International consortium offers guidelines, best practices for characterizing uncultivated viruses

December 17, 2018, Lawrence Berkeley National Laboratory
Credit: CC0 Public Domain

Microbes in, on and around the planet are said to outnumber the stars in the Milky Way Galaxy. The total number of viruses is expected to vastly exceed even that calculation.

While many viruses remain unknown and uncultivated, advances in and analyses have allowed researchers to identify more than 750,000 uncultivated virus genomes from metagenomic and metatranscriptomic data sets. In IMG/VR, a database for virus sequences established and maintained by researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, the viral diversity available has tripled within a single year.

As more and more researchers continue to assemble new genome sequences of uncultivated viruses, JGI researchers led a community effort to develop guidelines and best practices for defining virus data quality. In a report published December 17, 2018, in Nature Biotechnology, JGI partnered with a number of virus experts; as well as representatives from the Genomic Standards Consortium (GSC), an open-membership working body that engages the in the standards development process; and the International Committee on Taxonomy of Viruses, the premier authority on the official taxonomy of viruses which is currently re-evaluating virus classification based on sequence-based information.

Guidelines for Quality and Analyses

"Viruses are critical components of every microbial ecosystem. The JGI is especially interested in developing standards for virus genomes because we generate much of these data ourselves," said JGI research scientist and first author Simon Roux. "We are part of a small group of researchers who have scrutinized these data at length, have seen the metrics, and can provide guidance to help determine data quality. Additionally, in this paper, we've tried to provide not just standards, but also outline what type of analyses can be performed on these data, to help researchers who want to characterize their own novel viruses."

Cultured viruses already have their own data quality standards, but these cannot be directly applied to uncultured viruses, whose sequences are often incomplete and for which some properties can only be predicted indirectly using computational approaches.

"The uncultivated virus genome community has come together to define what is important to report and valuable to the research community," said GSC President Lynn Schriml of the Institute of Genome Sciences at University of Maryland School of Medicine. The GSC includes representatives from the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute, and the DNA Data Bank of Japan (DDBJ), who also collaborated on this article.

Categories of Virus Genome Quality

In the paper, Roux and his colleagues outlined the minimum amount of information for an uncultivated virus genome, including the source, methods of identification of the virus genome, and data quality. The JGI has previously developed standards for the minimum metadata to be reported with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases.

"The tremendous growth of virus sequence data, and microbiome data in general, necessitates robust standards and data quality metrics to allow the research community to leverage this data for comparative analyses," said JGI Metagenome Program head and study senior author Emiley Eloe-Fadrosh. "By establishing and promoting ',' the research community has the opportunity to break down barriers of data accessibility and reusability, thereby amplifying the research beyond the initial project scope."

The team proposed three categories of genome quality. "Genome fragments" are comprised of single or multiple fragments that are predicted to be less than 90 percent complete, or have no estimated genome size, and are minimally annotated. A "high-quality draft genome" is estimated to represent 90 percent or more of the complete expected genome sequence, in fragment(s) where any gaps span mostly repetitive regions. Finally, a "finished genome" would include both a complete genome comprised of a single contiguous sequence without gaps, and extensive annotation.

"If you're going to build a standard," Schriml noted, "it is essential to discuss what should be represented with the research community, taxonomists and database providers and to integrate these data needs into the standard." Schriml added journals have also started endorsing the application of the GSC's "Minimum Information about any (X) Sequence (MIxS)" guidelines, the umbrella under which the uncultivated standards and other similar community efforts reside. The GSC tracks the adoption of these standards developed over the past decade using records uploaded to the BioSample database. These records reflect individual samples collected, sequenced and annotated, and Schriml said that nearly 450,000 BioSample records currently reference MIxS guidelines, up from 326,000 records tracked in the spring.

Explore further: Defining standards for genomes from uncultivated microorganisms

More information: Minimum Information about an Uncultivated Virus Genome (MIUViG) Nature Biotechnology (2018). DOI: 10.1038/nbt.4306

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Osiris1
1 / 5 (1) Dec 17, 2018
"In, on, and around the planet"

Ah, an admission that life exists OFF of our world and not OF this world, probably EVER! The sequencing of this life will be a VERY interesting item! Evolution is ever happening and is not really at cross purposes of reasonable religions which ALWAYS have to change with existing conditions.

Most curious am I to find inklings as to how adaptive life really IS. Life as we do not or maybe ever knew it will be the order of the day. And not the ordure of the era as extreme religionists are wont to describe any deviation of 'doctrine'. Suspect 'other' members of the unit cell of the DNA triad of proteins.....other proteins of life's programming' ... will be found. Such life of course may be very different than we expect and use completely different programmed temperature and chemical tolerances.

May find that life can be virtually ....ANYWHERE. Our explorers will need to be 'decon' cleaned after even 'spacewalks' near Mars
Osiris1
1 / 5 (1) Dec 17, 2018
This is not to espouse agnosticism or atheism. GOD DOES exist, just not as radical protestants know Him. The late philosopher Catholic Priest Fr. Al McKnight and his Afrocentric view of humanity, which is really PanHumanic, bespoke all humans as 'Sparks of GOD'. I would say in extension that ALL sentient life are CELLs of GOD. EACH soul as a CELL. Cannot overemphasize this whether this idea is palatable to our human +or- 5std deviation extremes or not. In the world of multi-verses, multidimensional physics and many 6-D subsets of the same, malleable time and space, GOD and Heaven are not only possible but certain. We have no monopoly on this entity which probably does not have a 'sex' as we know Him who is an infinite construct all the souls in the universe. The Jews are right when they say in each prayer... 'King of the Universe'.
rrwillsj
not rated yet Dec 17, 2018
O old boy. Find me any evidence of life surviving on the Antarctic High Plateau Deserts.

We could have it for dessert!

As a materialist atheist, I am denying the validity of any & all of the tens of thousands of theologies & superstitions that afflict Mankind.

To say I disbelieve in a supernatural deity would be ridiculous. How could I ever prove or disprove such an assertion?
That doesn't make your belief system any less wrong.

Besides, the brat-deity keeps gurgling at me. It'll be hundreds of billions of years before it is mature enough to hold up it's end of an intelligent conversation.

Our bad luck to be "sooners" on one of the first mature Living Worlds.

Well, considering the effort we all are putting into screwing up this Biosphere? Our legacy is to be the classic "bad example" in the museums of future alien inhabited worlds.

I guess that'd be better than just going extinct without anyone else ever noticing our miserable ending?
torbjorn_b_g_larsson
5 / 5 (1) Dec 19, 2018
an admission that life exists OFF of our world


Please provide a reference exactly where a paper on "a community effort to develop guidelines and best practices for defining virus data quality" from observations describe viruses outside of GEO (since ISS and other non-sterile satellites carry virus remnants), or where they define viruses as "life" as most microbiologists do not.

If life had been observed elsewhere, it had been big news. Presumably the article somewhat fuzzily refer to wind carried viruses that permeate the atmosphere (or viruses carried by the technical artifacts I note above).

The rest is commentary based on humbug superstition instead of biology. And no, we now know 'gods' do not exist. It used to be no supporting evidence so not a fact, but recently we have observed the universe as a system and that it is 100 % mechanistic without anything else ever affecting it [see the robust and complete 3d data release in the Planck Legacy Archive].

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