There’s recently a type change on Agrobacterium tumefaciens, after Judicial Opinion 127. The new type strain is ATCC 4720, with a genome in GCA_011684035.1.
The current synonymization with A. fabacearum is somewhat expected as mentioned in the JO. The main issue here is that most members currently in s__Agrobacterium tumefaciens are probably going to be moved over to Agrobacterium radiobacter… if its type strain can have a passable assembly, that is. (GCF_963360635.1 seems fine)
I also raised the issue at NCBI, so maybe nothing will need to be manually done.
Thank you for bringing this to our attention. We are actively working on the next release of GTDB. Unfortunately, GCA_011684035.1 will not be a GTDB representative genome in this next release since it wasn’t designated as type material at the time species dereplication was performed. GCA_011684035.1 is in a species cluster represented by genome GCA_009649785.1 (CNPSo 675), the type strain of Agrobacterium fabacearum. Given the similarity of CNPSo 675 and ATCC 4720 this clustering is in agreement with GTDB generally using a 95% ANI criterion for delineating species. I have flagged this with a nomenclature expert (Maria Chuvochina), but I believe A. tumerfaciens has naming priority and we can reflect this in the name of this species cluster even if the selected GTDB representative will necessarily be GCA_009649785.1 in the next GTDB release.