"V体育官网入口" Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The . gov means it’s official. Federal government websites often end in VSports app下载. gov or . mil. Before sharing sensitive information, make sure you’re on a federal government site. .

Https

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely. V体育官网.

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

"V体育官网" Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective

Affiliations

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

"VSports最新版本" 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 VSports手机版. .

Keywords: human gut virome; microbiome; phage taxonomy; phageome; virome. V体育安卓版.

PubMed Disclaimer

VSports注册入口 - 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 V体育ios版. 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 VSports最新版本. 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.

References

    1. Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. 2020. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev 84:e00061-19. - PMC - PubMed
    1. International Committee on Taxonomy of Viruses Executive Committee. 2020. The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol 5:668–674. doi:10.1038/s41564-020-0709-x. - DOI - PMC - PubMed
    1. Turner D, Kropinski AM, Adriaenssens EM. 2021. A roadmap for genome-based phage taxonomy. Viruses 13:506. doi:10.3390/v13030506. - DOI - PMC - PubMed
    1. Adriaenssens E, Brister JR. 2017. How to name and classify your phage: an informal guide. Viruses 9:70. doi:10.3390/v9040070. - "V体育官网入口" DOI - PMC - PubMed
    1. Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee K-B, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit M-A, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, et al. . 2019. Minimum information about an uncultivated virus genome (MIUViG). Nat Biotechnol 37:29–37. doi:10.1038/nbt.4306. - DOI - PMC - PubMed

LinkOut - more resources