Improving Human Virome Studies: Updates to Virus Classification

The proposed phage proteomic tree by Rohwer and Edwards.

Taxonomy is an important aspect of microbiome research. Whether we are studying communities of bacteria, viruses, or other microbes, there are benefits to labeling microbes. Taxonomic names immediately give us information about their relationships to each other, such as similar bacteria being grouped into the same genus. Taxonomic identities also provide some information about an organism's functionality and/or clinical pathology. For example, by mentioning that a bacteria is a member of the genus Staphylococcus, you might think that it is a round, gram-positive bacterium that might inhabit the skin and is otherwise related to other members of that genus (including genomic relationships). In the end, the practice does what it aims to do, which is classify organisms in an informative way.

Although it might seem like a simple practice at first, it is actually a very complicated field that continues to improve due to the effort of many talented scientists. This is especially true for virus taxonomy. Although improving, phage taxonomy has continued to suffer from issues of ambiguity and inconsistency. In this post I want to go over the recently proposed improvements to phage taxonomic conventions. I feel this is particularly important to go over because it will impact the analyses done by human virome researchers, as well as virome researchers in general.

The manuscript outlining the changes is actually a very nice, short, and easy read, so I will direct you to it for details if you are interested. Overall, the changes reduce ambiguity and foster greater consistency in naming phages. Here is a list of the proposed changes, which are listed with greater detail in the manuscript itself.

1. Replace "phage" with "virus" in bacteriophage taxonomy names.

Example: "Escherichia phage T4" will become "Escherichia virus T4".

2. Removal of "like" from phage genus names.

Example: "Lambdalikevirus" will become "Lambdavirus".

3. Discontinuation of "phi" and other transliterated Greek letters.

Greek letters will be discouraged in names going forward.

4. Elimination of hyphens from taxon names.

Example: "Yersinia phage L-413C" will become "Yersinia virus L413C".

5. Specificity of isolation host in taxon name.

Example: "Enterobacteria phage T7" will become "Escherichia virus T7".

The group also discusses the ongoing efforts in using genomic similarity for defining virus genome similarity.  For example, viruses with greater than 40% amino acid sequence similarity have been categorized as being in the same genus. As is perhaps expected, this can result in somewhat uninformative categorizations that collect somewhat dissimilar viruses. This will be an area of development that we will have to continue watching.

So what can we take away from this? Honestly this is a important paper for those of us interested in virus ecology, and especially the human virome. In a lot of ways, our understanding of the human virome is only as good as our reference databases. By clearing up ambiguities and inconsistencies in these databases, we can improve our ability to discuss the communities we observe and better equip ourselves with an understanding of the phage relationships.

Thanks for hanging in there to the end. I know taxonomy can be a bit of a dry topic for people, but it really is important and something we all need to try to stay current with, particularly if we think a lot about microbiology. Be sure to check out the manuscript itself for the whole story. For even further reading, check out the paper by Thompson et al.  Finally, if you have any questions, comments, or concerns, please feel free to reach out either through the comment section below, Twitter, or email. I always love hearing from readers!

Works Cited

Krupovic, M., Dutilh, B., Adriaenssens, E., Wittmann, J., Vogensen, F., Sullivan, M., Rumnieks, J., Prangishvili, D., Lavigne, R., Kropinski, A., Klumpp, J., Gillis, A., Enault, F., Edwards, R., Duffy, S., Clokie, M., Barylski, J., Ackermann, H., & Kuhn, J. (2016). Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee Archives of Virology, 161 (4), 1095-1099 DOI: 10.1007/s00705-015-2728-0

Thompson, C., Amaral, G., Campeão, M., Edwards, R., Polz, M., Dutilh, B., Ussery, D., Sawabe, T., Swings, J., & Thompson, F. (2014). Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Archives of Microbiology, 197 (3), 359-370 DOI: 10.1007/s00203-014-1071-2