USCCN response: Genome sequences of bacteria should not qualify as type material

27 Feb USCCN response: Genome sequences of bacteria should not qualify as type material

Response to the Proposals for ICNP Changes by Whitman (2016, 2019)
Compiled by the US Culture Collection Network
24 February 2020

Co-authors of the response document:
Kyria Boundy-Mills, Executive Board, World Federation of Culture Collections; Steering Committee, US Culture Collection Network; Curator, Phaff Yeast Culture Collection, University of California Davis
Marco A. Riojas, Scientist, ATCC/BEI Resources
Manzour H. Hazbón, Senior Scientist, ATCC/BEI Resources
C.M. Lucy Joseph, Curator, UC Davis, Department of Viticulture and Enology Culture Collection
George M. Garrity, Michigan State University and NamesforLife, LLC
Ulrich Nübel, Leibniz Institute DSMZ, Germany

Background
Starting March 1, the International Committee on Systematics of Prokaryotes will vote on a proposed amendment to the International Code of Nomenclature of Prokaryotes to allow genome sequences to serve as type material, which will allow uncultured organisms to be formally named. (https://www.ncbi.nlm.nih.gov/pubmed/26902077).

The US Culture Collection Network (usccn.org) has served the communication needs of the US culture collection community since 2012, filling the role vacated when the US Federation of Culture Collections became inactive about 10 years ago. US collections have gathered at several USCCN workshops and symposia, visited each others’ collections, advocated for the interests of biological collections and their users, and co-authored numerous peer-reviewed publications educating the scientific community about collections.

Because the proposed change would impact US culture collections and their users, a virtual USCCN meeting was held 24 February 2020 to formulate a position statement regarding the Whitman proposals. The 21 participants included personnel of US and European culture collections and experts in nomenclature and taxonomy. Several additional interested parties submitted statements by email. This document summarizes the findings.

Nomenclature is a crucial tool used for communication in the basic sciences, as well as in applied fields such as medicine, food safety, biosecurity, agriculture, intellectual property, and others. Stability in nomenclature is essential to serve the needs of all these communities.

Findings

1. Benefits
   • Benefits of the proposals to US culture collections are minimal, and could possibly include:
   • It would be easier for collections to publish descriptions of new species. However, as they already preserve living organisms, this benefit would be minimal.
   • Culture collections could become repositories of DNA sequence data information. Again, this benefit would be minimal, because collections already preserve living organisms, and several also already are repositories of DNA sequence data.
2. Weaknesses
   • A number of serious concerns arose in the conversation. The primary concerns regard the purpose and strategy of the proposals.
   • General Consideration 4 and Principle 1 of the ICNP specifically restrict the ICNP to the formation and application of names to prokaryotes (with the current exclusion of the Cyanobacteria). It guarantees freedom of taxonomic thought, without which the field cannot adapt and advance to keep pace with our knowledge of prokaryotes. The current proposals by Whitman intermingle nomenclature with taxonomy in such a way as to clearly violate both General Consideration 4 and Principle 1. In other words, the ICNP applies to nomenclature; the proposed changes conflate taxonomy with nomenclature.
   • DNA sequence is a measurement, not a specimen. Taxonomic principles and technologies developed for prokaryotes tend to also be adopted in eukaryotic taxonomy, such as ribosomal sequencing, molecular phylogeny, etc. Similar recent proposals in other codes of nomenclature (zoological and algae, fungi and plants) have not been supported for numerous reasons echoed here. For example, a similar ICN change proposed at the International Commission on the Taxonomy of Fungi nomenclature session at the International Mycological Congress in Puerto Rico in 2018 was not supported because a DNA sequence is not a physical specimen.
   • Species concepts have evolved over many decades. A tradition of using polyphasic taxonomy has developed to capture multiple criteria for circumscribing species, for example detailing an organism’s morphology (morphological species concept), physiological characteristics and DNA sequences (phylogenetic species concept) and whether a group of organisms is reproductively isolated (biological species concept). Defining a species based only on DNA sequence relies on a single species concept, which is less robust than a polyphasic approach and also contravenes General Consideration 1 and Principle 1 (4).
   • The quantity and quality of DNA sequence that could serve as type is too broadly described in the proposal, and could include anything from small amplicons to metagenome sequences. Professional curation standards of the dataset are not detailed.
   • A type specimen must be permanent. Serious issues were identified with stability, quality, and availability of genome sequence data.
     • Many sequences have been deposited that are attributed to the wrong organism.
     • Some DNA sequences are not available to the scientific community.
     • DNA sequences deposited in GenBank are not permanent: many have been modified or removed.
     • Quality control standards for genome sequences are not specified in the proposal and vary greatly.
     • The genome sequence can differ dramatically based upon which assembly method is used.
     • Accepting genome sequences that cannot be replicated from a living type strain presents a temptation for unscrupulous researchers to invent fraudulent sequences simply for the purpose of making their mark in nomenclature.

