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The Global Catalogue of Microorganisms lists a bacterium called Achromobacter xerosis which is mentioned in several papers and patents. It once existed in the NCBI taxonomy database, with ID 216898. However, it is no longer there - going to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=216898 just yields a "No result found" page.

Why was this species removed from the NCBI's taxonomy? I haven't managed to find any documentation on why the NCBI would purge a species from their database, nor can I see any obvious reason to do so.

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For whatever it's worth, I queried NCBI support about this and got a reply:

To: info@ncbi.nlm.nih.gov
Subject: Reason for removal of a species from the taxonomy?

Hi,

I notice that the species Achromobacter xerosis used to be listed in the NCBI taxonomy at https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=216898 but no longer is. I haven't been able to track down any documentation hinting at why a species would ever be removed from the taxonomy. Is there any such documentation that I've missed, and are you able to explain why this species in particular was removed?

Thanks in advance for your time,
Mark

Reply:

Dear Mark Amery:
The NCBI Taxonomy database records exist to support data that are in other NCBI databases. A review of the Taxonomy database must have identified that we have no records for which Achromobacter xerosis is designated as the organism name.

regards,
Bonnie L. Maidak, Ph.D.
NCBI Help Desk
DHHS/NIH/NLM/NCBI

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Achromobacter xerosis was proposed in 1954 by Groupé et al. Currently, the genus Achromobacter (revived by Yabuuchi & Yano, 1981) comprises 21 species, but A. xerosis is not among them. It seems that A. xerosis has never been validly published.

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  • $\begingroup$ You've linked to your own website as a source for the claim that Achromobacter consists of 21 species, but I have no idea where I'm supposed to find that information. All I see is a download link for a password-protected PDF that I can't read since I don't have the password. $\endgroup$ – Mark Amery Apr 30 '18 at 19:25
  • $\begingroup$ It's also unclear to me whether the lack of a valid publication is grounds for exclusion of a species from the NCBI taxonomy. As I interpret support.ncbi.nlm.nih.gov/link/portal/28045/28049/Article/1474/…, it seems to suggest that valid names are preferred but that species without valid names may nonetheless be included in the taxonomy. As further evidence of this, note that ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi lists hundreds of species, not just 21! So I don't think that this is the full story. $\endgroup$ – Mark Amery Apr 30 '18 at 19:35
  • $\begingroup$ @MarkAmery: If you hover with your mouse over the picture you will see this text: "Download PDF | Password 1". Alternatively, visit DSMZ: dsmz.de $\endgroup$ – user37894 May 1 '18 at 15:03
  • $\begingroup$ @MarkAmery: It is impossible for a validly published bacterial species not be included, intentionally or inadvertently, in the list of recognized bacterial species for a period of 64 years. Note that a proposal of A. xerosis name is not necessarily a valid publication of the new bacterial species. Search IJSEM for validation lists: if you find A. xerosis, it was validly published; if you don't find it, it was not validly published: ijs.microbiologyresearch.org/content/journal/ijsem $\endgroup$ – user37894 May 1 '18 at 15:10
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    $\begingroup$ I'm not sure if you're missing my point or if I'm missing yours. Mine is this: NCBI does not seem to restrict itself to including only validly published species in its taxonomy, so as far as I can tell, whether A. xerosis was validly published is irrelevant to the question of why it was removed from the NCBI taxonomy. I don't see how your last two comments address that. $\endgroup$ – Mark Amery May 1 '18 at 15:38

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