Understanding and Analyzing Viral Communities with Shotgun Metagenomics (ASM 2014 Workshop)

Last week I attended the annual American Society for Microbiology (ASM) meeting in Boston.  This is a HUGE meeting (I'm talking thousands of microbiologists all in one place) with a lot going on.  There was so much going on that I decided to break my discussions on the meeting into a couple different posts.  This post is going to be about the viromics (the study of viral communities, which are called viromes) workshop I attended on the first day.

This year ASM hosted some really cool workshops where attendees could sign up (for a fee) and learn a lot more about a topic related to their research or interests.  I attended the viromics workshop (an all day workshop) because my research interests include viruses and viral communities (as you might have guessed by the title of this blog).  The workshop had an all-star lineup of renowned virome researchers including Forest Rohwer, Eric Wommack, Simon Roux, Matt Sullivan, Bonnie Hurwitz, and Mark Young.  This workshop was an awesome experience and I learned a lot.  In this post I am going to provide a brief overview of some of the main points of the workshop, as well as provide links to some resources in case you want more information.

Because the focus of the workshop was the metagenomic analysis of viromes, there was a lot of talk about the challenges facing this field of research, and how the field is addressing these challenges.  Some of the challenges facing the study of viral communities include the lack of robust taxonomic/phylogenetic marker genes (like the 16S rRNA genes used in bacteria), a lack of universal taxonomy, and a lack of robust markers which can link phages to their hosts.  There is also the technical challenge of even getting enough material to sequence (you have to collect a lot of ocean water to get enough viruses for sequencing).  To address these issues, researchers often amplify their phage DNA for sequencing using multiple displacement amplification (MDA) methods, and perform whole genome shotgun sequencing instead of amplicon sequencing (this is the method used for bacterial 16S rRNA studies).

Figure 1 Phylogenetic tree of 35 major known bacterial phyla, with the
three phyla primarily used for phage isolation highlighted in red.
This low amount of bacteria used for phage isolation is thought to
be a reason why so few phage genomes have been sampled.  Data
from [2] and figure generated myself.

Even with improved shotgun sequencing methods, most of the virome sequences fail to show any homology to the current viral genomes we have in our databases.  This means that the majority of viruses in the sequenced communities are unknown.  In fact, there was a report in 2003 that estimated less than 0.0002% of the global phage metagenome had been sampled (recent estimates suggest we have actually sampled more, but the number is still very low) [1].  One potential reason for our low level of phage genome sampling is the fact that the majority of phage isolates were grown on only 3 of the known 45 bacterial phyla (Figure 1).  All of these challenges, including the prevalence of unknown phage genomes, the lack of conserved marker genes, etc, are being addressed through efforts toward isolating/sequencing more phage genomes, and unique analysis approaches that allow us to extract useful information.  Viromics is still a relatively new and quickly evolving field that still needs a lot of work and standardization.

In addition to just discussing viral communities and related analysis methods, many of the speakers actually went through the analysis programs and resources that they are developing for public use.  Eric Wommack went over his program Virome, which is used for gene-focused analysis of viral communities.  Simon Roux went over his online program/server metaVIR, which allows for effective and broad virome sequence analysis.  Bonnie Hurwitz went over her online resource iVirus, which is being done in collaboration with iPlant.  This looks really cool because they are trying to tie together multiple different programs into one place, and are also focusing on providing flexible, high-powered computing resources for virome researchers who do not have these computational resources.  This is still in development but looks like a really awesome resource that you should definitely check out.  Overall, as Simon Roux pointed out, there are a lot of programs and resources available so it is important that we make use of multiple tools to get the best understanding of the viral communities.

There was of course a lot more that happened at the workshop, but this is a good general overview of what happened.  If you are interested in learning more, please follow some of the links to check out the specifics.  And of course, if you are really interested in learning more, think about heading to the ASM general meeting next year and attending one of their workshops for yourself.

Like I mentioned above, ASM was a huge meeting that I attended for four days.  Therefore, getting some of my summaries into writing (well, from my notebook to a more understandable blog format) is going to take a little time.  Stay tuned for more posts about ASM in the coming days.  And of course, feel free to contact me if you have any questions, comments, concerns, or just want to chat about ASM.  You can also stay up-to-date by finding me on Twitter.

Works Cited

1.  Rohwer, F. (2003). Global Phage Diversity Cell, 113 (2) DOI: 10.1016/S0092-8674(03)00276-9

2.  Holmfeldt, K., Solonenko, N., Shah, M., Corrier, K., Riemann, L., VerBerkmoes, N., & Sullivan, M. (2013). Twelve previously unknown phage genera are ubiquitous in global oceans Proceedings of the National Academy of Sciences, 110 (31), 12798-12803 DOI: 10.1073/pnas.1305956110