038/srep40424] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/07/2016] [Indexed: 01/15/2023] Open
Abstract
How temperate bacteriophages play a role in microbial infection and disease progression is not fully understood. They do this in part by carrying genes that promote positive evolutionary selection for the lysogen. Using Biolog phenotype microarrays and comparative metabolite profiling we demonstrate the impact of the well-characterised Shiga toxin-prophage ϕ24B on its Escherichia coli host MC1061. As a lysogen, the prophage alters the bacterial physiology by increasing the rates of respiration and cell proliferation. This is the first reported study detailing phage-mediated control of the E. coli biotin and fatty acid synthesis that is rate limiting to cell growth. Through ϕ24B conversion the lysogen also gains increased antimicrobial tolerance to chloroxylenol and 8-hydroxyquinoline. Distinct metabolite profiles discriminate between MC1061 and the ϕ24B lysogen in standard culture, and when treated with 2 antimicrobials. This is also the first reported use of metabolite profiling to characterise the physiological impact of lysogeny under antimicrobial pressure. We propose that temperate phages do not need to carry antimicrobial resistance genes to play a significant role in tolerance to antimicrobials.
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243
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Anand T, Bera BC, Vaid RK, Barua S, Riyesh T, Virmani N, Hussain M, Singh RK, Tripathi BN. Abundance of antibiotic resistance genes in environmental bacteriophages. J Gen Virol 2016; 97:3458-3466. [DOI: 10.1099/jgv.0.000639] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Taruna Anand
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Bidhan Ch. Bera
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Rajesh K. Vaid
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Sanjay Barua
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Thachamvally Riyesh
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Nitin Virmani
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana 125 001, India
| | - Mubarik Hussain
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
| | - Raj K. Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243 122, India
| | - Bhupendra N. Tripathi
- National Centre for Veterinary Type Culture Collection, Bagla Road, Hisar, Haryana 125 001, India
- ICAR-National Research Centre on Equines, Sirsa Road, Hisar, Haryana 125 001, India
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244
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Ly M, Jones MB, Abeles SR, Santiago-Rodriguez TM, Gao J, Chan IC, Ghose C, Pride DT. Transmission of viruses via our microbiomes. MICROBIOME 2016; 4:64. [PMID: 27912785 PMCID: PMC5134127 DOI: 10.1186/s40168-016-0212-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/24/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts. RESULTS Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals. Most of these viruses were bacteriophages, and each individual had distinct oral and gut viral ecology from their housemates despite the fact that some of their bacteriophages were shared. The distribution of bacteriophages over time within households indicated that they were frequently transmitted between the microbiomes of household contacts. CONCLUSIONS Because bacteriophages may shape human oral and gut bacterial ecology, their transmission to household contacts suggests they could have substantial roles in shaping the microbiota within a household.
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Affiliation(s)
- Melissa Ly
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - Shira R Abeles
- Department of Medicine, University of California, San Diego, 92093, USA
| | | | - Jonathan Gao
- Department of Pathology, University of California, San Diego, 92093, USA
| | - Ivan C Chan
- Department of Pathology, University of California, San Diego, 92093, USA
| | | | - David T Pride
- Department of Pathology, University of California, San Diego, 92093, USA.
- Department of Medicine, University of California, San Diego, 92093, USA.
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245
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Singer AC, Shaw H, Rhodes V, Hart A. Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators. Front Microbiol 2016; 7:1728. [PMID: 27847505 PMCID: PMC5088501 DOI: 10.3389/fmicb.2016.01728] [Citation(s) in RCA: 383] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/17/2016] [Indexed: 01/25/2023] Open
Abstract
The environment is increasingly being recognized for the role it might play in the global spread of clinically relevant antibiotic resistance. Environmental regulators monitor and control many of the pathways responsible for the release of resistance-driving chemicals into the environment (e.g., antimicrobials, metals, and biocides). Hence, environmental regulators should be contributing significantly to the development of global and national antimicrobial resistance (AMR) action plans. It is argued that the lack of environment-facing mitigation actions included in existing AMR action plans is likely a function of our poor fundamental understanding of many of the key issues. Here, we aim to present the problem with AMR in the environment through the lens of an environmental regulator, using the Environment Agency (England’s regulator) as an example from which parallels can be drawn globally. The issues that are pertinent to environmental regulators are drawn out to answer: What are the drivers and pathways of AMR? How do these relate to the normal work, powers and duties of environmental regulators? What are the knowledge gaps that hinder the delivery of environmental protection from AMR? We offer several thought experiments for how different mitigation strategies might proceed. We conclude that: (1) AMR Action Plans do not tackle all the potentially relevant pathways and drivers of AMR in the environment; and (2) AMR Action Plans are deficient partly because the science to inform policy is lacking and this needs to be addressed.
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Affiliation(s)
| | - Helen Shaw
- Department for Environment, Food and Rural Affairs London, UK
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