Issue 11 | January 3, 2019
6 min read

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

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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

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Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

The community board is empty this week. Be the first to post something for next week!

New reporting standards for uncultivated viral genomes

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Phage microbiologist and co-founder of Phage Directory

Co-founder

Phage Directory, Atlanta, GA, United States

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

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

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 <>={

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