Validation Request: Proposal to Grant an Exception under Rule 18a in Order to Validate the name ‘Omnitrophus fodinae’ #2
Replies: 9 comments 4 replies
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If this becomes the type material for this phyla, then it's low quality will continue to be propagated. From my understanding, even if a higher quality genome is generate in future, or it is even isolated, this genome will remain the type. My opinion is that while clearly an important taxa, an exception should not be made, although the name should have priority if someone else attempts to validate the name through the SeqCode. This would help reduce confusion of multiple names for a single taxa under the SeqCode, while retaining the standards. |
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Please note that this option is not consistent with the SeqCode (or any other code of nomenclature). The rules of priority are determined on the basis of validly published names, and the valid publication of names depends on the establishment of nomenclatural types. If the nomenclatural type (genome sequence) is not accepted, the species name cannot be considered validly published, and it therefore cannot be granted priority. The same applies to the phylum name: If the type genus is not validly published (due to the type species not being validly published), it cannot be used as nomenclatural type, and the phylum name has no priority. Under potential outcome A, the phylum will most likely be named after some other genus. Under potential outcome B, the name will be retained and priority respected, and the genome will be established as the permanent type for the species. |
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The main question here is whether the standard should be a fixed (and to some degree, arbitrary) threshold or if it should be accommodated on a case-by-case basis, if adequately justified. In fact, the SeqCode leaves open the possibility for standards to be lowered if the author justifies it appropriately (Appendix 1, comment b) |
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If this becomes the type material for this phyla... raw reads need to be provided. |
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I have mapped reads on existing assembly average depth looks good - 1323 from |
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Please keep in mind that this is a single-cell amplified genome (SAG), and the read coverage is expected to vary considerably, even within a contig, due to the MDA amplification. |
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I think this is an excellent example of why Rule 18a was worded in the way it is i.e. to allow a pragmatic (but not unregulated approach) to the typification of some taxa. Given the evidence presented that the sequence, whilst below the normal standard for QC, can serve as type (i.e. to unambiguously identify the taxon), then I think the requested exemption should be granted to ensure stability in nomenclature. However I must admit I am not expert in matters relating to sequence QC! |
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Thank you to all of you who have contributed to the discussion thus far. In my personal view (and in no official capacity here), there are several important things to keep in mind pertaining to this discussion (and potentially to future discussions similar to this one). i) If this name with the originally specified type does not get validated, there is no guarantee that the name "Omnitrophota" and those for the other taxonomic ranks will be retained. In fact, as other taxa in this phylum have already been named, with great potential to get validated under the SeqCode (many conform to all QC criteria), strict application of the rules in this case would mean that the name "Omnitrophota" will be "lost" and would have no standing in nomenclature going forward. The phylum name would thus be replaced with an appropriate name derived from the first validated genus name in the phylum and this new name would have standing in nomenclature, not "Omnitrophota". Thus, this would not ensure stability in nomenclature for this phylum as this would effect a name change for this phylum (and potentially lower taxonomic ranks). However, this may be preferable to some people, hence the request for public discussion. ii) Regarding whether the MQ type for this species could be replaced if a better quality genome becomes available - the steering committee considered this during development of the SeqCode, but the purpose of a nomenclatural type is to provide an anchor to the name and a means to unequivocally identify the taxon in the future. Thus, as stated by Riesco, Rule 18c states that if the type is lost or demonstrated to be ambiguous it may be replaced. In my personal opinion, unless the this SAG is shown to be contaminated or ambiguous in some other way, I wouldn't consider it as necessary to replace it in future, but I am personally open to discussion on this point if we came across it in the future. This is not to say that I do not think having a different reference genome (not nomenclatural type) for the taxon would be beneficial if a better quality genome becomes available. So, in my view, for comparative genomics/improved phenotype predictions/genome-enabled cultivation etc., I would support using the better quality genome, even if it isn't the nomenclatural type. But, some people may find having a different genome as type to the one used as a reference genome confusing, and it may not be desirable to some. iii) Regarding whether granting an exception here would lower the quality of all of the genomes used, I personally do not believe that this would be the case, as these