Detrimental Effects

• The detrimental effects of this proposal on US culture collections, their users, and science as a whole include:
• Type specimens are required because they constitute material for future research. Culture collections currently fill this critical need by providing such material. If the current proposal is adopted, users of collections would not have access to the living materials required to reproduce or extend characterization of organisms for research.
• The proposed taxonomy change impacts users of collections and nomenclature in the medical, food safety, biosecurity and many other fields. Regulatory agencies such as FDA, USDA, and EPA, intellectual property offices, and health insurance providers refer to specific species. Without type strains or other authenticated reference strains that are available for testing, quality control and validation, replicability is lost; without replicability, expanding knowledge of species in these fields is lost.
• Funding agencies such as NSF and the Department of Energy require that attribution and provenance of data generated by end users are recorded. Removing the requirement to preserve living type organisms can lead to problems with data use and public release of data, such as the data policies implemented by the Department of Energy, one of the major contributors of genome sequence data in the world.

Recommendations

• The proposed changes should not be adopted at this time. At the very least, the currently recommended changes should be tabled until additional proposed changes are made that address the serious flaws in the current proposed implementation, and all these changes should be evaluated in total.
• The ICSP should be more proactive about reaching out to stakeholders who may be affected to inform them when proposals are being brought to an official vote. Parties impacted by future proposed changes such as US culture collections and clinical and microbiological societies should be contacted in a timely manner so they can be more involved in future discussions.
• A broader range of parties impacted by changes to Candidatus species should be involved in discussions of changes in nomenclature.
• Rather than creating unnecessary disruption of the nomenclatural system, increased support and greater emphasis should be placed on development of methods for culturing, characterizing, and preserving currently unculturable and fastidious organisms.
• Specimens containing uncultured organisms should be preserved and made available to the scientific community. Appropriate support is needed to allow professionally managed collections to preserve mixed communities, and fastidious organisms, such as obligate symbionts within their host. It may be useful to consider a future proposal for amendment of the ICNP to allowing nomenclatural recognition of organisms in currently unrecognized formats (e.g. in vivo in animal models).

Summary circulated to ICNP community
(500 word limit)
Compiled by Marco Riojas, ATCC

The USCCN has identified numerous serious concerns regarding the proposed changes to the ICNP currently under consideration, particularly with respect to their purpose and strategy.

1. • General Consideration 4 and Principle 1 specifically restrict the ICNP to the formation and application of names to prokaryotes, guaranteeing freedom of taxonomic thought. The current proposals by Whitman intermingle nomenclature with taxonomy in such a way as to clearly violate both General Consideration 4 and Principle 1.
   • Recent similar proposals in the nomenclatural codes governing animals, algae, fungi, and plants have not been supported for numerous reasons, many equally applicable to prokaryotic nomenclature as well.
   • Serious issues exist with the proposed use of gene sequence data.
     • Many sequences have been deposited that are attributed to the wrong organism.
     • Deposited DNA sequences are not permanent: many have been modified or removed.
     • Genome sequence can differ dramatically based upon which assembly method is used.
     • Accepting gene sequences that cannot be replicated from a living type strain presents temptation for unscrupulous researchers to invent fraudulent sequences.

The current proposals would have many detrimental effects on US culture collections, their users, and science as a whole, including:

• Eliminating access to the living materials required to reproduce or extend characterization of organisms. Culture collections currently fill this critical need by providing such material.
• The proposed changes impact users of collections and nomenclature in the medical, food safety, biosecurity, and many other fields.
• Funding agencies such as NSF and DoE require attribution and provenance of data generated by users. Removing the requirement to preserve living type organisms can lead to problems with use and public release of data, e.g. data policies implemented by DoE, one of the major generators of genome sequence data in the world.

The USCCN recommends several actions regarding the current proposed changes and the overall process:

• The proposed changes should not be adopted at this time. At the very least, the currently recommended changes should be tabled until additional proposed changes are made that address the serious flaws in the current proposed implementation, and all these changes should be evaluated as a whole.
• The ICSP should be more proactive about reaching out to potentially affected stakeholders to inform them when proposals are being brought to an official vote. Parties (e.g., culture collections and clinical and microbiological societies) impacted by future proposed changes should be contacted in a timely manner so they can be more involved in discussions.
• Rather than creating unnecessary disruption of the nomenclatural system, greater emphasis should be placed on developing methods for culturing, characterization, and preservation of currently unculturable and fastidious organisms.
• Specimens containing uncultured organisms should be preserved and made available to the scientific community. Professionally managed collections could preserve fastidious organisms, such as obligate symbionts within their host. It may be useful to consider a future proposal for amendment of the ICNP to allowing nomenclatural recognition of organisms in currently unrecognized formats (e.g., in vivo in animal models).