SeqCode: naming prokaryotes from genome sequence data
Guests Marike Palmer and Miguel Rodriguez join hosts Lee Katz and Nabil-Fareed Alikhan to discuss SeqCode, a nomenclatural code that uses sequence data to name prokaryotes. They explain its relationship with the existing culture-based code, its genome quality requirements and disagreements over mass naming. The discussion shows why stable names matter for research and regulation, while distinguishing naming from the work of cultivating and understanding organisms.
In this episode
Why a parallel nomenclatural code?
SeqCode provides rules for naming prokaryotes using sequence data as nomenclatural types. The guests contrast this with the ICNP, which, as described in the episode, requires pure cultures deposited in two culture collections. A 2020 roadmap paper in Nature Microbiology outlined two routes: change the existing code to accept sequence data, or establish a parallel code.
Proposals to modify the ICNP were published in 2015 and 2016, but the International Committee on Systematics of Prokaryotes voted against the change in 2020. SeqCode followed further community workshops involving over 800 registrants from 42 countries. The guests emphasise compatibility rather than competition: cultivation remains valuable for physiology, and a future merger of the codes is an aspiration.
Governance and routes to registration
SeqCode has an executive board, committees and working groups, with elected and co-opted positions. The International Society for Microbial Ecology provides umbrella support, including hosting voting and discussion opportunities. Joining the SeqCode community does not require ISME membership.
The guests describe three validation routes. Their preferred route involves authors working with registry curators on names, descriptions and etymology while preparing a manuscript. A second allows registration after publication. A third, prospective route would coordinate nomenclatural review with partner journals’ manuscript review. SeqCode is not tied to one journal: a peer-reviewed manuscript in any journal can support registration, provided the naming and genome quality requirements are met.
The debate over naming 65,000 taxa
Miguel Rodriguez discusses a separate paper with Mark Pallen and Nabil-Fareed Alikhan proposing arbitrarily formed names for 65,000 taxa. At the time of recording, SeqCode required distinguishable linguistic roots, meaning many of those names could not be validated under it. Rodriguez argues that pronounceable invented words can be easier to remember than alphanumeric identifiers; OP9 and SAR11 also appear in the discussion as examples of identifier-based naming.
Marike Palmer outlines objections to mass naming without presenting every objection as her own position. These include naming organisms from other researchers’ data before their studies are complete, the memorability of meaningful names, and whether names should follow active investigation. Alikhan stresses that their proposed names were not intended to claim priority over better names supplied by researchers studying those organisms.
What genome quality is required?
The starting thresholds discussed are more than 90% genome completeness and less than 5% contamination. A 16S rRNA gene sequence alone is not accepted as a nomenclatural type. Including 16S is recommended, rather than compulsory, because it helps connect genome-based and 16S-based taxonomies.
Palmer explains that recovering the correct 16S sequence from a metagenome-assembled genome can be difficult. Making it mandatory could encourage authors to attach an incorrect sequence. Quality standards sit in an appendix and can be reviewed. Smaller sets of housekeeping genes are discussed only as a possible future option for difficult organisms, such as obligate intracellular parasites—not an accepted alternative at the time.
When completeness estimates are misleading
Rodriguez names CheckM, CheckM2 and MiGA when discussing estimates based on conserved genes. Such estimates can be problematic for deep-branching CPR organisms, endosymbionts with reduced genomes, and cells containing numerous non-identical chromosomes. He gives the striking example of an apparent 1,000% contamination estimate for a biologically valid genome representation.
Registry submissions still require completeness and contamination estimates. However, authors can explain why those estimates may be unsuitable for their organism. Curators can consider smaller exceptions, while substantial questions may go to the Reconciliation Commission and Standards Working Group. The approach combines conservative entry requirements with a mechanism for reviewing biological exceptions.
Stable names and recognisable records
The guests argue that regulated names for uncultivated organisms can help agencies refer consistently and uniquely to taxa with clinical or environmental significance. They also note that pathovars, serovars and biovars are not regulated by either SeqCode or the ICNP, although regulatory agencies already use genomic information to define relevant groups.
SeqCode assigns accession numbers to registered lists containing one or more names and encourages authors to report them in publications. In ordinary use, a SeqCode name remains an italicised Latin or Latinised binomial. For formal references to nomenclatural types, Rodriguez describes a superscript capital TS, distinguishing it from the capital T used under the ICNP.