exceptions would be considered on a case-by-case basis (when proposed by the contributors). I also only really anticipate this issue for historical names that are widely used in literature, where names were assigned prior to any QC standards, as going forward all new names are expected to be based on HQ genomes, although the SeqCode leaves room for changes if/when required. So the question here becomes whether stability in nomenclature for higher taxonomic ranks widely used in literature and by the scientific community, is more important than a strict application of the rules of the SeqCode - and this remains to be seen based on the community's comments. Thus, under outcome "A. Reject the proposal to validate the name “Omnitrophus fodinae” because there is not enough evidence to support the taxon description.", the phylum name "Omnitrophota" will be replaced with a different phylum name, while under outcome "B. Accept the proposal to validate the name “Omnitrophus fodinae” based on the medium-quality draft genome.", a medium-quality SAG will serve as nomenclatural type for this taxon (but could open the door for more historical name exceptions), and would be unlikely to be replaced with a better genome in my opinion. |
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When reading the proposal, I became curious about the experimental basis for the % completion. Is it possible that this parameter is underestimated? As I understand it, many of the other characterized genomes in this phylum are small, and the cells are also believed be small. If this is true, are the current methods to estimate the % coverage reliable for this cell type? Aren't these methods based on the experience with cultured organisms, which are often much larger? |
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I can expand a little on this in a personal capacity, as one of the authors on the Seymour et al., 2023 paper (https://doi.org/10.1038/s41564-022-01319-1). We did try various different approaches to estimate completeness, including both CheckM versions (CheckM2 uses machine learning to accommodate taxa with systematically reduced genomes) and a custom "Omnitrophota"-specific marker set for CheckM1, and the automated Registry estimates are done in MiGA. However, all these different approaches consistently delivered estimates of ~70% completeness or below. But as you stated, we also show that "Omnitrophota" genomes are reduced despite relatively complete metabolic pathways being encoded by these genomes. So, yes, it is still possible that despite our best efforts, we are still not in a position to have an accurate completeness estimate, and we probably wouldn't have one (or a better idea of its accuracy) until we have a genome of this species that have been assembled to replicon level, or at least several genomes that are closer related to this species than what we have currently. But for the moment, these estimates are the best we can do. |
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It's great to see diverse viewpoints here, but in my opinion this is exactly why Rule 18a allows exceptions. We should strive for stability in nomenclature (see Principle 1 of SeqCode (https://disc-genomics.uibk.ac.at/seqcode/page/seqcode) and ICNP (https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000778)). The only reason this exception was requested is to retain the phylum name Omnitrophota because it is well known. As summarized above, this phylum name or close derivatives appears in 33 titles or abstracts, but in fact many more papers use this phylum name. As stated by Marike Palmer above, if an exception is not granted, then a different type genus would be selected from Seymour et al., 2023 (https://doi.org/10.1038/s41564-022-01319-1; assuming these names are validated). Most likely the phylum name would be changed based on the genus Velamenicoccus as the nomenclatural type, because there is a complete genome and a very good study, although the name has orthographic problems (Kizina et al., 2022; https://journals.asm.org/doi/10.1128/aem.02407-21). A decision to change the name would be antithetical to Principle 1 and be confusing and frustrating for the scientific community. As described above, the genome of Omnitrophus fodinae is not a low-quality genome and it is suitable for comparative studies to recognize the taxon. In the future, when better genomes are obtained from this genus and/or species, they can be used as references. My hope is that this example is used as a guide for similar exceptions in the future. In full disclosure, I am an author on the Rinke et al., 2013 paper and the Seymour et al., 2023 paper. |
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It appears to me that the strongest argument against the exception so far is the possibility of polluting databases, potentially resulting in error propagation (e.g., as raised by @thh32). I believe this is an important and delicate topic, and it's worth careful consideration. However, I note that:
Given the above reasons, I would consider the risk of error propagation arising from this exception as minimal, and the benefits of accepting this exception much greater than its risks. |
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Request for Decision and Community Discussion
Marike Palmer (@MarikePalmer), Maria Chuvochina (@uqmchuvo), Taylor Priest (@tpriest0), Luis M. Rodriguez-R (@lmrodriguezr)
Validation request: proposal to grant an exception under Rule 18a in order to validate the name ‘Omnitrophus fodinae’
Author/s of the original request: Chris Rinke (1)
Reason for request: type material does not meet the quality standards, but abundant evidence of the species existence and novelty has been accumulated in the literature.
