Q: Why are a 'type strain' and a 'reference strain' usually not the same?
Type strains form the backbone of prokaryotic systematics as nomenclatural types of
species and subspecies, and comparisons with established type strains are mandatory
when classifying novel strains (PMID: 19700448).
The good news is that the TYGS is designed to automatically determine type strains
closely related to your query genome(s).
On contrary, the term 'reference strain' is often used synonymously with the term
'type strain' but in fact the former term is not sharply defined and just an
arbitrary label which can basically be put on any strain, even on those which are
in fact no type strains. But this can lead to serious taxonomic confusions,
if strains are falsely mistaken as type strains. That is, be careful when preparing
your dataset and when collecting lists of 'reference strains' from other web pages.