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. 2021 Aug 31;6(4):e0079921.
doi: 10.1128/mSystems.00799-21. Epub 2021 Aug 17.

Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective

Evelien M Adriaenssens  1
Affiliations

Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective

Evelien M Adriaenssens. mSystems. .

Abstract

Bacteriophages (phages) have been known for over a century, but only in the last 2 decades have we really come to appreciate how abundant and diverse they are. With that realization, research groups across the globe have shown the importance of phage-based processes in a myriad of environments, including the global oceans and soils, and as part of the human microbiome. Through advances in sequencing technology, genomics, and bioinformatics, we know that the morphological diversity of bacteriophages originally used for taxonomy is eclipsed by their genomic diversity. Because we currently do not have a complete taxonomic framework or naming scheme to describe this diversity, crucial information from virome and microbiome studies is being lost. In this commentary, I will discuss recent advances in taxonomy and its importance for studies of the microbiome with examples of the human gut phageome and make recommendations for future analyses.

Keywords: human gut virome; microbiome; phage taxonomy; phageome; virome.

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Conflict of interest statement

Conflict of Interest Disclosures: E.M.A. reports grants from the Biotechnology and Biological Sciences Research Council (BBSRC) during the conduct of the study. She is the Chair of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV).

Conflict of Interest Disclosures: E.M.A. reports grants from the Biotechnology and Biological Sciences Research Council (BBSRC) during the conduct of the study. She is the Chair of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV).

Figures

FIG 1
FIG 1
Overview of the virus ranks containing bacteriophages as of Master Species List 36 (https://talk.ictvonline.org/files/master-species-lists/m/msl/12314 [accessed June 2021]). The order Caudovirales is indicated in gray as it is scheduled for deletion. The family Picobirnaviridae outlined in red was originally recognized as a family of animal-associated viruses, but is now bioinformatically predicted to be made up of bacteriophages.
FIG 2
FIG 2
Phage diversity analysis of three gut phageome samples. (A) Heatmap of the number of uncultivated virus genomes (UViGs) per family grouped at the viral family level using Diamond BLASTX against the viral RefSeq database release 99 and lowest common ancestor assignment using Megan6. (B) vConTACT2 network analysis of UViGs from three samples and all published complete phage genomes of the INPHARED pipeline on 24 January 2021. Families are colored according to the INPHARED metadata, with selected families indicated in the legend. Archaeal viruses and the taxa of nontailed phages except for microviruses were removed.
See this image and copyright information in PMC

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