Capsid and Tail

a weekly phage periodical
Issue 11: Uncultivated viral genomes
January 3, 2019

New reporting standards for uncultivated viral genomes

Have you submitted genome sequences for phages that haven’t been cultured yet? Here’s what you should report if and when you do.

Last week, we announced a new set of reporting standards for uncultivated viral genome sequences. This week, we’re shining light on what these standards are, how they came to be, and why we should all take note.

We’re also introducing a new section this week: the Community Board! Submit requests to the phage community for phages (for any reason, not just therapy), or for collaborations, recommendations, potential supervisors, etc., and we’ll post them here. We hope you’ll give it a try!

What's New

Phage Futures Congress (January 29-30, 2019) is fast-approaching! Speakers include representatives of the FDA (Scott Stibitz, Cara Fiore), biotech (Xavier Duportet, Carl Merril), academia (Martha Clokie, Betty Kutter, Steffanie Strathdee) and the non-profit sector (Tobi Nagel). If you haven’t registered yet, it’s not too late! - use code PHDI10 for 10% off.

Phage Futures 2019

Promotion

Mark your calendars for another exciting translational phage conference! The Bacteriophage Therapy Summit will take place in Boston, Massachusetts March 26-27, 2019. The meeting will focus on the discovery, translation and acceleration of phage research into targeted therapeutics. Register here and use code 12259PHD for 10% off.

Bacteriophage Summit 2019

Promotion

The American Society for Microbiology will host ASM Microbe 2019 in San Francisco June 20-24, and the abstract submission deadline is Jan. 15, 2019—submit yours here!

ConferenceMicrobiology

Did you know ASM has a phage group called Division M?. Members are invited to attend Division M’s Business Meeting on June 21 at 5 PM (at ASM Microbe 2019) for food, drinks and (phage) conversation!

CommunityMeetup

Not one but TWO interesting new phage methods papers have just been published by KU Leuven researchers. The first, by Hanne Hendrix et al. details how to screen for growth-inhibitory proteins made by phages. The second, by Jeroen De Smet et al. shows how to identify phage-host protein interactions.

MethodsPhage Research
2018-12-21

The Center for Innovative Phage Applications and Therapeutics (IPATH) at the University of California, San Diego is seeking a postdoctoral fellow to investigate the effects of phages in altering the human microbiome and in combating pathogens. The work will be performed under the mentorship of Dr. David Pride, MD, PhD.

Postdoc
2018-12-21Expiring Soon

The lab of Ignacio Mir-Sanchis at Umeå University in Sweden has two funded postdoctoral positions open. Both positions will focus on gene expression and replication of Staphylococcal mobile genetic elements (including phages!). Apply here by Jan. 31, 2019.

Postdoc
2018-12-21

Edze Westra of the University of Exeter has an upcoming postdoctoral position that will focus on virus communication systems. The project will involve collaboration with Rotem Sorek, Angus Buckling, Kai Papenfort and Sylvain Gandon. Contact Dr. Westra for details!

Postdoc
2018-11-30Expiring Soon

Ellie Jameson, Andrew Millard and Freya Harrison have an opening for a co-supervised PhD student to work on the potential of natural phage communities in biofilm degradation at the University of Warwick. Apply by Jan. 31, 2019.

PhD
2018-11-30

The University of Massachusetts Medical School has an opening for a tenure-track assistant professor position in virology. Apply by May 13, 2019.

Tenure-trackAssistant Prof

Community Board

Have a question or request for the phage community? Post it here and reach > 200 phage enthusiasts spanning academia, industry, medicine, and beyond. Feel free to be creative about what you might ask! (e.g. collaborations, advice, seeking opportunities)

Have a question or request for the phage community? Post it here and reach > 200 phage enthusiasts spanning academia, industry, medicine, and beyond. Feel free to be creative about what you might ask! (e.g. collaborations, advice, seeking opportunities)

Phage Request2018-12-31

Citrobacter phages for a sea turtle

On New Year’s Eve, we got a request for Citrobacter phages to treat a sea turtle’s antibiotic-resistant shell infection. If you can help, please email [email protected]!

THANK YOU to the labs of @GroseLab of BYU, @RandallJDeJong and @insectmicrobejr of Calvin College, @phage4lyfe of MSU, @BryanGibb2 of NYIT, and Ben Chan of Yale for offering to supply/test phages so far!