Highlights
- 00:01:39 — The community effort behind SeqCode and the need to name uncultivated organisms
- 00:05:05 — Governance, voting membership and elected versus co-opted positions
- 00:09:44 — Three routes for validating names through the SeqCode registry
- 00:18:00 — Plan A: modifying the existing culture-based nomenclatural code
- 00:19:29 — The proposals, the 2020 rejection and subsequent community workshops
- 00:24:20 — A separate proposal for arbitrarily formed names for 65,000 taxa
- 00:26:01 — Objections to mass naming using other researchers’ data
- 00:33:44 — Genome quality thresholds and the standards working group
- 00:37:00 — Why completeness and contamination estimates fail for some taxa
- 00:38:33 — Reporting quality estimates and explaining exceptions to curators
- 00:40:09 — Stable names for uncultivated taxa with regulatory significance
- 00:42:30 — Accession numbers for registered lists in publications
In their own words
And that’s why we aimed for trying to keep that compatibility between the codes as far as we could.
— Marike Palmer, 00:15:42
Who is talking
- Lee Katz (host)
- Nabil-Fareed Alikhan (host)
- Marike Palmer (guest, School of Life Sciences, University of Nevada Las Vegas)
- Miguel Rodriguez (guest, University of Innsbruck, Departments of Microbiology and the Digital Science Center (DiSC))
Also mentioned: Mark Pallen.
Tools and resources mentioned
SeqCode registry, CheckM, CheckM2, MiGA.
Questions this episode answers
Does SeqCode replace the ICNP?
No. The guests describe it as a parallel code designed to remain compatible with the ICNP. They support continued cultivation efforts and hope the systems might eventually merge.
Can a prokaryote be named under SeqCode using only 16S?
Not under the requirements discussed in this episode. SeqCode requires a high-quality genome; 16S is recommended within it but is not compulsory.
What are SeqCode’s genome quality thresholds?
The episode gives thresholds of more than 90% completeness and less than 5% contamination. Authors must submit estimates, but can explain limitations or unusual biology for curator review.
Are arbitrarily formed names accepted by SeqCode?
At the time of recording, names required distinguishable linguistic roots. Many names in the discussed 65,000-taxon proposal therefore could not be validated without a change to the code.
This page was written from a machine transcript of the episode and checked against it. Listen to the episode for the whole conversation.
Show notes
We are back talking about systematics, and SeqCode; a nomenclatural code for prokaryotes described from sequence data. Marike Palmer is a Postdoctoral researcher in the School of Life Sciences at the University of Nevada Las Vegas and Miguel Rodriguez is an Assistant Professor of Bioinformatics at the University of Innsbruck in the departments of Microbiology and the Digital Science Center (DiSC).
Link to paper: https://www.nature.com/articles/s41564-022-01214-9 History paper: https://www.sciencedirect.com/science/article/pii/S0723202022000121
They discussed the SeqCode, a nomenclature code for Prokaryotes described from sequence data. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer explained that the impetus for the SeqCode was the need to accommodate previously uncultivated organisms under a specific nomenclature code. She emphasized that the SeqCode was written to allow any peer-reviewed publication, but noted that the authors have designed three paths of validation in the SeqCode. They hope that anyone proposing a name will work with the curriculum team to ensure the best quality descriptions, names, etymology, and solidification.
Rodriguez discussed the SeqCode’s governance, which is already in place, and they have made them public so that anyone interested can join the SeqCode community. The governance structure comprises an executive board, committees, and working groups. The position’s co-opted members hold some of the committees of these committees, while some are chosen by ballot.
The hosts sought to clarify the relationship between the Isme Society, which is backing the SeqCode, and the wider field in general. Rodriguez explained that ISME is simply providing support as an umbrella organization for the SeqCode.
Palmer and Rodriguez clarified that the SeqCode is not a competing code but rather a parallel one that aims to accommodate previously uncultivated organisms. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer noted that most scientists culture prokaryotes not for naming but to advance their knowledge of these organisms through physiology experiments. They emphasized that the new system is the result of a long collaborative effort that involved many different viewpoints and philosophies.
The episode also discussed the practical requirements for naming under the new system, which include standards for the completeness and contamination levels required in the genome sequence data. Palmer noted that while the 16S rRNA gene sequence was not required for naming, it was recommended for improved accuracy in cross-talk between different taxonomies. The conversation highlighted the importance and challenges of naming microorganisms and the ongoing efforts to create a system that is inclusive of all microorganisms, both cultivated and uncultivated.
Rodriguez and Palmer also discussed the SeqCode, a nature code for naming prokaryotes described from sequence data. They agreed that high-quality genomes should be the main control types to ensure the system builds up rather than breaks down. They noted the challenge of obtaining full genomes of some organisms, such as obligate intracellular parasites but suggested obtaining housekeeping genes as a potential solution. They further explained the technical issue of estimating completeness or contamination for many taxa, but Palmer confirmed that registering a name on the SeqCode registry requires adding such estimates.
It emphasized the importance of collaboration within the scientific community and the need to create a system that is inclusive of all microorganisms. It also highlighted the challenges inherent in the process of naming microorganisms but demonstrated that it is an ongoing process, and that scientists are working to create a system that is accurate, practical, and beneficial for all.