Effective publication: Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). https://doi.org/10.1038/nature12352
Proposed type genome
Single-Cell Amplified Genome GCA_000405945.1 [65.01% Completeness, 0.56% Contamination (CheckM2); 70.8% Completeness, 0.9% Contamination (Automated Registry Estimate by MiGA); Complete 16S rRNA and 23S rRNA genes phylogenetically concordant with other marker genes]
Evidence for taxon and its novelty
In the original publication (Rinke et al., 2013), four SAGs were identified based on a Small Sub-Unit (SSU) ribosomal RNA (rRNA) gene phylogeny as belonging to the candidate grouping OP3, previously identified from rRNA gene sequences (Hugenholtz et al., 1998; Glöckner et al., 2010). Phylogenetic reconstruction based on 38 marker sequences also supported delineation of these four genomes as distinct from other phyla (Rinke et al., 2013), and the highest estimated quality SAG (GCA_000405945.1 = SCGC AAA011-A17) was selected to serve as type for a novel phylum. Since the initial proposal, the novelty of this taxon has further been supported by phylum-level phylogenomics and comparative genomics study (Seymour et al., 2023), where phylogenies inferred from 4 different conserved marker sets, comprising 56 to 120 marker sequences, along with overall genome relatedness indices, Average Nucleotide and Amino Acid Identity (ANI and AAI), support its novelty and its exclusivity of other taxa represented by medium- or high-quality genomes belonging to the phylum (grouping into >200 putative species clusters).
(i) The species can be unambiguously identified using genomic metrics and phylogenetic analyses; (ii) the proposed type genome is a representative genome of the species cluster bearing this name in GTDB; (iii) the publication that introduce this species and its associated phylum name has been cited over thousand times and these names have been used in literature for a decade; (iv) it is the first genomic representative of the phylum.
Classification: ‘Omnitrophus’, ‘Omnitrophaceae’, ‘Omnitrophales’, ‘Omnitrophia’, ‘Omnitrophota’ (syn. ‘Omnitrophica’, OP3)
Submitter comments: “This genome has lower completeness than suggested by standards, but we request lowering of the requirement here, because this is a historical name and allows us to keep the nomenclature for the entire phylum. Despite several attempts at recovering a higher completeness genome from metagenomic data, there has been no other genomes recovered for the genus, thus in order to retain the historical genus through phylum names with the least amount of confusion, we request special consideration for validation with this genome as type.”
Taxon description: “This species is the type of the genus Omnitrophus. No data on cell size in the species is available. This species is represented by only one medium-quality genome, however, for historical significance, this genome serves as the nomenclatural type for the species. The %GC content of the genome is 49.56%. The estimated genome size is 2.9 Mb, with the available genome estimated to be 65 % complete. The genome available for this species encodes 2 very large ORFs with domains typically implicated in eukaryotic cell adhesion. This organism originated from groundwater sampled at Homestake Mine (Sanford Lab Homestake), South Dakota. The nomenclatural type for the species is the genome GCA_000405945.1.”
Historical significance
The effective publication (Rinke et al., 2013) has accrued 1,365 citations at the time of writing, and the derived phylum name “Omnitrophota” (= “Omnitrophica”) is found in the title or the abstract of 33 journal articles (Clarivate Web of Science).
Relevant SeqCode Rules and Recommendations
Rule 18a
“The type of a species or subspecies is a designated DNA sequence that is compliant with the
minimum standards designated by the SeqCode Committee for genome, metagenome-assembled
genome, or single-amplified genome sequences […] Upon recommendations of the SeqCode Committee or subcommittees on the taxonomy of specific groups, the SeqCode Committee may approve other minimal standards as suitable types for specific groups.”
Appendix I, Data quality necessary for completion of SeqCode Registry*
Required
-Type genome assembly quality for MAGs and SAGs: >90% complete and <5% contaminated (modified from Bowers et al., 2017). For isolates, read coverage ≥10x (Field et al., 2008).
-Agreement between genome and 16S rRNA taxonomic assignments
Recommended
* Data quality will be assessed by automated pipelines or other approaches. Exceptions for lower data quality should be justified by authors in the effective publication.
Reconciliation Commission comments
As the effective publication predates any recommended community quality standards, and any recommendations in the SeqCode, no justification for lowering data quality standards was provided in the effective publication. However, justification in the SeqCode Registry was provided. We request opinions from the SeqCode community on whether this taxon name can be validated based on the proposed genome sequence so that the genus name can serve as a nomenclatural type for higher taxonomic ranks including the rank of phylum, thus preserving the historical name for this taxon. Any additional attempts to recover a better quality genome for this species failed (personal communication).
Potential outcomes
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