Thanks also to @chngin_the_wrld and @phagehunter of @ipath_ucsd for helping coordinate efforts!

Lastly, thanks to the 200+ people on Twitter who’ve helped spread the word about this turtle to 20,000+ people and counting!

Phage TherapyVeterinary Medicine

New reporting standards for uncultivated virus genomes

Many of you have probably published a genome sequence for a new phage you’ve isolated. But huge numbers of genome sequences for viruses that haven’t yet been cultured are now being generated. This is thanks to the field of viral metagenomics, where DNA of all viruses in an environmental sample is analyzed at once.

Last week, we announced the publication of a new set of reporting standards for uncultivated viral genome (UViG) sequences. They’re called MIUViG standards (Minimum Information for Uncultivated Virus Genomes).

This week, we’re shining light on what these standards are, how they came to be, and why we should all take note.

What’s an uncultivated viral genome?

A genome sequence of a virus that’s never been propagated in the lab. Thanks to metagenomics and metatranscriptomics, more and more of these sequences are coming in.

How many uncultivated viral genome sequences have been collected?

Apparently, about 750,000 in the last 2 years alone. This is 5x higher than the number of genomes from viruses that HAVE been cultivated. Uncultivated viruses actually account for 95% of the viral genome sequence diversity in public databases.

What can these sequences tell us?

Understanding the diversity of viruses on our planet (most of which are probably phages) can tell us a lot about ecosystems and the roles of microbes within them.

Why do uncultivated viral genomes need (their own set of) standards?

If everyone used the same reporting standards, viruses found in different places, with different techniques, and by different people, could be compared more easily. This would allow much more information to be extracted from the massive amount of data being collected around the world.

Current standards for metadata reporting for other kinds of genomes, which are maintained by the Genomic Standards Consortium, don’t quite work for uncultivated viruses.

Uncultivated viruses are so much more diverse than other organisms, and their identification depends on computational methods. This means that the completeness and quality of their genomes, their taxonomy and their ecology each need to be evaluated in a way that takes these unique aspects into account.

Who made the new set of standards?

This was a joint effort by government and academic researchers in 15 countries (US, UK, Netherlands, Canada, France, Belgium, South Africa, Egypt, Germany, Australia, Japan, Spain, Austria, Colombia and Switzerland). The effort was led by the US Department of Energy Joint Genome Institute.

What needs to be reported?

Mandatory information* includes:

  • Source (type of dataset)
  • Genome assembly software
  • Virus identification software (tool you used to determine that the sequence was viral)
  • Predicted genome type and structure
  • Detection type
  • Number of contigs
  • Assembly quality (see below)

*The reasons why this info is so important for uncultivated viruses, as well as instructions on how to do these analyses, are clearly detailed in the MIUViG standards paper.

Three new classifications for genome quality

  • Genome fragments: fragments <90 percent complete, no estimated genome size, minimal annotation
  • High-quality draft genome: >90 % of the complete expected genome sequence, gaps span mostly repetitive regions
  • Finished genome: complete genome, single contiguous sequence, no gaps, extensive annotation

Are you avoiding these pitfalls?

  • Misidentification of a cellular sequence as viral
  • Partial genomes assembled as circular contigs
  • Errors in gene prediction
  • Inaccurate functional annotation
  • Clustering of partial genomes
  • Taxonomic classification
  • Read mapping from nonquantitative datasets

Where should you submit your data?

Submit your sequence and metadata to any International Nucleotide Sequence Database Collaboration (INSDC) member database, such as:

Other interesting tidbits

If you’d like to learn more, please read the paper (open access) by Roux et al., which was our main source for this issue.

Thanks for reading!
– Jessica <>={

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology

Stay updated on phage research, phage therapy, and phage jobs by getting Capsid & Tail every week!

Have an idea for a story, news to share, or wanting to write an opinion piece? Get in touch at [email protected] or tweet @phagedirectory

For every issue of Capsid & Tail, we are committed to getting our facts straight, but we’re not experts in the information we’re bringing to you. If you feel that we’ve missed an important viewpoint, or if you have something to add, please reach out to us by emailing [email protected]. We’d love to hear from you, and we’d be happy to revisit topics we’ve covered (ideally with added information and viewpoints from community members like you!).

Lastly, please reach out if you’re interested in writing for us, or have suggestions for future issues!