We should first explain how these inappropriate names appeared. We have insisted to use the directory name at the NCBI FTP site as genome name. However, in November 2013 NCBI announced that they would not release genomes of different strains of the same species as before. In a period thereafter NCBI sometimes put several genomes in a directory and we had to extract the data and to assign a name from the “Source” line of the GenBank file. This caused some confusion. For example, as of February 27, 2015, a directory name at NCBI remained “archaeon_Mx1201_uid196597” and we had to change it to: Candidatus_Methanomethylophilus_alvus_Mx1201_uid196597 Now all “wrong names” as pointed out by the Reviewer no longer appear in figures. In the text we tried to refer to their names as complete as possible.
However, I am personally not convinced that whole genomes bring additional advantages, or if we are better off by just using a conserved set of proteins.