Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2019 Oct 28;17(1):84.
doi: 10.1186/s12915-019-0704-y.

Studying the Gut Virome in the Metagenomic Era: Challenges and Perspectives

Affiliations
Free PMC article
Review

Studying the Gut Virome in the Metagenomic Era: Challenges and Perspectives

Sanzhima Garmaeva et al. BMC Biol. .
Free PMC article

Abstract

The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.

Conflict of interest statement

The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Viruses can be classified based on various characteristics. These terms are used continuously throughout this manuscript. While all characters are important in determining taxonomic relationships, sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa [6]
Fig. 2
Fig. 2
Size distributions of genomes and virions of the most prevalent virus families in the gut. Values are given for the prototype virus of each family. Prokaryotic viruses are shown in red, eukaryotic viruses in blue. Structural information as well as genome sizes have been exported from the ICTV Online Report [24]. The prevalence of each family in the human gut has been inferred from the following studies: Inoviridae [20, 25], Circoviridae, Adenoviridae, Microviridae, Podoviridae, Myoviridae, Siphoviridae [26], Anelloviridae [–27], CrAss-like [28, 29]. dsDNA double-stranded DNA. ssDNA single-stranded DNA
Fig. 3
Fig. 3
The steps in metagenomic study of the virome. Nucleic acid extraction: the virome can be studied by extraction of nucleic acids from both fractions of the total microbial community which includes bacteria and viruses (left) and purified viral-like particles (VLPs; right), and different types of VLP-enriching techniques might be applied to obtain the latter fraction (see main text for details). Genomic library preparation: the extracted viral genetic material is subjected to sequencing after genomic library preparation. Both the choice of genomic library preparation technique and the sequencing coverage can affect the representation of specific members of the viral community in the sample (see discussion in the main text). Quality control: the raw sequencing reads are further trimmed of sequencing adapters, and low-quality and overrepresented reads are discarded. Virome annotation: there are two main ways of studying viral communities—read-mapping to closed reference databases or de novo assembly of viral genomes with optional, but advised, validation of contigs via reference databases

Similar articles

See all similar articles

Cited by 3 articles

References

    1. Cobián Güemes AG, Youle M, Cantú VA, Felts B, Nulton J, Rohwer F. Viruses as winners in the game of life. Annu Rev Virol. 2016;3:197–214. doi: 10.1146/annurev-virology-100114-054952. - DOI - PubMed
    1. Galtier M, De Sordi L, Sivignon A, de Vallée A, Maura D, Neut C, et al. Bacteriophages targeting adherent invasive Escherichia coli strains as a promising new treatment for Crohn’s disease. J Crohn’s Colitis. 2017;11:jjw224. doi: 10.1093/ecco-jcc/jjw224. - DOI - PubMed
    1. Barr JJ, Auro R, Furlan M, Whiteson KL, Erb ML, Pogliano J, et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc Natl Acad Sci U S A. 2013;110:10771–10776. doi: 10.1073/pnas.1305923110. - DOI - PMC - PubMed
    1. Rohwer F, Prangishvili D, Lindell D. Roles of viruses in the environment. Environ Microbiol. 2009;11:2771–2774. doi: 10.1111/j.1462-2920.2009.02101.x. - DOI - PubMed
    1. Suttle CA. Marine viruses — major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–812. doi: 10.1038/nrmicro1750. - DOI - PubMed

Publication types

LinkOut - more resources

Feedback