Research on the human virome: where are we and what is next

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Abstract

The National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health convened a Working Group on the Microbiome in Cardiovascular, Pulmonary and Hematologic Health and Diseases from June 25, 2014, to June 26, 2014. The Working Group’s central goal was to define what major microbiome research areas warranted additional study in the context of heart, lung, and blood (HLB) diseases. The Working Group identified studies of the human virome a key priority.

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Most cited references 25

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The airway epithelium: soldier in the fight against respiratory viruses.

Marjolaine Vareille, Elisabeth Kieninger, Michael R. Edwards … (2011)

The airway epithelium acts as a frontline defense against respiratory viruses, not only as a physical barrier and through the mucociliary apparatus but also through its immunological functions. It initiates multiple innate and adaptive immune mechanisms which are crucial for efficient antiviral responses. The interaction between respiratory viruses and airway epithelial cells results in production of antiviral substances, including type I and III interferons, lactoferrin, β-defensins, and nitric oxide, and also in production of cytokines and chemokines, which recruit inflammatory cells and influence adaptive immunity. These defense mechanisms usually result in rapid virus clearance. However, respiratory viruses elaborate strategies to evade antiviral mechanisms and immune responses. They may disrupt epithelial integrity through cytotoxic effects, increasing paracellular permeability and damaging epithelial repair mechanisms. In addition, they can interfere with immune responses by blocking interferon pathways and by subverting protective inflammatory responses toward detrimental ones. Finally, by inducing overt mucus secretion and mucostasis and by paving the way for bacterial infections, they favor lung damage and further impair host antiviral mechanisms.

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The virome in mammalian physiology and disease.

Herbert Virgin (2014)

The virome contains the most abundant and fastest mutating genetic elements on Earth. The mammalian virome is constituted of viruses that infect host cells, virus-derived elements in our chromosomes, and viruses that infect the broad array of other types of organisms that inhabit us. Virome interactions with the host cannot be encompassed by a monotheistic view of viruses as pathogens. Instead, the genetic and transcriptional identity of mammals is defined in part by our coevolved virome, a concept with profound implications for understanding health and disease. Copyright © 2014 Elsevier Inc. All rights reserved.

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Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.

David T. Pride, Julia Salzman, Matthew Haynes … (2012)

Viruses are the most abundant known infectious agents on the planet and are significant drivers of diversity in a variety of ecosystems. Although there have been numerous studies of viral communities, few have focused on viruses within the indigenous human microbiota. We analyzed 2 267 695 virome reads from viral particles and compared them with 263 516 bacterial 16S rRNA gene sequences from the saliva of five healthy human subjects over a 2- to 3-month period, in order to improve our understanding of the role viruses have in the complex oral ecosystem. Our data reveal viral communities in human saliva dominated by bacteriophages whose constituents are temporally distinct. The preponderance of shared homologs between the salivary viral communities in two unrelated subjects in the same household suggests that environmental factors are determinants of community membership. When comparing salivary viromes to those from human stool and the respiratory tract, each group was distinct, further indicating that habitat is of substantial importance in shaping human viromes. Compared with coexisting bacteria, there was concordance among certain predicted host-virus pairings such as Veillonella and Streptococcus, whereas there was discordance among others such as Actinomyces. We identified 122 728 virulence factor homologs, suggesting that salivary viruses may serve as reservoirs for pathogenic gene function in the oral environment. That the vast majority of human oral viruses are bacteriophages whose putative gene function signifies some have a prominent role in lysogeny, suggests these viruses may have an important role in helping shape the microbial diversity in the human oral cavity.

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Author and article information

Contributors

Shimian Zou:

ORCID: http://orcid.org/0000-0002-4331-2739

301-435-0074 , 301-480-1046 , shimian.zou@nih.gov

Lis Caler: lis.caler@nih.gov

Sandra Colombini-Hatch: hatchs@nhlbi.nih.gov

Simone Glynn: glynnsa@nhlbi.nih.gov

Pothur Srinivas: srinivap@nhlbi.nih.gov

Journal

Journal ID (nlm-ta): Microbiome

Journal ID (iso-abbrev): Microbiome

Title: Microbiome

Publisher: BioMed Central (London )

ISSN (Electronic): 2049-2618

Publication date (Electronic): 24 June 2016

Publication date PMC-release: 24 June 2016

Publication date Collection: 2016

Volume: 4

Electronic Location Identifier: 32

Affiliations

National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD 20892-7950 USA

Author information

Shimian Zou http://orcid.org/0000-0002-4331-2739

Article

Publisher ID: 177

DOI: 10.1186/s40168-016-0177-y

PMC ID: 4919837

PubMed ID: 27341799

SO-VID: 45302311-a1d5-42bb-83c0-9e7b065de0d5

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 15 April 2016

Date accepted : 10 June 2016

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Keywords: microbiome,virome,heart,lung,blood,hiv

Data availability:

Keywords: microbiome, virome, heart, lung, blood, hiv

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Most cited references 25

The airway epithelium: soldier in the fight against respiratory viruses.

The virome in mammalian physiology and disease.

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome.

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