Working with the Nagoya protocol

The protocol was implemented 12 October 2014. Meaning that only samples taken after this day are covered by the protocol. 

The paper of Overmann & Scholz 2017 describes the implications with prokaryotic strains. 
A point made in this paper is that most prokaryotes are globally distributed and that many of the concepts made in the Nagoya protocol are difficult to apply to microorganisms.  

One-strain species. 
The many problems have been described in the paper of Christensen et al. 2001
Unfortunately the problem has increased tremendously since that paper was published. In IJSEM, the majority publications are one-strains species and even one-strain genera. 
For different reasons we have been able to limit one-strain species and one-strain genera in the Pasteurellaceae.

No type strains?
It has been proposed to accept the genomic sequence instead of the deposition of type strains with two culture collections to accept a validly name a species. The proposal in IJSEM is outlining these ideas. 
Several problems can be foreseen if this proposal is implemented:
- the scientific data supporting the description of the species cannot be reproduced since the original material (DNA or culture material) is no longer available
- standards for whole DNA sequencing change and current methods may be outdated in a few years and then the species names will also be outdated 
- clinical microbiologists or other parts of the scientific society will develop an independent and more robust taxonomy 

Origins of type strains of species of Pasteurellaceae
Avibacterium paragallinarumIPDH 2403 isolated by K.-H. Hinz in 1970/71 from coryza in N. Germany. 

Muribacter muris: J. J. Ackerman in 1979 from mouse in USA. 

Rodentibacter pneumotropicus: M8.19.48 isolated by E. Jawetz probably in 1948 from mouse in USA. 

Pasteurella dagmatis: S. D. Henriksen 953/90 before 1961, from human nose in Norway.

Pasteurella multocida: W-9217 before 1962  from pig in Canada.