Bacterial type strains - Type status invalid?

I am curator of the national culture collection of New Zealand (ICMP): https://www.gbif.org/dataset/3c6e7390-3b56-11dc-8c19-b8a03c50a862 we hold bacterial, fungal, and chromist living cultures, frozen in liquid nitrogen.

Sometime over the past year there has been a change to the ‘issues’ in GBIF, and now valid bacterial type strains have the message “Type status invalid”. E.g.: https://www.gbif.org/occurrence/1315968484

Is this a data publishing issue with the text for ‘type status’? “type strain” is a valid term for bacteria.

Thanks

2 Likes

Thanks, @Bevan, for alerting us to this. That indeed appears to be a missing term in our Type vocabulary that we may want to add.

Just to make sure: there are currently eight “strain” (ex-type) types in http://rs.gbif.org/vocabulary/gbif/type_status.xml. None of these seem to be relevant to your case, as they refer to strains extracted from type material - correct?

Would https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000778, Rules 18a-c, be the appropriate reference for use of the term “type strain”? And if so, what is the convention of use of designating a culture as a type strain as opposed to a “holotype” (18b) or a “neotype” (18c)? From a naive perspective, the combination of basisOfRecord=living and type=holotype should express the same, but may be too far from common use. How relevant is the expression of the type status in bacterial strain collections?

Many thanks,
Andrea

1 Like

Hi,

Thanks for the reply @ahahn, yes none of the ex-types work for bacteria, although they do work fine for the fungal ex-holotype etc. cultures, we have. The chart below shows all the types in the ICMP by organism, they all work well except for the bacterial ones.

I straddle the world of both fungal and bacterial taxonomy and have described species under both nomenclature codes, they really are quite separate. Although rule 18b says “the type strain and may be referred to as the holotype” this never happens in practice. I searched a few major global bacterial collections, and they all use “type strain”:

I suggest adding “type strain” and “neotype strain” to your Type vocabulary. I doubt more are needed. Terms such as isotype, paratype, epitype are meaningless under the prokaryote code.

In my chart above you can also see “pathotype strain” these refer to a subspecific nomenclature the ‘pathovar standards’: https://www.isppweb.org/about_tppb_naming.asp (written by my predecessor) which is outside the formal prokaryote code. I don’t suggest adding these as they are outside the code, and the GBIF taxonomy can’t (or won’t?) deal with these names. But in case you are interested here are some examples:

Cheers,
Bevan

2 Likes

Thanks you, @Bevan. I opened an issue here to extend the type vocabulary, based on your feedback.
Best regards,
Andrea

2 Likes